diff --git a/.DS_Store b/.DS_Store
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diff --git a/docs/amazons3.md b/docs/amazons3.mdx
similarity index 88%
rename from docs/amazons3.md
rename to docs/amazons3.mdx
index 95c6cfb4cb..611083c760 100644
--- a/docs/amazons3.md
+++ b/docs/amazons3.mdx
@@ -1,5 +1,3 @@
-(amazons3-page)=
-
 # Amazon S3
 
 Nextflow includes support for AWS S3 storage. Files stored in an S3 bucket can be accessed transparently in your pipeline script like any other file in the local file system.
@@ -20,7 +18,7 @@ The usual file operations can be applied to a path handle with the above notatio
 println file('s3://my-bucket/data/sequences.fa').text
 ```
 
-See {ref}`working-with-files` and the {ref}`stdlib-types-path` reference to learn more about available file operations.
+See [Working with files][working-with-files] and the [Path][stdlib-types-path] reference to learn more about available file operations.
 
 ## Security credentials
 
@@ -96,4 +94,9 @@ aws {
 
 ## Advanced configuration
 
-Read {ref}`AWS configuration<config-aws>` section to learn more about advanced S3 client configuration options.
+See [AWS configuration][config-aws] for more information about advanced S3 client configuration options.
+
+
+[config-aws]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#aws
+[stdlib-types-path]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#path
+[working-with-files]: /nextflow_docs/nextflow_repo/docs/working-with-files.mdx
\ No newline at end of file
diff --git a/docs/aws.mdx b/docs/aws.mdx
new file mode 100644
index 0000000000..aef7ce7d8d
--- /dev/null
+++ b/docs/aws.mdx
@@ -0,0 +1,545 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Amazon Web Services
+
+:::tip
+This page describes how to manually set up and use Nextflow with AWS Cloud.
+You may be interested in using [Batch Forge](https://docs.seqera.io/platform/latest/compute-envs/aws-batch) in [Seqera Platform](https://seqera.io/platform/),
+which automatically creates the required AWS infrastructure for you with minimal intervention.
+:::
+
+## AWS security credentials
+
+Nextflow uses the [AWS security credentials](https://docs.aws.amazon.com/general/latest/gr/aws-sec-cred-types.html) to make programmatic calls to AWS services.
+
+The AWS credentials are selected from the following sources, in order of descending priority:
+
+1. Nextflow configuration file - `aws.accessKey` and `aws.secretKey`. See [aws][config-aws] for more details.
+
+2. A custom profile in `$HOME/.aws/credentials` and/or `$HOME/.aws/config`. The profile can be supplied from the `aws.profile` config option, or the `AWS_PROFILE` or `AWS_DEFAULT_PROFILE` environmental variables.
+
+3. Environment variables - `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY`.
+
+4. The `default` profile in `~/.aws/credentials` and/or `~/.aws/config`.
+
+5. Single Sign-On (SSO) credentials. See the [AWS documentation](https://docs.aws.amazon.com/cli/latest/userguide/sso-configure-profile-token.html) for more details.
+
+
+    <AddedInVersion version="23.07.0-edge" />
+
+6. EC2 instance profile credentials. See the [AWS documentation](http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/iam-roles-for-amazon-ec2.html) and [this blog post](https://aws.amazon.com/blogs/security/granting-permission-to-launch-ec2-instances-with-iam-roles-passrole-permission/) for more details.
+
+The AWS region is selected from the following sources, in order of descending priority:
+
+1. Nextflow configuration file - `aws.region`
+2. Environment variables - `AWS_REGION` or `AWS_DEFAULT_REGION`
+3. EC2 instance metadata (if Nextflow is running in an EC2 instance)
+
+SSO credentials and instance profile credentials are the most recommended because they don't require you to manage and distribute AWS keys explicitly. SSO credentials are ideal for launching pipelines from outside of AWS (e.g. your laptop), while instance profile credentials are ideal for launching pipelines within AWS (e.g. an EC2 instance).
+
+## AWS IAM policies
+
+[IAM policies](https://docs.aws.amazon.com/IAM/latest/UserGuide/access_policies.html) are the mechanism used by AWS to define permissions for IAM identities. In order to access certain AWS services, the proper policies must be attached to the identity associated to the AWS credentials.
+
+Minimal permissions policies to be attached to the AWS account used by Nextflow are:
+
+- To use AWS Batch:
+
+  ```json
+  "batch:CancelJob"
+  "batch:DescribeComputeEnvironments"
+  "batch:DescribeJobDefinitions"
+  "batch:DescribeJobQueues"
+  "batch:DescribeJobs"
+  "batch:ListJobs"
+  "batch:RegisterJobDefinition"
+  "batch:SubmitJob"
+  "batch:TagResource"
+  "batch:TerminateJob"
+  ```
+
+- To view [EC2](https://aws.amazon.com/ec2/) instances:
+
+  ```json
+  "ec2:DescribeInstanceAttribute"
+  "ec2:DescribeInstances"
+  "ec2:DescribeInstanceStatus"
+  "ec2:DescribeInstanceTypes"
+  "ecs:DescribeContainerInstances"
+  "ecs:DescribeTasks"
+  ```
+
+- To pull container images from [ECR](https://aws.amazon.com/ecr/) repositories:
+
+  ```json
+  "ecr:BatchCheckLayerAvailability"
+  "ecr:BatchGetImage"
+  "ecr:DescribeImages"
+  "ecr:DescribeImageScanFindings"
+  "ecr:DescribeRepositories"
+  "ecr:GetAuthorizationToken"
+  "ecr:GetDownloadUrlForLayer"
+  "ecr:GetLifecyclePolicy"
+  "ecr:GetLifecyclePolicyPreview"
+  "ecr:GetRepositoryPolicy"
+  "ecr:ListImages"
+  "ecr:ListTagsForResource"
+  ```
+
+  Alternatively, you can use AWS provided `AmazonEC2ContainerRegistryReadOnly` managed policy.
+
+:::note
+If you are running Fargate or Fargate Spot, you may need the following policies in addition to the listed above:
+  ```json
+  "ec2:DescribeSubnets"
+  "ecs:CreateCluster"
+  "ecs:DeleteCluster"
+  "ecs:DescribeClusters"
+  "ecs:ListClusters"
+  ```
+:::
+
+### S3 policies
+
+Nextflow also requires policies to access [S3 buckets](https://aws.amazon.com/s3/) in order to use the work directory, pull input data, and publish results.
+
+Depending on the pipeline configuration, the above actions can be done all in a single bucket but, more likely, spread across multiple buckets. Once the list of buckets used by the pipeline is identified, there are two alternative ways to give Nextflow access to these buckets:
+
+1. Grant access to all buckets by attaching the policy `"s3:*"` to the IAM identity. This works only if buckets do not set their own access policies (see point 2);
+
+2. For more fine grained control, assign to each bucket the following policy (replace the placeholders with the actual values):
+
+    ```json
+    {
+        "Version": "2012-10-17",
+        "Id": "<my policy id>",
+        "Statement": [
+            {
+                "Sid": "<my statement id>",
+                "Effect": "Allow",
+                "Principal": {
+                    "AWS": "<ARN of the nextflow identity>"
+                },
+                "Action": [
+                    "s3:GetObject",
+                    "s3:PutObject",
+                    "s3:DeleteObject",
+                    "s3:PutObjectTagging",
+                    "s3:AbortMultipartUpload"
+                ],
+                "Resource": "arn:aws:s3:::<bucket name>/*"
+            },
+            {
+                "Sid": "AllowSSLRequestsOnly",
+                "Effect": "Deny",
+                "Principal": "*",
+                "Action": "s3:*",
+                "Resource": [
+                    "arn:aws:s3:::<bucket name>",
+                    "arn:aws:s3:::<bucket name>/*"
+                ],
+                "Condition": {
+                    "Bool": {
+                        "aws:SecureTransport": "false"
+                    }
+                }
+            }
+        ]
+    }
+    ```
+
+See the [bucket policy documentation](https://docs.aws.amazon.com/config/latest/developerguide/s3-bucket-policy.html) for additional details.
+
+## AWS Batch
+
+[AWS Batch](https://aws.amazon.com/batch/) is a managed computing service that allows the execution of containerised workloads in the AWS cloud infrastructure. It dynamically provisions the optimal quantity and type of compute resources (e.g., CPU or memory optimized compute resources) based on the volume and specific resource requirements of the jobs submitted.
+
+Nextflow provides built-in support for AWS Batch, allowing the seamless deployment of Nextflow pipelines in the cloud, in which tasks are offloaded as Batch jobs.
+
+See [AWS Batch][awsbatch-executor] to learn more about the `awsbatch` executor in Nextflow.
+
+### AWS CLI
+
+:::tip
+The need for the AWS CLI is considered a legacy requirement for the deployment of Nextflow pipelines with AWS Batch.
+Instead, consider using [Wave][wave-page] and [Fusion][fusion-page] to facilitate access to S3 without using the AWS CLI.
+:::
+
+Nextflow uses the [AWS command line tool](https://aws.amazon.com/cli/) (`aws`) to stage input files and output files between S3 and the task containers.
+
+The `aws` command can be made available by either (1) installing it in the container image(s) or (2) installing it in a [custom AMI][aws-custom-ami]` to be used instead of the default AMI when configuring AWS Batch.
+
+### Get started
+
+1. In the AWS Console, navigate to **AWS Batch** and create a [Compute environment](http://docs.aws.amazon.com/batch/latest/userguide/compute_environments.html) (CE).
+
+   1. If you are using a custom AMI (see following sections), the AMI ID must be specified in the CE configuration
+   2. Make sure to select an AMI (either custom or existing) with Docker installed (see following sections)
+   3. Make sure the policy `AmazonS3FullAccess` (granting access to S3 buckets) is attached to the instance role configured for the CE
+   4. If you plan to use Docker images from Amazon ECS container, make sure the `AmazonEC2ContainerServiceforEC2Role` policy is also attached to the instance role
+
+2. In the AWS Console, create (at least) one [Job Queue](https://docs.aws.amazon.com/batch/latest/userguide/job_queues.html) and bind it to the Compute environment.
+
+3. In the AWS Console, create an S3 bucket for the work directory (see below). You can also create separate buckets for input data and results, as needed.
+
+4. Make sure that every process in your pipeline specifies a Docker container with the [container][process-container] directive.
+
+5. Make sure that all of your container images are published in a Docker registry that can be reached by AWS Batch, such as [Docker Hub](https://hub.docker.com/), [Quay](https://quay.io/), or [Elastic Container Registry](https://aws.amazon.com/ecr/).
+
+### Configuration
+
+To configure your pipeline for AWS Batch:
+
+1. Specify the AWS Batch [executor][awsbatch-executor]
+2. Specify the AWS Batch queue with the [queue][process-queue] directive
+3. Specify any Batch job container options with the [containerOptions][process-containerOptions] directive.
+
+An example `nextflow.config` file is shown below:
+
+```groovy
+process {
+    executor = 'awsbatch'
+    queue = 'my-batch-queue'
+    container = 'quay.io/biocontainers/salmon'
+    containerOptions = '--shm-size 16000000 --ulimit nofile=1280:2560 --ulimit nproc=16:32'
+}
+
+aws {
+    batch {
+        // NOTE: this setting is only required if the AWS CLI is installed in a custom AMI
+        cliPath = '/home/ec2-user/miniconda/bin/aws'
+    }
+    region = 'us-east-1'
+}
+```
+
+:::tip
+Each process can be configured with its own queue by using the [queue][process-queue] directive in the process definition or via [Process selectors][config-process-selectors] in your Nextflow configuration.
+:::
+
+## Container Options
+
+<AddedInVersion version="21.12.1-edge" />
+
+The [containerOptions][process-containerOptions] directive can be used to control the properties of the container execution associated with each Batch job.
+
+The following container options are currently supported:
+
+```
+-e, --env string
+    Set environment variables (format: <name> or <name>=<value>)
+--init
+    Run an init inside the container that forwards signals and reaps processes
+--memory-swap int
+    The total amount of swap memory (in MiB) the container can use: '-1' to enable unlimited swap
+--memory-swappiness int
+    Tune container memory swappiness (0 to 100) (default -1)
+--privileged
+    Give extended privileges to the container
+--read-only
+    Mount the container's root filesystem as read only
+--shm-size int
+    Size (in MiB) of /dev/shm
+--tmpfs string
+    Mount a tmpfs directory (format: <path>:<options>,size=<int>), size is in MiB
+-u, --user string
+    Username or UID (format: <name|uid>[:<group|gid>])
+--ulimit string
+    Ulimit options (format: <type>=<soft limit>[:<hard limit>])
+```
+
+Container options may be passed in long form (e.g `--option value`) or short form (e.g. `-o value`) where available.
+
+Few examples:
+
+```nextflow
+containerOptions '--tmpfs /run:rw,noexec,nosuid,size=128 --tmpfs /app:ro,size=64'
+
+containerOptions '-e MYVAR1 --env MYVAR2=foo2 --env MYVAR3=foo3 --memory-swap 3240000 --memory-swappiness 20 --shm-size 16000000'
+
+containerOptions '--ulimit nofile=1280:2560 --ulimit nproc=16:32 --privileged'
+```
+
+Check the [AWS documentation](https://docs.aws.amazon.com/batch/latest/APIReference/API_ContainerProperties.html) for further details.
+
+## Custom AMI
+
+There are several reasons why you might need to create your own [AMI (Amazon Machine Image)](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AMIs.html) to use in your Compute Environments:
+
+- You do not want to install the AWS CLI into each of your Docker images and would rather provide it through the AMI
+- The existing AMI (selected from the marketplace) does not have Docker installed
+- You need to attach more storage to your EC2 instance (the default ECS instance AMI has only a 30GB EBS volume which is not enough for most data pipelines)
+- You need to install additional software that is not available in your Docker image
+
+### Create your custom AMI
+
+From the EC2 Dashboard, select **Launch Instance**, then select **Browse more AMIs**. In the new page, select
+**AWS Marketplace AMIs**, and then search for `Amazon ECS-Optimized Amazon Linux 2 (AL2) x86_64 AMI`. Select the AMI and continue as usual to configure and launch the instance.
+
+:::note
+The selected instance has a root volume of 30GB. Make sure to increase its size or add a second EBS volume with enough storage for real genomic workloads.
+:::
+
+When the instance is running, SSH into it (or connect with the Session Manager service), install the AWS CLI, and install any other tool that may be required (see following sections).
+
+Finally, select **Create Image** from the EC2 Dashboard to create a new AMI from the running instance (you can also do it through the AWS CLI).
+
+The new AMI ID needs to be specified when creating the Batch Compute Environment.
+
+:::warning
+Any additional software must be installed on the EC2 instance *before* creating the AMI.
+:::
+
+
+### AWS CLI installation
+
+:::tip
+The need for the AWS CLI is considered a legacy requirement for the deployment of Nextflow pipelines with AWS Batch.
+Instead, consider using [Wave][wave-page] and [Fusion][fusion-page] to facilitate access to S3 without using the AWS CLI.
+:::
+
+The [AWS CLI](https://aws.amazon.com/cli) should be installed in your custom AMI using a self-contained package manager such as [Conda](https://conda.io). That way, you can control which version of Python is used by the AWS CLI (which is written in Python).
+
+If you don't use Conda, the `aws` command will attempt to use the version of Python that is installed in the container, and it won't be able to find the necessary dependencies.
+
+The following snippet shows how to install AWS CLI with [Miniconda](https://conda.io/miniconda.html) in the home folder:
+
+```bash
+cd $HOME
+sudo yum install -y bzip2 wget
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/miniconda
+$HOME/miniconda/bin/conda install -c conda-forge -y awscli
+rm Miniconda3-latest-Linux-x86_64.sh
+```
+
+Afterwards, verify that the AWS CLI package works correctly:
+
+```console
+$ ./miniconda/bin/aws --version
+aws-cli/1.29.20 Python/3.11.4 Linux/4.14.318-241.531.amzn2.x86_64 botocore/1.31.20
+```
+
+:::note
+The `aws` tool will be placed in a directory named `bin` in the main installation folder. Modifying this directory structure after the tool is installed will cause it to not work properly.
+:::
+
+To configure Nextflow to use this installation, specify the `aws.batch.cliPath` option in the Nextflow configuration as shown below:
+
+```groovy
+aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
+```
+
+Replace the path above with the one matching the location where the `aws` tool is installed in your AMI.
+
+:::warning
+The grandparent directory of the `aws` tool will be mounted into the container at the same path as the host, e.g. `/home/ec2-user/miniconda`, which will shadow existing files in the container. Make sure you use a path that is not already present in the container.
+:::
+
+### Docker installation
+
+Docker is required by Nextflow to execute tasks on AWS Batch. The **Amazon ECS-optimized Amazon Linux 2023 AMI** has Docker installed, however, if you create your AMI from a different AMI that does not have Docker installed, you will need to install it manually.
+
+The following snippet shows how to install Docker on an Amazon EC2 instance:
+
+```bash
+# install Docker
+sudo yum update -y
+sudo yum install docker
+
+# start the Docker service
+sudo service docker start
+
+# empower your user to run Docker without sudo
+sudo usermod -a -G docker ec2-user
+```
+
+You must log out and log back in again to use the new `ec2-user` permissions.
+
+These steps must be done *before* creating the AMI from the current EC2 instance.
+
+### Amazon ECS container agent installation
+
+The [ECS container agent](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ECS_agent.html) is a component of Amazon Elastic Container Service (Amazon ECS) and is responsible for managing containers on behalf of ECS. AWS Batch uses ECS to execute containerized jobs, therefore it requires the agent to be installed on EC2 instances within your Compute Environments.
+
+The ECS agent is included in the **Amazon ECS-optimized Amazon Linux 2023 AMI** . If you use a different base AMI, you can also install the agent on any EC2 instance that supports the Amazon ECS specification.
+
+To install the agent, follow these steps:
+
+```bash
+sudo yum install ecs-init
+sudo systemctl enable --now ecs
+```
+
+To test the installation:
+
+```bash
+curl -s http://localhost:51678/v1/metadata | python -mjson.tool
+```
+
+:::note
+The `AmazonEC2ContainerServiceforEC2Role` policy must be attached to the instance role in order to be able to connect the EC2 instance created by the Compute Environment to the ECS container.
+:::
+
+:::note
+The `AmazonEC2ContainerRegistryReadOnly` policy should be attached to the instance role in order to get read-only access to Amazon EC2 Container Registry repositories.
+:::
+
+## Jobs & Execution
+
+### Custom job definition
+
+Nextflow automatically creates the Batch [Job definitions](http://docs.aws.amazon.com/batch/latest/userguide/job_definitions.html) needed to execute tasks in your pipeline, so you don't need to define them beforehand.
+
+However, sometimes you may still need to specify a custom **Job Definition** to fine tune the configuration of a specific job, for example to define custom mount paths.
+
+To do that, first create a **Job Definition** in the AWS Console (or by other means). Note the name of the Job definition you created. You can then associate a process execution with this Job definition by using the [container][process-container] directive and specifying, in place of the container image name, the Job definition name prefixed by `job-definition://`, as shown below:
+
+```groovy
+process.container = 'job-definition://your-job-definition-name'
+```
+
+### Hybrid workloads
+
+Nextflow allows the use of multiple executors in the same workflow application. This feature enables the deployment of hybrid workloads in which some jobs are executed in the local computer or local computing cluster and some jobs are offloaded to AWS Batch.
+
+To enable this feature, use one or more [Process selectors][config-process-selectors] in your Nextflow configuration to apply the AWS Batch configuration to the subset of processes that you want to offload. For example:
+
+```groovy
+process {
+    withLabel: bigTask {
+        executor = 'awsbatch'
+        queue = 'my-batch-queue'
+        container = 'my/image:tag'
+    }
+}
+
+aws {
+    region = 'eu-west-1'
+}
+```
+
+With the above configuration, processes with the `bigTask` [label][process-label] will run on AWS Batch, while the remaining processes will run in the local computer.
+
+Then launch the pipeline with the -bucket-dir option to specify an AWS S3 path for the jobs computed with AWS Batch and, optionally, the -work-dir to specify the local storage for the jobs computed locally:
+
+```bash
+nextflow run <script or project name> -bucket-dir s3://my-bucket/some/path
+```
+
+:::warning
+The AWS S3 path needs to contain at least one sub-directory (e.g. `s3://my-bucket/work` rather than `s3://my-bucket`).
+:::
+
+:::note
+Nextflow will automatically manage the transfer of input and output files between the local and cloud environments when using hybrid workloads.
+:::
+
+### Volume mounts
+
+User provided container volume mounts can be provided as shown below:
+
+```groovy
+aws {
+    region = 'eu-west-1'
+    batch {
+        volumes = '/tmp'
+    }
+}
+```
+
+Multiple volumes can be specified as a comma-separated list of paths. The usual Docker volume mount syntax can be used to specify complex volumes where the container path is different from the host path or the volume should be *read-only*. For example:
+
+```groovy
+aws {
+    region = 'eu-west-1'
+    batch {
+        volumes = ['/tmp', '/host/path:/mnt/path:ro']
+    }
+}
+```
+
+The above snippet defines two volume mounts for the jobs executed in your pipeline. The first volume mounts the host path `/tmp` to the same path in the container, with the *read-write* access mode. The second volume mounts the host path `/host/path` to `/mnt/path` in the container, with the *read-only* access mode.
+
+### Troubleshooting
+
+**Problem**: The Pipeline execution terminates with an AWS error message similar to the one shown below:
+
+```
+JobQueue <your queue> not found
+```
+
+Make sure you have defined a AWS region in the Nextflow configuration file and it matches the region in which your Batch environment has been created.
+
+**Problem**: A process execution fails reporting the following error message:
+
+```
+Process <your task> terminated for an unknown reason -- Likely it has been terminated by the external system
+```
+
+This may happen when Batch is unable to execute the process script. A common cause of this problem is that the Docker container image you have specified uses a non standard [entrypoint](https://docs.docker.com/engine/reference/builder/#entrypoint) which does not allow the execution of the Bash launcher script required by Nextflow to run the job.
+
+This may also happen if the AWS CLI doesn't run correctly.
+
+Other places to check for error information:
+
+- The `.nextflow.log` file.
+- The Job execution log in the AWS Batch dashboard.
+- The [CloudWatch](https://aws.amazon.com/cloudwatch/) logs found in the `/aws/batch/job` log group.
+
+**Problem**: A process execution is stalled in the `RUNNABLE` status and the pipeline output is similar to the one below:
+
+```
+executor >  awsbatch (1)
+process > <your process> (1) [  0%] 0 of ....
+```
+
+It may happen that the pipeline execution hangs indefinitely because one of the jobs is held in the queue and never gets executed. In AWS Console, the queue reports the job as `RUNNABLE` but it never moves from there.
+
+There are multiple reasons why this can happen. They are mainly related to the Compute Environment workload/configuration, the docker service or container configuration, network status, etc.
+
+This [AWS page](https://aws.amazon.com/premiumsupport/knowledge-center/batch-job-stuck-runnable-status/) provides several resolutions and tips to investigate and work around the issue.
+
+## AWS Fargate
+
+<AddedInVersion version="23.12.0-edge" />
+
+Nextflow provides experimental support for the execution of [AWS Batch jobs with Fargate resources](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html).
+
+AWS Fargate is a technology that you can use with AWS Batch to run containers without having to manage servers or  EC2 instances.
+With AWS Fargate, you no longer have to provision, configure, or scale clusters of virtual machines to run containers.
+
+To enable the use of AWS Fargate in your pipeline use the following settings in your `nextflow.config` file:
+
+```groovy
+process.executor = 'awsbatch'
+process.queue = '<AWS BATCH QUEUE>'
+aws.region = '<AWS REGION>'
+aws.batch.platformType = 'fargate'
+aws.batch.jobRole = 'JOB ROLE ARN'
+aws.batch.executionRole = 'EXECUTION ROLE ARN'
+wave.enabled = true
+```
+
+See the AWS documentation for details how to create the required AWS Batch queue for Fargate, the Batch Job Role
+and the Batch Execution Role.
+
+:::note
+Nextflow uses [s5cmd](https://github.com/peak/s5cmd) to download the task input data and upload the task outputs.
+To enable this capability, you need to enable the Wave service in the Nextflow configuration, as shown in the above example. See [Wave][] for more details.
+:::
+
+## Advanced configuration
+
+See [aws][config-aws] to learn more about advanced configuration options.
+
+[awsbatch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#aws-batch
+[aws-custom-ami]: /nextflow_docs/nextflow_repo/docs/aws.mdx#custom-ami
+[config-aws]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#aws
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-containerOptions]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#containeroptions
+[process-label]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#label
+[process-queue]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#queue
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
diff --git a/docs/azure.mdx b/docs/azure.mdx
new file mode 100644
index 0000000000..ed52caf664
--- /dev/null
+++ b/docs/azure.mdx
@@ -0,0 +1,714 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Azure
+
+## Overview
+
+Nextflow provides built-in support for Azure Cloud Services. It enables you to:
+
+- Store and access data using Azure Blob Storage and Azure file shares.
+- Execute workflows using Azure Batch.
+
+:::tip
+For automated Azure infrastructure setup, consider using [Batch Forge](https://docs.seqera.io/platform/latest/compute-envs/azure-batch#compute-environment) in [Seqera Platform](https://seqera.io/platform/).
+:::
+
+## Quick start
+
+To run pipelines with Azure Batch:
+
+1. Create an Azure Batch account in the Azure portal.
+
+2. Increase the quotas in your Azure Batch account to the pipeline's needs. Quotas impact the number of pools, CPUs, and jobs you can create.
+
+3. Create a storage account and Azure Blob Storage in the same region as the Batch account.
+
+4. Add the following settings to your Nextflow configuration file:
+
+    - Add authentication and account details. See [Authentication](#authentication) for configuration examples.
+
+    - Set `process.executor` to `azurebatch` to make Nextflow submit tasks to Azure Batch.
+
+    - Set `workDir` to a working directory on Azure Blob Storage. For example, `az://<BLOB_CONTAINER>/work`, where `BLOB_CONTAINER` is a blob container in your storage account.
+
+5. Launch your pipeline with the above configuration:
+
+    ```bash
+    nextflow run <PIPELINE_NAME>
+    ```
+
+:::tip
+You can list Azure regions with:
+
+```bash
+az account list-locations -o table
+```
+:::
+
+## Authentication
+
+Nextflow supports three authentication methods for Azure services, listed in order of security and recommended usage:
+
+- [Managed identities](#managed-identities): The most secure option, available only within Azure. Uses Azure-managed credentials without storing secrets.
+
+- [Service principals](#service-principals): A secure and flexible method that works across environments. Uses Microsoft Entra credentials for authentication.
+
+- [Access keys](#access-keys): The most basic and least secure method. Relies on direct access keys for authentication.
+
+### Required roles
+
+The following role assignments are required to use Azure services:
+
+For Azure Storage:
+
+- Storage Blob Data Reader
+- Storage Blob Data Contributor
+
+For Azure Batch:
+
+- Batch Data Contributor
+
+To assign roles to a managed identity or service principal, see the [Azure documentation](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current).
+
+### Managed identities
+
+<AddedInVersion version="24.05.0-edge" />
+
+
+[Managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) is the recommended authentication method when running Nextflow within Azure. It automatically manages credentials without requiring you to store secrets.
+
+When using a managed identity, an Azure resource can authenticate based on what it is rather than using access keys. For example, Nextflow can submit jobs to Azure Batch and access private storage accounts without additional credentials if it is running on Azure Virtual Machines with a managed identity and the necessary permissions.
+
+There are two types of managed identities:
+
+- System-assigned managed identity
+- User-assigned managed identity
+
+**System-assigned managed identity**
+
+A system-assigned identity is tied to a specific Azure resource. To use it:
+
+1. Enable [system-assigned managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-to-configure-managed-identities?pivots=qs-configure-portal-windows-vm#system-assigned-managed-identity) on your Azure resource.
+
+2. Configure the required role assignments. See [Required roles](#required-roles) for more information.
+
+3. Add the following configuration:
+
+```groovy
+azure {
+    managedIdentity {
+        system = true
+    }
+    storage {
+        accountName = '<STORAGE_ACCOUNT_NAME>'
+    }
+    batch {
+        accountName = '<BATCH_ACCOUNT_NAME>'
+        location = '<BATCH_ACCOUNT_LOCATION>'
+    }
+}
+```
+
+Replace the following:
+
+- `STORAGE_ACCOUNT_NAME`: your Azure storage account name
+- `BATCH_ACCOUNT_NAME`: your Azure Batch account name
+- `BATCH_ACCOUNT_LOCATION`: your Azure Batch account location
+
+:::tip
+Nextflow uses the `AZURE_MANAGED_IDENTITY_SYSTEM` environment variable if the managed identity is not set in the Nextflow configuration file. Set this to `true` to enable a system-assigned managed identity.
+:::
+
+**User-assigned managed identity**
+
+A user-assigned identity can be shared across multiple Azure resources and its lifecycle is not tied to any specific resource. See the [Azure documentation](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/managed-identity-best-practice-recommendations#choosing-system-or-user-assigned-managed-identities) for more information.
+
+To use user-assigned managed identity:
+
+1. Create a [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-manage-user-assigned-managed-identities?pivots=identity-mi-methods-azp#create-a-user-assigned-managed-identity).
+
+2. Configure the required role assignments.
+
+3. [Assign the identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/how-to-configure-managed-identities?pivots=qs-configure-portal-windows-vm#user-assigned-managed-identity) to your Azure resource.
+
+4. Add the following configuration:
+
+```groovy
+azure {
+    managedIdentity {
+        clientId = '<USER_ASSIGNED_MANAGED_IDENTITY_CLIENT_ID>'
+    }
+    storage {
+        accountName = '<STORAGE_ACCOUNT_NAME>'
+    }
+    batch {
+        accountName = '<BATCH_ACCOUNT_NAME>'
+        location = '<BATCH_ACCOUNT_LOCATION>'
+    }
+}
+```
+
+Replace the following:
+
+- `USER_ASSIGNED_MANAGED_IDENTITY_CLIENT_ID`: your user assigned managed identity client ID
+- `STORAGE_ACCOUNT_NAME`: your Azure Storage account name
+- `BATCH_ACCOUNT_NAME`: your Azure Batch account name
+- `BATCH_ACCOUNT_LOCATION`: your Azure Batch account location
+
+:::tip
+Nextflow uses the `AZURE_MANAGED_IDENTITY_USER` environment variable if the managed identity client ID is not provided in the Nextflow configuration file.
+:::
+
+### Service principals
+
+<AddedInVersion version="22.11.0-edge" />
+
+[Service principal](https://learn.microsoft.com/en-us/entra/identity-platform/app-objects-and-service-principals) credentials can be used to access Azure Batch and Storage accounts.
+
+Similar to a managed identity, a service principal is an application identity that can have specific permissions and role-based access. Unlike managed identities, service principals require a secret key for authentication. The secret key is less secure, but it allows you to authenticate with Azure resources when operating outside of the Azure environment, such as from your local machine or a non-Azure cloud.
+
+To create a service principal, follow the steps in the [Register a Microsoft Entra app and create a service principal](https://learn.microsoft.com/en-us/entra/identity-platform/howto-create-service-principal-portal) guide and add the credentials to your Nextflow configuration file. For example:
+
+```groovy
+azure {
+    activeDirectory {
+        servicePrincipalId = '<SERVICE_PRINCIPAL_CLIENT_ID>'
+        servicePrincipalSecret = '<SERVICE_PRINCIPAL_CLIENT_SECRET>'
+        tenantId = '<TENANT_ID>'
+    }
+    storage {
+        accountName = '<STORAGE_ACCOUNT_NAME>'
+    }
+    batch {
+        accountName = '<BATCH_ACCOUNT_NAME>'
+        location = '<BATCH_ACCOUNT_LOCATION>'
+    }
+}
+```
+
+:::tip
+Nextflow uses the following environment variables if storage settings are not set in the Nextflow config file:
+
+- `AZURE_CLIENT_ID`: your Azure service principal application ID
+- `AZURE_CLIENT_SECRET`: your Azure service principal secret
+- `AZURE_TENANT_ID`: your Azure Entra account tenant ID
+:::
+
+### Access keys
+
+The basic authentication method uses direct access keys. While easy to set up, it's less secure than managed identities or service principals because it provides full access to your resources. This approach requires you to obtain and manage the access keys for your Azure Batch and Storage accounts.
+
+You can find your access keys in the Azure portal:
+
+- For Storage accounts, navigate to your Storage account and select **Access keys** in the left-hand navigation menu.
+- For Batch accounts, navigate to your Batch account and select **Keys** in the left-hand navigation menu.
+
+Keep access keys secure and rotate them regularly. Use environment variables instead of hardcoding keys in configuration files, especially in shared or version-controlled environments:
+
+```groovy
+azure {
+    storage {
+        accountName = '<STORAGE_ACCOUNT_NAME>'
+        accountKey = '<STORAGE_ACCOUNT_KEY>'
+    }
+    batch {
+        accountName = '<BATCH_ACCOUNT_NAME>'
+        accountKey = '<BATCH_ACCOUNT_KEY>'
+        location = '<LOCATION>'
+    }
+}
+```
+
+You can also use a Shared Access Token (SAS) instead of an account key to provide time-limited access to your storage account:
+
+```groovy
+azure.storage.sasToken = '<SAS_TOKEN>'
+```
+
+:::tip
+When creating a SAS token, make sure to enable `Read`, `Write`, `Delete`, `List`, `Add`, `Create` permissions for the `Container` and `Object` resource types. The value of `sasToken` should be stripped of the leading `?` character.
+:::
+
+:::tip
+Nextflow uses the following environment variables if storage settings are not provided in the Nextflow configuration file:
+
+- `AZURE_STORAGE_ACCOUNT_NAME`: your Azure Storage account name
+- `AZURE_STORAGE_ACCOUNT_KEY`: your Azure Storage account key
+- `AZURE_BATCH_ACCOUNT_NAME`: your Azure Batch account name
+- `AZURE_BATCH_ACCOUNT_KEY`: your Azure Batch account key
+- `AZURE_STORAGE_SAS_TOKEN`: your Azure Storage account SAS token
+:::
+
+## Azure Blob Storage
+
+Azure Storage provides several services for storing and accessing data in Azure. Nextflow primarily supports Azure Blob Storage for most workloads. Limited support is available for Azure file shares for specific use cases.
+
+Nextflow uses the `az://` URI scheme to enable transparent access to files stored in Azure Blob Storage. Once Azure Storage is configured, you can use this scheme to reference files in any blob container as if they were local. For example, the path `/path/to/file.txt` in a container named `my-container` can be accessed as follows:
+
+```groovy
+file('az://my-container/path/to/file.txt')
+```
+
+The Blob storage account name and key need to be provided in the Nextflow configuration file as shown below:
+
+```groovy
+azure {
+    storage {
+        accountName = '<BLOB_ACCOUNT_NAME>'
+    }
+}
+```
+
+:::tip
+Nextflow uses the following environment variables if storage settings are not provided in the Nextflow configuration file:
+
+- `AZURE_STORAGE_ACCOUNT_NAME`: your Azure Storage account name
+- `AZURE_STORAGE_ACCOUNT_KEY`: your Azure Storage account access key
+- `AZURE_STORAGE_SAS_TOKEN`: a shared access signature (SAS) token for Azure Storage access
+:::
+
+## Azure Batch
+
+[Azure Batch](https://learn.microsoft.com/en-us/azure/batch/) is a managed computing service that enables large-scale parallel and high-performance computing (HPC) batch jobs in Azure. Nextflow provides a built-in executor for Azure Batch, allowing you to offload workflow tasks to the cloud.
+
+Nextflow integrates seamlessly with Azure Batch to:
+
+- Dynamically create and manage compute pools based on workflow requirements.
+- Automatically scale nodes up and down as needed during workflow execution.
+- Support both regular and low-priority VMs for cost optimization.
+- Manage task dependencies and data transfers between Azure Storage and compute nodes.
+
+This section describes how to configure and use Azure Batch with Nextflow for efficient cloud-based workflow execution. For comprehensive information about Azure Batch features and capabilities, refer to the [official Azure Batch documentation](https://learn.microsoft.com/en-us/azure/batch/).
+
+### Overview
+
+Nextflow integrates with Azure Batch by mapping its execution model to Azure Batch's structure. A Nextflow process corresponds to an Azure Batch job, and every execution of that process (a Nextflow task) becomes an Azure Batch task. These Azure Batch tasks are executed on compute nodes within an Azure Batch pool, which is a collection of virtual machines that can scale up or down based on an autoscale formula.
+
+Nextflow manages these pools dynamically. You can assign processes to specific, pre-existing pools using the process `queue` directive. Nextflow will create it if it doesn't exist and `azure.batch.allowPoolCreation` is set to `true`. Alternatively, `autoPoolMode` enables Nextflow to automatically create multiple pools based on the CPU and memory requirements defined in your processes.
+
+An Azure Batch task is created for each Nextflow task. This task first downloads the necessary input files from Azure Blob Storage to its assigned compute node. It then runs the process script. Finally, it uploads any output files back to Azure Blob Storage.
+
+Nextflow ensures that the corresponding Azure Batch jobs are marked as terminated when the pipeline completes. The compute pools, if configured for auto-scaling, automatically scale down according to their defined formula to minimize costs. Nextflow can also be configured to delete these node pools after pipeline completion.
+
+To use Azure Batch, set the `executor` directive to `azurebatch` in your Nextflow configuration file and add a work directory on Azure Blob Storage:
+
+```groovy
+process {
+    executor = 'azurebatch'
+}
+
+workDir = 'az://<BLOB_CONTAINER>/work'
+
+azure {
+    storage {
+        accountName = '<STORAGE_ACCOUNT_NAME>'
+    }
+    batch {
+        location = '<LOCATION>'
+        accountName = '<BATCH_ACCOUNT_NAME>'
+        autoPoolMode = true
+        allowPoolCreation = true
+    }
+}
+```
+
+:::note
+The work directory must be a subdirectory, for example, `az://container/work`, not `az://container`.
+:::
+
+Finally, launch your pipeline with the above configuration:
+
+```bash
+nextflow run <PIPELINE_NAME>
+```
+
+### Quotas
+
+Azure Batch enforces quotas on resources like pools, jobs, and VMs.
+
+- **Pools:** There is a limit on the number of pools that can exist at one time. Nextflow throws an error if it attempts to create a pool when this quota is exhausted. To proceed, you must delete existing pools.
+
+- **Active jobs:** There is a limit on the number of active jobs. Completed jobs should be terminated. If this limit is reached, Nextflow throws an error. You must terminate or delete jobs before you run additional pipelines.
+
+- **VM cores:** Each Azure VM family has a maximum core quota. If you request a VM family size for which you lack sufficient core quota, any jobs and tasks created by Nextflow will remain pending, as the pool cannot scale due to the quota. This can cause your pipeline to hang indefinitely.
+
+You can increase your quota on the Azure Portal by opening your Batch account and selecting **Quotas** in the left-hand menu, then request an increase in quota numbers.
+
+### Pools
+
+Nextflow supports two approaches for managing Batch pools: auto pools and named pools. These approaches are described in the following sections.
+
+:::warning
+Clean up the Batch pools or use auto-scaling to avoid additional charges in the Batch account.
+:::
+
+### Auto pools
+
+When using the `autoPoolMode` mode, Nextflow automatically creates pools of compute nodes appropriate for your pipeline.
+
+The `cpus` and `memory` directives are used to find the smallest machine type in the Azure machine family, specified by the `machineType` directive, that satisfies the requested resources. If memory is not specified, 1 GB of memory is requested per CPU. When no options are specified, it uses one compute node of type *Standard_D4_v3*.
+
+To use `autoPoolMode`, enable it in the `azure.batch` config scope:
+
+```groovy
+azure {
+    batch {
+        autoPoolMode = true
+        allowPoolCreation = true
+    }
+}
+
+process {
+    machineType = 'Standard_D4_v3'
+    cpus = 4
+    memory = 16.GB
+}
+```
+
+You can specify multiple machine families per process using glob patterns in the `machineType` directive:
+
+```groovy
+// D or E v5 machines with data disk
+process.machineType = "Standard_D*d_v5,Standard_E*d_v5"
+```
+
+For example, the following process creates a pool of *Standard_E8d_v5* machines when using `autoPoolMode`:
+
+```groovy
+process EXAMPLE_PROCESS {
+    machineType "Standard_E*d_v5"
+    cpus 8
+    memory 8.GB
+
+    script:
+    """
+    echo "cpus: ${task.cpus}"
+    """
+}
+```
+
+Additional notes:
+
+- For tasks using fewer than 4 CPUs, Nextflow creates pools with 4x CPUs to enable task packing.
+- For tasks using fewer than 8 CPUs, Nextflow uses 2x CPUs.
+- This behavior can be overridden by specifying an exact machine type (e.g., *Standard_E2d_v5*).
+- Regexes can be used to avoid certain machine types (e.g., `Standard_*[^p]_v*` avoids ARM-based machines).
+- The pool is not removed when the pipeline terminates unless `azure.batch.deletePoolsOnCompletion` is enabled in your Nextflow configuration file.
+
+### Named pools
+
+The `queue` directive can be used to specify the ID of the Azure Batch compute pool that should be used for a process.
+
+When `azure.batch.allowPoolCreation = true` is set in your configuration, Nextflow creates the pools on-demand. Otherwise, the pool must be available in the Batch environment when Nextflow submits tasks.
+
+Each pool can be configured separately in the Nextflow configuration. For example:
+
+```groovy
+azure {
+    batch {
+        pools {
+            small {
+                vmType = 'Standard_D2_v2'
+                vmCount = 5
+            }
+            large {
+                vmType = 'Standard_D8_v3'
+                vmCount = 2
+            }
+        }
+    }
+}
+
+process {
+    withLabel: small_jobs {
+        queue = 'small'
+    }
+    withLabel: large_jobs {
+        queue = 'large'
+    }
+}
+```
+
+The above example defines the configuration for two node pools, `small` and `large`. The `small` pool provisions 10 compute nodes of type *Standard_D2_v2*, and the `large` pool provisions 5 nodes of type *Standard_E2_v3*. See the [azure][config-azure] configuration scope for the list of available configuration options.
+
+:::warning
+Pool names may contain alphanumeric characters, hyphens, and underscores. Hyphenated names must be quoted, e.g., `'pool-1'`.
+:::
+
+**Requirements for pre-existing named pools**
+
+The target pool must satisfy the following requirements when Nextflow is configured to use a pool that is already available in the Batch account:
+
+- The pool must be declared as `dockerCompatible` (Container Type property).
+
+- The task slots per node must match the number of cores for the selected VM. Otherwise, Nextflow returns an error of the form "Azure Batch pool 'ID' slots per node does not match the VM num cores (slots: N, cores: Y)".
+
+- Unless you are using Fusion, all tasks must have the `azcopy` command line tool available in the path. If `azure.batch.copyToolInstallMode = 'node'`, every node must have `azcopy` available at `$AZ_BATCH_NODE_SHARED_DIR/bin/`.
+
+### Auto-scaling
+
+Azure Batch can automatically scale pools based on the parameters you define. With automatic scaling, Batch dynamically adds nodes to a pool as task demands increase and removes nodes as task demands decrease.
+
+To enable this feature for pools created by Nextflow, add `autoScale = true` to the corresponding pool configuration scope. For example, when using the `autoPoolMode`:
+
+```groovy
+azure {
+    batch {
+        pools {
+            <POOL_NAME> {
+                autoScale = true
+                vmCount = 5        // Initial count
+                maxVmCount = 50    // Maximum count
+            }
+        }
+    }
+}
+```
+
+The default auto-scaling formula initializes the pool with the number of VMs specified by the `vmCount` option. It dynamically scales up the pool based on the number of pending tasks. The pool limit is defined by `maxVmCount`. The formula automatically scales the pool down to zero nodes to minimize costs when no jobs are submitted for execution. The default formula is shown below:
+
+```
+// Get pool lifetime since creation.
+lifespan = time() - time("{{poolCreationTime}}");
+interval = TimeInterval_Minute * {{scaleInterval}};
+
+// Compute the target nodes based on pending tasks.
+$samples = $PendingTasks.GetSamplePercent(interval);
+$tasks = $samples < 70 ? max(0, $PendingTasks.GetSample(1)) : max( $PendingTasks.GetSample(1), avg($PendingTasks.GetSample(interval)));
+$targetVMs = $tasks > 0 ? $tasks : max(0, $TargetDedicatedNodes/2);
+targetPoolSize = max(0, min($targetVMs, {{maxVmCount}}));
+
+// For first interval deploy 1 node, for other intervals scale up/down as per tasks.
+$TargetDedicatedNodes = lifespan < interval ? {{vmCount}} : targetPoolSize;
+$NodeDeallocationOption = taskcompletion;
+```
+
+The `azure.batch.pools.<POOL_NAME>.scaleFormula` setting can be used to specify custom formulas.
+
+### Task authentication
+
+By default, Nextflow creates SAS tokens for specific containers and passes them to tasks to enable file operations with Azure Storage. SAS tokens expire after a set period of time. The expiration time is 48 hours by default and can be configured using `azure.storage.tokenDuration` in your configuration.
+
+<AddedInVersion version="25.05.0-edge" />
+
+:::warning
+Only available when using [Fusion filesystem](./fusion.mdx).
+:::
+
+You can also authenticate to Azure Storage using a managed identity when using Fusion.
+
+To do this:
+
+1. Create a user-assigned managed identity with the Azure Storage Blob Data Contributor role for your storage account.
+2. Attach the user-assigned managed identity to the node pool manually.
+3. Set `azure.batch.poolIdentityClientId` to this identity in your configuration.
+
+```groovy
+azure {
+    batch {
+        poolIdentityClientId = '<MANAGED_IDENTITY_CLIENT_ID>'
+    }
+}
+```
+
+Each task authenticates as the managed identity, and downloads and uploads files to Azure Storage using these credentials. It is possible to attach more than one managed identity to a pool. Fusion uses the identity specified by `azure.batch.poolIdentityClientId`.
+
+### Task packing
+
+Each Azure Batch node is allocated a specific number of task slots that determine how many tasks can run concurrently on that node. The number of slots is calculated based on the virtual machine's available CPUs. Nextflow intelligently assigns task slots to each process based on the proportion of total node resources requested through the `cpus`, `memory`, and `disk` directives.
+
+For example, consider a *Standard_D4d_v5* machine with 4 vCPUs, 16 GB of memory, and 150 GB local disk:
+
+- If a process requests `cpus 2`, `memory 8.GB`, or `disk 75.GB`, two task slots are allocated (50% of resources), allowing two tasks to run concurrently on the node.
+
+- If a process requests `cpus 4`, `memory 16.GB`, or `disk 150.GB`, four task slots are allocated (100% of resources), allowing one task to run on the node.
+
+Resource overprovisioning can occur if tasks consume more than their allocated share of resources. For instance, the node described above may become overloaded and fail if a task with `cpus 2` uses more than 8 GB of memory or 75 GB of disk space. Make sure to accurately specify resource requirements to ensure optimal performance and prevent task failures.
+
+:::warning
+Azure virtual machines come with fixed storage disks that are not expandable. Tasks will fail if the tasks running concurrently on a node use more storage than the machine has available.
+:::
+
+### Task containers
+
+Every process in your pipeline must specify a container in order to be executed on Azure Batch.
+
+Nextflow supports both public and private container images. You can pull public images from repositories such as [https://community.wave.seqera.io](https://community.wave.seqera.io). You must authenticate for any private images that you use. Ensure the Batch pool has access when using a private registry like Azure Container Registry (ACR). Provide ACR credentials in the `azure.registry` configuration scope:
+
+```groovy
+azure {
+    registry {
+        server = '<REGISTRY_SERVER>'     // e.g., 'myregistry.azurecr.io'
+        userName = '<REGISTRY_USER>'
+        password = '<REGISTRY_PASSWORD>'
+    }
+}
+```
+
+:::tip
+Nextflow uses the following environment variables if the registry credentials are not provided in the Nextflow configuration file:
+
+- `AZURE_REGISTRY_USER_NAME`: the username for Azure Container Registry authentication
+- `AZURE_REGISTRY_PASSWORD`: the password for Azure Container Registry authentication
+:::
+
+Container images from public registries such as Docker Hub can be used without additional configuration, even when a private registry is specified in the `azure.registry` scope. The Docker runtime on Azure Batch VMs automatically uses the appropriate registry based on the container image specified for the task.
+
+### VM images
+
+When Nextflow creates a pool of compute nodes, it selects:
+
+- The virtual machine image reference (defines the operating system (OS) and software to be installed on the node).
+- The Batch node agent SKU (a program that runs on each node and provides the interface between the node and the Azure Batch service).
+
+These settings determine the operating system, version, and available features for each compute node in your pool.
+
+By default, Nextflow creates pool nodes suitable for most bioinformatics workloads based on Ubuntu 22.04. You can customize the OS in your pool configuration to meet specific requirements.
+
+Below are example configurations for common operating systems used in scientific computing:
+
+**Ubuntu 22.04 (default)**
+
+```groovy
+azure {
+    batch {
+        pools {
+            <POOL_NAME> {
+                sku = "batch.node.ubuntu 22.04"
+                offer = "ubuntu-hpc"
+                publisher = "microsoft-dsvm"
+            }
+        }
+    }
+}
+```
+
+**CentOS 8**
+
+```groovy
+azure {
+    batch {
+        pools {
+            <POOL_NAME> {
+                sku = "batch.node.centos 8"
+                offer = "centos-container"
+                publisher = "microsoft-azure-batch"
+            }
+        }
+    }
+}
+```
+
+### Advanced features
+
+**Virtual networks**
+
+Pools can be configured to use virtual networks to connect to your existing network infrastructure.
+
+```groovy
+azure.batch.pools.<POOL_NAME>.virtualNetwork = '<SUBNET_ID>'
+```
+
+The subnet ID must be in the following format:
+
+```
+/subscriptions/<SUBSCRIPTION>/resourceGroups/<GROUP>/providers/Microsoft.Network/virtualNetworks/<VNET>/subnets/<SUBNET>
+```
+
+Nextflow can submit tasks to existing pools that are already attached to a virtual network without requiring additional configuration.
+
+:::warning
+Virtual networks require Microsoft Entra authentication (service principal or managed identity).
+:::
+
+**Start tasks**
+
+Start tasks are optional commands that run when a node joins the pool. They are useful for setting up the node environment or for running other commands that need to be executed when the node is created.
+
+```groovy
+azure {
+    batch {
+        pools {
+            <POOL_NAME> {
+                startTask {
+                    script = 'echo "Hello, world!"'
+                    privileged = true  // optional, defaults to false
+                }
+            }
+        }
+    }
+}
+```
+
+**Azure file shares**
+
+Azure file shares provide fully managed file shares that can be mounted to compute nodes. Files become immediately available in the file system and can be accessed as local files within processes.
+
+The Azure file share must exist in the storage account configured for Blob Storage. You must provide the name of the source Azure file share and mount path (the path where the files are mounted). Additional mount options can also be set for further customization of the mounting process. See the [Azure Files documentation](https://learn.microsoft.com/en-us/azure/storage/files/storage-files-introduction) for more information.
+
+For example:
+
+```groovy
+azure {
+    storage {
+        fileShares {
+            references {  // any name of your choice
+                mountPath = '/mnt/references'
+                mountOptions = '-o vers=3.0,dir_mode=0777,file_mode=0777,sec=ntlmssp'  // optional
+            }
+        }
+    }
+}
+```
+
+:::warning
+File shares must be authenticated using a storage account key. Managed identity and service principal are not supported.
+:::
+
+**Hybrid workloads**
+
+It is possible to use multiple executors in the same Nextflow pipeline. This feature enables the deployment of hybrid workloads in which some tasks are executed locally (or on an HPC cluster) and some tasks are offloaded to Azure Batch.
+
+Use process selectors in your Nextflow configuration to execute specific processes with Azure Batch. For example:
+
+```groovy
+process {
+    withLabel: bigTask {
+        executor = 'azurebatch'
+        queue = 'my-batch-pool'
+        container = 'my/image:tag'
+    }
+}
+
+bucketDir = 'az://my-container/some/path'
+
+azure {
+    storage {
+        accountName = '<STORAGE_ACCOUNT_NAME>'
+        accountKey = '<STORAGE_ACCOUNT_KEY>'
+    }
+    batch {
+        location = '<LOCATION>'
+        accountName = '<BATCH_ACCOUNT_NAME>'
+        accountKey = '<BATCH_ACCOUNT_KEY>'
+    }
+}
+```
+
+With the above configuration, processes labeled as `bigTask` run on Azure Batch and use `bucketDir` as the work directory, while all other processes run locally and use the local work directory specified by `workDir`. Nextflow handles file transfers between the local and remote work directories.
+
+Launch the pipeline with the above configuration:
+
+```bash
+nextflow run <PIPELINE_NAME>
+```
+
+:::note
+When using Fusion, `bucketDir` is not needed as all tasks will use the remote work directory. Specify `workDir` instead.
+:::
+
+## Advanced configuration
+
+See the [azure][config-azure] configuration scope for the list of available configuration options.
+
+[config-azure]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#azure
diff --git a/docs/cache-and-resume.mdx b/docs/cache-and-resume.mdx
new file mode 100644
index 0000000000..32b1564d8a
--- /dev/null
+++ b/docs/cache-and-resume.mdx
@@ -0,0 +1,258 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Caching and resuming
+
+One of the core features of Nextflow is the ability to cache task executions and re-use them in subsequent runs to minimize duplicate work. Resumability is useful both for recovering from errors and for iteratively developing a pipeline. It is similar to [checkpointing](https://en.wikipedia.org/wiki/Application_checkpointing), a common practice used by HPC applications.
+
+You can enable resumability in Nextflow with the `-resume` flag when launching a pipeline with `nextflow run`. In most cases, that is all you need to do and resumability will "just work". This page describes Nextflow's caching behavior in more detail in order to help advanced users understand how the cache works and troubleshoot it when it doesn't work.
+
+## Task cache
+
+All task executions are automatically saved to the task cache, regardless of the `-resume` option (so that you always have the option to resume later). The task cache is a key-value store, where each key-value pair corresponds to a previously-executed task.
+
+The task cache is used in conjunction with the [work directory](#work-directory) to recover cached tasks in a resumed run. It is also used by the [`log`][cli-log] sub-command to query task metadata.
+
+### Task hash
+
+The task hash is computed from the following metadata:
+
+- Session ID (see `workflow.sessionId` in the [workflow][stdlib-namespaces-workflow] namespace)
+- Task name (see `name` in [Trace file][trace-report])
+- Task container image (if applicable)
+- Task [environment modules][process-module] (if applicable)
+- Task [Conda environment][process-conda] (if applicable)
+- Task [Spack environment][process-spack] and [CPU architecture][process-arch>] (if applicable)
+- Task [inputs][process-input]
+- Task [script][process-script]
+- Any global variables referenced in the task script
+- Any task [`ext`][process-ext] properties referenced in the task script
+- Any [bundled scripts][bundling-executables] used in the task script
+- Whether the task is a [stub run][process-stub]
+
+:::note
+Nextflow also includes an incrementing component in the hash generation process, which allows it to iterate through multiple hash values until it finds one that does not match an existing execution directory. This mechanism typically aligns with task retries (i.e., task attempts), however this is not guaranteed.
+:::
+
+<ChangedInVersion version="23.09.2-edge">
+The [`ext`][process-ext] directive was added to the task hash.
+</ChangedInVersion>
+
+Nextflow computes this hash for every task when it is created but before it is executed. If resumability is enabled and there is an entry in the task cache with the same hash, Nextflow tries to recover the previous task execution. A cache hit does not guarantee that the task will be resumed, because it must also recover the task outputs from the [work directory](#work-directory).
+
+Files are hashed differently depending on the caching mode. See the [`cache`][process-cache] directive for more details.
+
+### Task entry
+
+The task entry is a serialized blob of the task metadata required to resume a task, including the fields used by the [Trace file][trace-report] and the task input variables.
+
+### Cache stores
+
+The default cache store uses the `.nextflow/cache` directory, relative to the launch directory (i.e. `workflow.launchDir`), to store the task cache, with a separate subdirectory for each session ID backed by [LevelDB](https://github.com/dain/leveldb).
+
+Due to the limitations of LevelDB, the database for a given session ID can only be accessed by one reader/writer at a time. This means, for example, that you cannot use `nextflow log` to query the task metadata for a pipeline run while it is still running.
+
+<AddedInVersion version="23.07.0-edge" />
+
+The cloud cache is an alternative cache store that uses cloud storage instead of the local cache directory. You can use it by setting the `NXF_CLOUDCACHE_PATH` environment variable to the desired cache path (e.g. `s3://my-bucket/cache`) and providing the necessary credentials.
+
+The cloud cache is particularly useful when launching Nextflow from within the cloud, where the default cache would be lost once the pipeline completes and the VM instance is terminated. Furthermore, because it is backed by cloud storage, it can support multiple readers and writers.
+
+## Work directory
+
+While the [task cache](#task-cache) stores the task metadata for subsequent runs, the work directory stores various files used during a pipeline run.
+
+Each task uses a unique directory based on its hash. When a task is created, Nextflow stages the task input files, script, and other helper files into the task directory. The task writes any output files to this directory during its execution, and Nextflow uses these output files for downstream tasks and/or publishing.
+
+When a previous task is retrieved from the task cache on a resumed run, Nextflow then checks the corresponding task directory in the work directory. If all the required outputs are present and the exit code is valid, then the task is successfully cached; otherwise, the task is re-executed.
+
+For this reason, it is important to preserve both the task cache (`.nextflow/cache`) and work directories in order to resume runs successfully. You can use the [`clean`][cli-clean] command to delete specific runs from the cache.
+
+## Troubleshooting
+
+Cache failures occur when a task that was supposed to be cached was re-executed or a task that was supposed to be re-executed was cached.
+
+Common causes of cache failures include:
+
+- [Resume not enabled](#resume-not-enabled)
+- [Cache directive disabled](#cache-directive-disabled)
+- [Modified inputs](#modified-inputs)
+- [Inconsistent file attributes](#inconsistent-file-attributes)
+- [Race condition on a global variable](#race-condition-on-a-global-variable)
+- [Non-deterministic process inputs](#non-deterministic-process-inputs)
+
+### Resume not enabled
+
+The `-resume` option is required to resume a pipeline. Ensure you enable `-resume` in your run command or your Nextflow configuration file.
+
+### Cache directive disabled
+
+The `cache` directive is enabled by default. However, you can disable or modify its behavior for a specific process. For example:
+
+```nextflow
+process FOO {
+  cache false
+  // ...
+}
+```
+
+Ensure that the `cache` directive has not been disabled. See [cache][process-cache]  for more information.
+
+### Modified inputs
+
+Modifying inputs that are used in the task hash invalidates the cache. Common causes of modified inputs include:
+
+- Changing input files
+- Resuming from a different session ID
+- Changing the process name
+- Changing the calling workflow name
+- Changing the task container image or Conda environment
+- Changing the task script
+- Changing a bundled script used by the task
+
+Nextflow calculates a hash for an input file using its full path, last modified timestamp, and file size. If any of these attributes change, Nextflow re-executes the task.
+
+:::warning
+If a process modifies its input files, it cannot be resumed. Avoid processes that modify their own input files as this is considered an anti-pattern.
+:::
+
+### Inconsistent file attributes
+
+Some shared file systems, such as NFS, may report inconsistent file timestamps, which can invalidate the cache when using the standard caching mode.
+
+To resolve this issue, use the `'lenient'` [caching mode][process-cache] to ignore the last modified timestamp and use only the file path and size.
+
+### Race condition on a global variable
+
+Race conditions can disrupt the caching behavior of your pipeline. For example:
+
+```nextflow
+channel.of(1,2,3).map { v -> X=v; X+=2 }.view { v -> "ch1 = $v" }
+channel.of(1,2,3).map { v -> X=v; X*=2 }.view { v -> "ch2 = $v" }
+```
+
+In the above example, `X` is declared in each `map` closure. Without the `def` keyword, the variable `X` is global to the entire script. Because operators are executed concurrently and `X` is global, there is a *race condition* that causes the emitted values to vary depending on the order of the concurrent operations. If these values were passed to a process as inputs, the process would execute different tasks during each run due to the race condition.
+
+To resolve this issue, avoid declaring global variables in closures:
+
+```nextflow
+channel.of(1,2,3).map { v -> def X=v; X+=2 }.view { v -> "ch1 = $v" }
+```
+
+<AddedInVersion version="25.04.0">
+The [strict syntax][strict-syntax-page] does not allow global variables to be declared in closures.
+</AddedInVersion>
+
+### Non-deterministic process inputs
+
+A process that merges inputs from different sources non-deterministically may invalidate the cache. For example:
+
+```nextflow
+workflow {
+    ch_bam = channel.of( ['1', '1.bam'], ['2', '2.bam'] )
+    ch_bai = channel.of( ['2', '2.bai'], ['1', '1.bai'] )
+    check_bam_bai(ch_bam, ch_bai)
+}
+
+process check_bam_bai {
+    input:
+    tuple val(id), file(bam)
+    tuple val(id), file(bai)
+
+    script:
+    """
+    check_bam_bai $bam $bai
+    """
+}
+```
+
+In the above example, the inputs will be merged without matching on `id`, in a similar manner as the [`merge`][operator-merge] operator. As a result, the inputs are incorrect and non-deterministic.
+
+To resolve this issue, use the `join` operator to join the channels into a single input channel before invoking the process:
+
+```nextflow
+workflow {
+    ch_bam = channel.of( ['1', '1.bam'], ['2', '2.bam'] )
+    ch_bai = channel.of( ['2', '2.bai'], ['1', '1.bai'] )
+    check_bam_bai(ch_bam.join(ch_bai))
+}
+
+process check_bam_bai {
+    input:
+    tuple val(id), file(bam), file(bai)
+
+    script:
+    """
+    check_bam_bai $bam $bai
+    """
+}
+```
+
+## Tips
+
+### Resuming from a specific run
+
+Nextflow resumes from the previous run by default. If you want to resume from an earlier run, simply specify the session ID for that run with the `-resume` option:
+
+```bash
+nextflow run rnaseq-nf -resume 4dc656d2-c410-44c8-bc32-7dd0ea87bebf
+```
+
+You can use the [`log`][cli-log] command to view all previous runs as well as the task executions for each run.
+
+### Comparing the hashes of two runs
+
+One way to debug a resumed run is to compare the task hashes of each run using the `-dump-hashes` option.
+
+1. Perform an initial run: `nextflow -log run_initial.log run <pipeline> -dump-hashes`
+2. Perform a resumed run: `nextflow -log run_resumed.log run <pipeline> -dump-hashes -resume`
+3. Extract the task hash lines from each log (search for `cache hash:`)
+4. Compare the runs with a diff viewer
+
+While some manual effort is required, the final diff can often reveal the exact change that caused a task to be re-executed.
+
+<AddedInVersion version="23.10.0" />
+
+When using `-dump-hashes json`, the task hashes can be more easily extracted into a diff. Here is an example Bash script to perform two runs and produce a diff:
+
+```bash
+nextflow -log run_1.log run $pipeline -dump-hashes json
+nextflow -log run_2.log run $pipeline -dump-hashes json -resume
+
+get_hashes() {
+    cat $1 \
+    | grep 'cache hash:' \
+    | cut -d ' ' -f 10- \
+    | sort \
+    | awk '{ print; print ""; }'
+}
+
+get_hashes run_1.log > run_1.tasks.log
+get_hashes run_2.log > run_2.tasks.log
+
+diff run_1.tasks.log run_2.tasks.log
+```
+
+You can then view the `diff` output or use a graphical diff viewer to compare `run_1.tasks.log` and `run_2.tasks.log`.
+
+<AddedInVersion version="25.04.0">
+Nextflow now has a built-in way to compare two task runs. See the [Data lineage][data-lineage-page] guide for details.
+</AddedInVersion>
+
+[bundling-executables]: /nextflow_docs/nextflow_repo/docs/sharing.mdx#the-bin-directory
+[data-lineage-page]: /nextflow_docs/nextflow_repo/docs/tutorials/data-lineage.mdx
+[cli-clean]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#clean
+[cli-log]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#log
+[operator-join]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#join
+[process-arch]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#arch
+[process-cache]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cache
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
+[process-ext]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#ext
+[process-input]: /nextflow_docs/nextflow_repo/docs/process.mdx#inputs
+[operator-merge]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#merge
+[process-module]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#module
+[process-script]: /nextflow_docs/nextflow_repo/docs/process.mdx#script
+[process-spack]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#spack
+[process-stub]: /nextflow_docs/nextflow_repo/docs/process.mdx#stub
+[stdlib-namespaces-workflow]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-namespaces.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[trace-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
diff --git a/docs/channel.md b/docs/channel.md
deleted file mode 100644
index 3b4d099ff9..0000000000
--- a/docs/channel.md
+++ /dev/null
@@ -1,79 +0,0 @@
-(dataflow-page)=
-
-# Dataflow
-
-Nextflow uses a **dataflow** programming model to define workflows declaratively. In this model, {ref}`processes <process-page>` in a pipeline are connected to each other through *dataflow channels* and *dataflow values*.
-
-(dataflow-type-channel)=
-
-## Channels
-
-A *dataflow channel* (or simply *channel*) is an asynchronous sequence of values.
-
-The values in a channel cannot be accessed directly, but only through an operator or process. For example:
-
-```nextflow
-channel.of(1, 2, 3).view { v -> "channel emits ${v}" }
-```
-
-```console
-channel emits 1
-channel emits 2
-channel emits 3
-```
-
-### Factories
-
-A channel can be created by factories in the `channel` namespace. For example, the `channel.fromPath()` factory creates a channel from a file name or glob pattern, similar to the `files()` function:
-
-```nextflow
-channel.fromPath('input/*.txt').view()
-```
-
-See {ref}`channel-factory` for the full list of channel factories.
-
-### Operators
-
-Channel operators, or *operators* for short, are functions that consume and produce channels. Because channels are asynchronous, operators are necessary to manipulate the values in a channel. Operators are particularly useful for implementing glue logic between processes.
-
-Commonly used operators include:
-
-- {ref}`operator-combine`: emit the combinations of two channels
-
-- {ref}`operator-collect`: collect the values from a channel into a list
-
-- {ref}`operator-filter`: select the values in a channel that satisfy a condition
-
-- {ref}`operator-flatMap`: transform each value from a channel into a list and emit each list element separately
-
-- {ref}`operator-grouptuple`: group the values from a channel based on a grouping key
-
-- {ref}`operator-join`: join the values from two channels based on a matching key
-
-- {ref}`operator-map`: transform each value from a channel with a mapping function
-
-- {ref}`operator-mix`: emit the values from multiple channels
-
-- {ref}`operator-view`: print each value in a channel to standard output
-
-See {ref}`operator-page` for the full list of operators.
-
-(dataflow-type-value)=
-
-## Values
-
-A *dataflow value* is an asynchronous value.
-
-Dataflow values can be created using the {ref}`channel.value <channel-value>` factory, and they are created by processes (under {ref}`certain conditions <process-out-singleton>`).
-
-A dataflow value cannot be accessed directly, but only through an operator or process. For example:
-
-```nextflow
-channel.value(1).view { v -> "dataflow value is ${v}" }
-```
-
-```console
-dataflow value is 1
-```
-
-See {ref}`stdlib-types-value` for the set of available methods for dataflow values.
diff --git a/docs/channel.mdx b/docs/channel.mdx
new file mode 100644
index 0000000000..eeffd80636
--- /dev/null
+++ b/docs/channel.mdx
@@ -0,0 +1,88 @@
+# Dataflow
+
+Nextflow uses a **dataflow** programming model to define workflows declaratively. In this model, [processes][process-page] in a pipeline are connected to each other through *dataflow channels* and *dataflow values*.
+
+## Channels
+
+A *dataflow channel* (or simply *channel*) is an asynchronous sequence of values.
+
+The values in a channel cannot be accessed directly, but only through an operator or process. For example:
+
+```nextflow
+channel.of(1, 2, 3).view { v -> "channel emits ${v}" }
+```
+
+```console
+channel emits 1
+channel emits 2
+channel emits 3
+```
+
+### Factories
+
+A channel can be created by factories in the `channel` namespace. For example, the `channel.fromPath()` factory creates a channel from a file name or glob pattern, similar to the `files()` function:
+
+```nextflow
+channel.fromPath('input/*.txt').view()
+```
+
+See [Channel factories][channel-factory] for the full list of channel factories.
+
+### Operators
+
+Channel operators, or *operators* for short, are functions that consume and produce channels. Because channels are asynchronous, operators are necessary to manipulate the values in a channel. Operators are particularly useful for implementing glue logic between processes.
+
+Commonly used operators include:
+
+- [combine][operator-combine]: emit the combinations of two channels
+- [collect][operator-collect]: collect the values from a channel into a list
+- [filter][operator-filter]: select the values in a channel that satisfy a condition
+- [flatMap][operator-flatMap]: transform each value from a channel into a list and emit each list element separately
+- [groupTuple][operator-grouptuple]: group the values from a channel based on a grouping key
+- [join][operator-join]: join the values from two channels based on a matching key
+- [map][operator-map]: transform each value from a channel with a mapping function
+- [mix][operator-mix]: emit the values from multiple channels
+- [view][operator-view]: print each value in a channel to standard output
+
+See [Operators][operator-page] for the full list of operators.
+
+## Values
+
+A *dataflow value* is an asynchronous value.
+
+Dataflow values can be created using the [value][channel-value] factory, and they are created by processes (under [certain conditions][process-out-singleton]).
+
+A dataflow value cannot be accessed directly, but only through an operator or process. For example:
+
+```nextflow
+channel.value(1).view { v -> "dataflow value is ${v}" }
+```
+
+```console
+dataflow value is 1
+```
+
+See [Value][stdlib-types-value] for the set of available methods for dataflow values.
+
+[channel-of]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#of
+[channel-path]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#frompath
+[operator-map]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#map
+[operator-flatmap]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#flatmap
+[process-output]: /nextflow_docs/nextflow_repo/docs/process.mdx#outputs
+[channel-value]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#value
+[operator-first]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#first
+[operator-collect]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#collect
+[operator-reduce]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#reduce
+[process-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[process-out-singleton]: /nextflow_docs/nextflow_repo/docs/process.mdx#singleton-outputs
+[process-multiple-input-channels]: /nextflow_docs/nextflow_repo/docs/process.mdx#multiple-input-channels
+[channel-factory]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[operator-combine]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#combine
+[operator-filter]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#filter
+[operator-flatMap]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#flatmap
+[operator-grouptuple]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#grouptuple
+[operator-join]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#join
+[operator-mix]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#mix
+[operator-view]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#view
+[operator-page]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx
+[stdlib-types-value]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#valuev
diff --git a/docs/cli.md b/docs/cli.mdx
similarity index 72%
rename from docs/cli.md
rename to docs/cli.mdx
index 160c04d500..7124767cb8 100644
--- a/docs/cli.md
+++ b/docs/cli.mdx
@@ -1,13 +1,11 @@
-(cli-page)=
-
 # Command line
 
 Nextflow provides a robust command line interface (CLI) for the management and execution of pipelines.
 
-Simply run `nextflow` with no options or `nextflow -h` to see the list of available top-level options and commands. See {ref}`cli-reference` for the full list of subcommands with examples.
+Simply run `nextflow` with no options or `nextflow -h` to see the list of available top-level options and commands. See [CLI reference][cli-reference] for the full list of subcommands with examples.
 
-:::{note}
-Nextflow options use a single dash prefix, e.g. `-resume`. Do not confuse with double dash notation, e.g. `--resume`, which is instead used for {ref}`Pipeline parameters <cli-params>`.
+:::note
+Nextflow options use a single dash prefix, for example, `-resume`. Do not confuse with double dash notation, for example, `--resume`, which is instead used for [Pipeline parameters][cli-params].
 :::
 
 ## Basic usage
@@ -16,147 +14,157 @@ Nextflow options use a single dash prefix, e.g. `-resume`. Do not confuse with d
 
 Use the specified configuration file(s) overriding any defaults.
 
-```console
-$ nextflow -C my.config COMMAND [arg...]
+```bash
+nextflow -C my.config COMMAND [arg...]
 ```
 
 The `-C` option is used to override *all* settings specified in the default config file. For soft override, please refer the `-c` option.
 
 - Override **any** default configuration with a custom configuration file:
 
-  ```console
-  $ nextflow -C my.config run nextflow-io/hello
+  ```bash
+  nextflow -C my.config run nextflow-io/hello
   ```
 
 ### JVM properties
 
 Set JVM properties.
 
-```console
-$ nextflow -Dkey=value COMMAND [arg...]
+```bash
+nextflow -Dkey=value COMMAND [arg...]
 ```
 
 This option allows the definition of custom Java system properties that can be used to properly configure or fine tuning the JVM instance used by the Nextflow runtime.
 
-For specifying other JVM level options, please refer to the {ref}`config-env-vars` section.
+For specifying other JVM level options, see the [Environment variables][config-env-vars] section.
 
 - Add JVM properties to the invoked pipeline:
 
-  ```console
-  $ nextflow -Dfile.encoding=UTF-8 run nextflow-io/hello
+  ```bash
+  nextflow -Dfile.encoding=UTF-8 run nextflow-io/hello
   ```
 
 ### Execution as a background job
 
 Execute `nextflow` in the background.
 
-```console
-$ nextflow -bg COMMAND [arg...]
+```bash
+nextflow -bg COMMAND [arg...]
 ```
 
 The `-bg` option is used to invoke the nextflow execution in the background and allows the user to continue interacting with the terminal. This option is similar to `nohup` in behavior.
 
 - Invoke any execution as a background job:
 
-  ```console
-  $ nextflow -bg run nextflow-io/hello
+  ```bash
+  nextflow -bg run nextflow-io/hello
   ```
 
 ### Soft configuration override
 
 Add the specified file to configuration set.
 
-```console
-$ nextflow -c nxf.config COMMAND [arg...]
+```bash
+nextflow -c nxf.config COMMAND [arg...]
 ```
 
 The `-c` option is used to append a new configuration to the default configuration. The `-c` option allows us to update the config in an additive manner. For **hard override**, refer to the `-C` option.
 
 - Update *some* fields of the default config for any pipeline:
 
-  ```console
-  $ nextflow -c nxf.config run nextflow-io/hello
+  ```bash
+  nextflow -c nxf.config run nextflow-io/hello
   ```
 
 ### Help
 
 Print the help message.
 
-```console
-$ nextflow -h
+```bash
+nextflow -h
 ```
 
 The `-h` option prints out the overview of the CLI interface and enumerates the top-level *options* and *commands*.
 
 ### Execution logs
 
-Sets the path of the nextflow log file.
+Sets the path of the Nextflow log file.
 
-```console
-$ nextflow -log custom.log COMMAND [arg...]
+```bash
+nextflow -log custom.log COMMAND [arg...]
 ```
 
 The `-log` option takes a path of the new log file which will be used instead of the default `.nextflow.log` or to save logs files to another directory.
 
 - Save all execution logs to the custom `/var/log/nextflow.log` file:
 
-  ```console
-  $ nextflow -log /var/log/nextflow.log run nextflow-io/hello
+  ```bash
+  nextflow -log /var/log/nextflow.log run nextflow-io/hello
   ```
 
 ### Quiet execution
 
 Disable the printing of information to the terminal.
 
-```console
-$ nextflow -q COMMAND [arg...]
+```bash
+nextflow -q COMMAND [arg...]
 ```
 
 The `-q` option suppresses the banner and process-related info, and exits once the execution is completed. Please note that it does not affect any explicit print statement within a pipeline.
 
 - Invoke the pipeline execution without the banner and pipeline information:
 
-  ```console
-  $ nextflow -q run nextflow-io/hello
+  ```bash
+  nextflow -q run nextflow-io/hello
   ```
 
 ### Logging to a syslog server
 
 Send logs to [Syslog](https://en.wikipedia.org/wiki/Syslog) server endpoint.
 
-```console
-$ nextflow -syslog localhost:1234 COMMAND [arg...]
+```bash
+nextflow -syslog localhost:1234 COMMAND [arg...]
 ```
 
 The `-syslog` option is used to send logs to a Syslog logging server at the specified endpoint.
 
 - Send the logs to a Syslog server at specific endpoint:
 
-  ```console
-  $ nextflow -syslog localhost:1234 run nextflow-io/hello
+  ```bash
+  nextflow -syslog localhost:1234 run nextflow-io/hello
   ```
 
 ### Version
 
 Print the Nextflow version information.
 
-```console
-$ nextflow -v
+```bash
+nextflow -v
 ```
 
 The `-v` option prints out information about Nextflow, such as the version and build. The `-version` option, in addition, prints out the citation reference and official website.
 
-- The short version:
+- The `-v` option prints out information about Nextflow, such as the version and build.:
+
+  ```bash
+  nextflow -v
+  ```
+
+  This prints an output similar to the following:
 
   ```console
-  $ nextflow -v
   nextflow version 20.07.1.5412
   ```
 
-- The full version info with citation and website link:
+- The `-version` option in addition prints out the citation reference and official website.:
+
+  ```bash
+  nextflow -version
+  ```
+
+  This prints an output similar to the following:
 
   ```console
-  $ nextflow -version
   N E X T F L O W
   version 20.07.1 build 5412
   created 24-07-2020 15:18 UTC (20:48 IDT)
@@ -166,7 +174,7 @@ The `-v` option prints out information about Nextflow, such as the version and b
 
 ## Running pipelines
 
-The main purpose of the Nextflow CLI is to run Nextflow pipelines with the `run` command. Nextflow can execute a local script (e.g. `./main.nf`) or a remote project (e.g. `github.com/nextflow-io/hello`).
+The main purpose of the Nextflow CLI is to run Nextflow pipelines with the `run` command. Nextflow can execute a local script (e.g., `./main.nf`) or a remote project (e.g., `github.com/nextflow-io/hello`).
 
 ### Launching a remote project
 
@@ -186,34 +194,40 @@ nextflow run http://github.com/nextflow-io/hello
 
 If the project is found, it will be automatically downloaded to the Nextflow home directory (`$HOME/.nextflow` by default) and cached for subsequent runs.
 
-:::{note}
-You must use the `-hub` option to specify the hosting service if your project is hosted on a service other than GitHub, e.g. `-hub bitbucket`. However, the `-hub` option is not required if you use the project URL.
+:::note
+You must use the `-hub` option to specify the hosting service if your project is hosted on a service other than GitHub, e.g., `-hub bitbucket`. However, the `-hub` option is not required if you use the project URL.
 :::
 
+Try this feature by running the following command:
+
+```bash
+nextflow run nextflow-io/hello
+```
+
+It will download a trivial example from the repository published at [http://github.com/nextflow-io/hello](http://github.com/nextflow-io/hello) and execute it on your computer.
+
 If the `owner` is omitted, Nextflow will search your cached pipelines for a pipeline that matches the name specified. If no pipeline is found, Nextflow will try to download it using the `organization` name defined by the `NXF_ORG` environment variable (`nextflow-io` by default).
 
-:::{tip}
-To access a private repository, specify the access credentials using the `-user` command line option. Then follow the interactive prompts to enter your password. Alternatively, define your private repository access credentials using Git. See {ref}`Git configuration <git-page>` for more information.
+:::note
+To access a private repository, specify the access credentials using the `-user` command line option. Then follow the interactive prompts to enter your password. Alternatively, define your private repository access credentials using Git. See [Git configuration][git-page] for more information.
 :::
 
 ### Using a specific revision
 
 Any Git branch, tag, or commit of a project repository can be used when launching a pipeline by specifying the `-r` option:
 
-```console
-$ nextflow run nextflow-io/hello -r mybranch
+```bash
+nextflow run nextflow-io/hello -r mybranch
 ```
 
 or
 
-```console
-$ nextflow run nextflow-io/hello -r v1.1
+```bash
+nextflow run nextflow-io/hello -r v1.1
 ```
 
 These commands will execute two different project revisions based on the given Git branch/tag/commit.
 
-(cli-params)=
-
 ### Pipeline parameters
 
 Pipeline scripts can define *parameters* that can be overridden on the command line.
@@ -238,36 +252,36 @@ params {
 
 The above parameter can be specified on the command line as `--alpha`:
 
-```console
-$ nextflow run main.nf --alpha Hello
+```bash
+nextflow run main.nf --alpha Hello
 ```
 
-:::{note}
+:::note
 Parameters that are specified on the command line without a value are set to `true`.
 :::
 
-:::{note}
+:::note
 Parameters that are specified on the command line in kebab case (e.g., `--alpha-beta`) are automatically converted to camel case (e.g., `--alphaBeta`). Because of this, a parameter defined as `alphaBeta` in the pipeline script can be specified on the command line as `--alphaBeta` or `--alpha-beta`.
 :::
 
-:::{warning}
+:::note
 When a command line parameter includes one or more glob characters, i.e. wildcards like `*` or `?`, the parameter value must be enclosed in quotes to prevent Bash expansion and preserve the glob characters. For example:
 
-```console
-$ nextflow run <pipeline> --files "*.fasta"
+```bash
+nextflow run main.nf --files "*.fasta"
 ```
 :::
 
 Parameters specified on the command line can be also specified in a params file using the `-params-file` option.
 
-```console
-$ nextflow run main.nf -params-file pipeline_params.yml
+```bash
+nextflow run main.nf -params-file pipeline_params.yml
 ```
 
 The `-params-file` option loads parameters for your Nextflow pipeline from a JSON or YAML file. Parameters defined in the file are equivalent to specifying them directly on the command line. For example, instead of specifying parameters on the command line:
 
-```console
-$ nextflow run main.nf --alpha 1 --beta two
+```bash
+nextflow run main.nf --alpha 1 --beta two
 ```
 
 Parameters can be represented in YAML format:
@@ -286,14 +300,14 @@ Or in JSON format:
 }
 ```
 
-:::{note}
-Parameter values in the params file can reference the following {ref}`built-in variables <config-constants>`: `baseDir`, `projectDir`, `launchDir`.
+:::note
+Parameter values in the params file can reference the following [built-in variables][config-constants]: `baseDir`, `projectDir`, `launchDir`.
 :::
 
 Parameters are applied in the following order (from lowest to highest priority):
 
-1. Parameters defined in pipeline scripts (e.g. `main.nf`)
-2. Parameters defined in {ref}`config files <config-params>`
+1. Parameters defined in pipeline scripts (e.g., `main.nf`)
+2. Parameters defined in [config files][config-params]
 3. Parameters specified in a params file (`-params-file`)
 4. Parameters specified on the command line (`--something value`)
 
@@ -313,7 +327,7 @@ nextflow list
 
 This prints a list similar to the following:
 
-```
+```console
 cbcrg/ampa-nf
 cbcrg/piper-nf
 nextflow-io/hello
@@ -324,8 +338,13 @@ nextflow-io/examples
 
 By using the `info` command you can show information from a downloaded project. For example:
 
+```bash
+nextflow info hello
+```
+
+This prints an output similar to the following:
+
 ```console
-$ nextflow info hello
 project name: nextflow-io/hello
 repository  : http://github.com/nextflow-io/hello
 local path  : $HOME/.nextflow/assets/nextflow-io/hello
@@ -343,14 +362,14 @@ Starting from the top it shows: the project name; the Git repository URL; the lo
 
 The `pull` command allows you to download a project from a GitHub repository or to update it if that repository has already been downloaded. For example:
 
-```console
-$ nextflow pull nextflow-io/hello
+```bash
+nextflow pull nextflow-io/hello
 ```
 
 Alternatively, you can use the repository URL as the name of the project to pull:
 
-```console
-$ nextflow pull https://github.com/nextflow-io/hello
+```bash
+nextflow pull https://github.com/nextflow-io/hello
 ```
 
 Downloaded pipeline projects are stored in your directory `$HOME/.nextflow/assets` directory.
@@ -359,8 +378,8 @@ Downloaded pipeline projects are stored in your directory `$HOME/.nextflow/asset
 
 The `view` command shows the content of the pipeline script you have pulled. For example:
 
-```console
-$ nextflow view nextflow-io/hello
+```bash
+nextflow view nextflow-io/hello
 ```
 
 By adding the `-l` option to the example above it will list the content of the repository.
@@ -369,11 +388,11 @@ By adding the `-l` option to the example above it will list the content of the r
 
 The `clone` command allows you to copy a Nextflow pipeline project to a directory of your choice. For example:
 
-```console
-$ nextflow clone nextflow-io/hello target-dir
+```bash
+nextflow clone nextflow-io/hello target-dir
 ```
 
-If the destination directory is omitted the specified project is cloned to a directory with the same name as the pipeline base name (e.g. `hello`) in the current directory.
+If the destination directory is omitted the specified project is cloned to a directory with the same name as the pipeline base name (e.g., `hello`) in the current directory.
 
 The `clone` command can be used to inspect or modify the source code of a pipeline project. You can eventually commit and push back your changes by using the usual Git/GitHub workflow.
 
@@ -384,3 +403,10 @@ Downloaded pipelines can be deleted by using the `drop` command, as shown below:
 ```bash
 nextflow drop nextflow-io/hello
 ```
+
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[cli-reference]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx
+[config-constants]: /nextflow_docs/nextflow_repo/docs/config.mdx#constants
+[config-env-vars]: /nextflow_docs/nextflow_repo/docs/reference/env-vars.mdx
+[config-params]: /nextflow_docs/nextflow_repo/docs/config.mdx#parameters
+[git-page]: /nextflow_docs/nextflow_repo/docs/cli.mdx
diff --git a/docs/conda.mdx b/docs/conda.mdx
new file mode 100644
index 0000000000..a6a70d45b9
--- /dev/null
+++ b/docs/conda.mdx
@@ -0,0 +1,218 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Conda environments
+
+[Conda](https://conda.io/) is an open source package and environment management system that simplifies the installation and the configuration of complex software packages in a platform agnostic manner.
+
+Nextflow has built-in support for conda that allows the configuration of workflow dependencies using conda recipes and environment files.
+
+This allows Nextflow applications to use popular tool collections such as [Bioconda](https://bioconda.github.io) and the [Python Package index](https://pypi.org/), whilst taking advantage of the configuration flexibility provided by Nextflow.
+
+## Prerequisites
+
+This feature requires the conda or [Miniconda](https://conda.io/miniconda.html) package manager to be installed on your system.
+
+## How it works
+
+Nextflow automatically creates and activates the conda environment(s) given the dependencies specified by each process.
+
+Dependencies are specified by using the [conda][process-conda] directive, providing either the names of the required conda packages, the path of a conda environment yaml file, or the path of an existing conda environment directory.
+
+:::note
+Conda environments are stored on the file system. By default, Nextflow instructs conda to save the required environments in the pipeline work directory. The same environment may be created/saved multiple times across multiple executions when using different work directories.
+:::
+
+You can specify the directory where the conda environments are stored using the `conda.cacheDir` configuration property. When using a computing cluster, make sure to use a shared file system path accessible from all compute nodes. See [Configuration][config-conda] for details about conda configuration.
+
+:::warning
+The conda environment feature is not supported by executors that use remote object storage as a work directory. For example, AWS Batch.
+:::
+
+### Enabling conda environment
+
+<AddedInVersion version="22.08.0-edge" />
+
+The use of conda recipes specified using the [conda][process-conda] directive needs to be enabled explicitly in the pipeline configuration file (i.e., `nextflow.config`):
+
+```groovy
+conda.enabled = true
+```
+
+Alternatively, it can be specified by setting the variable `NXF_CONDA_ENABLED=true` in your environment or by using the `-with-conda` command line option.
+
+### Use conda package names
+
+Conda package names can be specified using the `conda` directive. Multiple package names can be specified by separating them with a blank space. For example:
+
+```nextflow
+process hello {
+  conda 'bwa samtools multiqc'
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+Using the above definition, a conda environment that includes BWA, Samtools and MultiQC tools is created and activated when the process is executed.
+
+The usual conda package syntax and naming conventions can be used. The version of a package can be specified after the package name as shown here `bwa=0.7.15`.
+
+The name of the channel where a package is located can be specified prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
+
+### Use conda environment files
+
+Conda environments can also be defined using one or more conda environment files. This is a file that lists the required packages and channels structured using the YAML format. For example:
+
+```yaml
+name: my-env
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - star=2.5.4a
+  - bwa=0.7.15
+```
+
+Read the conda documentation for more details about how to create [environment files](https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually).
+
+The path of an environment file can be specified using the `conda` directive:
+
+```nextflow
+process hello {
+  conda '/some/path/my-env.yaml'
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+:::warning
+The environment file name **must** have a `.yml` or `.yaml` extension or else it won't be properly recognised.
+:::
+
+### Python Packages from PyPI
+
+Conda environment files can also be used to install Python packages from the [PyPI repository](https://pypi.org/), through the `pip` package manager (which must also be explicitly listed as a required package):
+
+```yaml
+name: my-env-2
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - pip
+  - pip:
+    - numpy
+    - pandas
+    - matplotlib
+```
+
+### Conda text files
+
+It is possible to provide dependencies by listing each package name as a separate line in a plain text file. For example:
+
+```
+bioconda::star=2.5.4a
+bioconda::bwa=0.7.15
+bioconda::multiqc=1.4
+```
+
+:::note
+Dependency files must be a text file with the `.txt` extension.
+:::
+
+### Conda lock files
+
+The final method for providing packages to conda is by using [conda lock files](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#identical-conda-envs).
+
+To generate a lock file from an existing conda environment, run the following command:
+
+```bash
+conda list --explicit > spec-file.txt
+```
+
+If you're using Mamba or Micromamba, use this command instead:
+
+```bash
+micromamba env export --explicit > spec-file.txt
+```
+
+You can also download Conda lock files from [Wave](https://seqera.io/wave/) container build pages.
+
+These files list every package and its dependencies, so Conda doesn't need to perform dependency resolution. This makes environment setup faster and more reproducible.
+
+Each file includes package URLs and, optionally, an MD5 hash for verifying file integrity:
+
+```
+# micromamba env export --explicit
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+# .. and so on
+```
+
+To use a conda lock file with Nextflow, set the `conda` directive to the path of the lock file.
+
+:::note
+Conda lock files must be a text file with the `.txt` extension.
+:::
+
+### Use existing conda environments
+
+If you already have a local conda environment, you can use it in your workflow specifying the installation directory of such environment by using the `conda` directive:
+
+```nextflow
+process hello {
+  conda '/path/to/an/existing/env/directory'
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+### Use Mamba to resolve packages
+
+:::warning{title="Experimental: may change in a future release."}
+:::
+
+It is also possible to use [mamba](https://github.com/mamba-org/mamba) to speed up the creation of conda environments. For more information on how to enable this feature please refer to [conda][config-conda].
+
+## Best practices
+
+When a `conda` directive is used in any `process` definition within the workflow script, conda tool is required for the workflow execution.
+
+Specifying the conda environments in a separate configuration [profile][config-profiles] is therefore recommended to allow the execution via a command line option and to enhance the workflow portability. For example:
+
+```groovy
+profiles {
+  conda {
+    process.conda = 'samtools'
+  }
+
+  docker {
+    process.container = 'biocontainers/samtools'
+    docker.enabled = true
+  }
+}
+```
+
+The above configuration snippet allows the execution either with conda or Docker specifying `-profile conda` or `-profile docker` when running the workflow script.
+
+## Advanced settings
+
+Conda advanced configuration settings are described in the [conda][config-conda] section on the Nextflow configuration page.
+
+[config-conda]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#conda
+[config-profiles]: /nextflow_docs/nextflow_repo/docs/config.mdx#config-profiles
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
diff --git a/docs/config.mdx b/docs/config.mdx
new file mode 100644
index 0000000000..9a0fc32b70
--- /dev/null
+++ b/docs/config.mdx
@@ -0,0 +1,352 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Configuration
+
+## Configuration file
+
+When a pipeline script is launched, Nextflow looks for configuration files in multiple locations. Since each configuration file may contain conflicting settings, they are applied in the following order (from lowest to highest priority):
+
+1. The config file `$HOME/.nextflow/config` (or `$NXF_HOME/config` when [NXF_HOME][nxf-env-vars] is set).
+2. The config file `nextflow.config` in the project directory
+3. The config file `nextflow.config` in the launch directory
+4. Config files specified using the `-c <config-files>` option
+
+:::tip
+You can alternatively use the `-C <config-file>` option to specify a fixed set of configuration files and ignore all other files.
+:::
+
+## Syntax
+
+The Nextflow configuration syntax is based on the Nextflow script syntax. It is designed for setting configuration options in a declarative manner while also allowing for dynamic expressions where appropriate.
+
+A Nextflow config file may consist of any number of *assignments*, *blocks*, and *includes*. Config files may also contain comments in the same manner as scripts.
+
+See [syntax-page] for more information about the Nextflow script syntax.
+
+### Assignments
+
+A config assignment consists of a config option and an expression separated by an equals sign:
+
+```groovy
+workDir = 'work'
+docker.enabled = true
+process.maxErrors = 10
+```
+
+A config option consists of an *option name* prefixed by any number of *scopes* separated by dots. Config scopes are used to group related config options. See [Configuration options][config-options] for the full set of config options.
+
+The expression is typically a literal value such as a number, boolean, or string. However, any expression can be used:
+
+```groovy
+params.helper_file = "${projectDir}/assets/helper.txt"
+```
+
+### Blocks
+
+A config scope can also be specified as a block, which may contain multiple configuration options. For example:
+
+```groovy
+// dot syntax
+docker.enabled = true
+docker.runOptions = '-u $(id -u):$(id -g)'
+
+// block syntax
+docker {
+    enabled = true
+    runOptions = '-u $(id -u):$(id -g)'
+}
+```
+
+As a result, deeply nested config options can be assigned in various ways. For example, the following three assignments are equivalent:
+
+```groovy
+executor.retry.maxAttempt = 5
+
+executor {
+    retry.maxAttempt = 5
+}
+
+executor {
+    retry {
+maxAttempt = 5
+    }
+}
+```
+
+### Includes
+
+A configuration file can include any number of other configuration files using the `includeConfig` keyword:
+
+```groovy
+process.executor = 'sge'
+process.queue = 'long'
+process.memory = '10G'
+
+includeConfig 'path/extra.config'
+```
+
+Relative paths are resolved against the location of the including file.
+
+:::note
+Config includes can also be specified within config blocks. However, config files should only be included at the top level or in a [profile](#config-profiles) so that the included config file is valid on its own and in the context in which it is included.
+:::
+
+## Constants
+
+The following constants are globally available in a Nextflow configuration file:
+
+##### `baseDir: Path`
+
+<DeprecatedInVersion version="20.04.0" />
+
+Alias for `projectDir`.
+
+##### `launchDir: Path`
+
+The directory where the workflow was launched.
+
+##### `projectDir: Path`
+
+The directory where the main script is located.
+
+##### `workDir: Path`
+
+The directory where the workflow work directory is located.
+
+##### `secrets: Map<String,String>`
+
+Map of pipeline secrets. See [Secrets][secrets-page] for more information.
+
+## Functions
+
+The following functions are globally available in a Nextflow configuration file:
+
+##### `env( name: String ) -> String`
+
+Get the value of the environment variable with the specified name in the Nextflow launch environment.
+
+## Parameters
+
+Pipeline parameters can be defined in the config file using the `params` scope:
+
+```groovy
+params.alpha = 123
+params.beta = 'string value .. '
+
+params {
+    gamma = true
+    delta = "params.alpha is ${params.alpha}"
+}
+```
+
+See [Pipeline parameters][cli-params] for information about how to specify pipeline parameters.
+
+:::note
+When including a config file, the included config is evaluated with the parameters that are defined before the include. Parameters defined after the include are not visible to the included config.
+:::
+
+## Process configuration
+
+The `process` scope allows you to specify [process directives][process-reference] separately from the pipeline code.
+
+For example:
+
+```groovy
+process {
+    executor = 'sge'
+    queue = 'long'
+    clusterOptions = '-pe smp 10 -l virtual_free=64G,h_rt=30:00:00'
+}
+```
+
+By using this configuration, all processes in your pipeline will be executed through the SGE cluster, with the specified settings.
+
+### Process selectors
+
+The `withLabel` selectors allow the configuration of all processes annotated with a [label][process-label] directive as shown below:
+
+```groovy
+process {
+    withLabel: big_mem {
+        cpus = 16
+        memory = 64.GB
+        queue = 'long'
+    }
+}
+```
+
+The above configuration example assigns 16 cpus, 64 Gb of memory and the `long` queue to all processes annotated with the `big_mem` label.
+
+In the same manner, the `withName` selector allows the configuration of a specific process in your pipeline by its name. For example:
+
+```groovy
+process {
+    withName: hello {
+cpus = 4
+memory = 8.GB
+queue = 'short'
+    }
+}
+```
+
+The `withName` selector applies both to processes defined with the same name and processes included under the same alias. For example, `withName: hello` will apply to any process originally defined as `hello`, as well as any process included under the alias `hello`.
+
+Furthermore, selectors for the alias of an included process take priority over selectors for the original name of the process. For example, given a process defined as `hello` and included as `sayHello`, the selectors `withName: hello` and `withName: sayHello` will both be applied to the process, with the second selector taking priority over the first.
+
+:::tip
+Label and process names do not need to be enclosed with quotes, provided the name does not include special characters (`-`, `!`, etc) and is not a keyword or a built-in type identifier. When in doubt, you can enclose the label name or process name with single or double quotes.
+:::
+
+### Selector expressions
+
+Both label and process name selectors allow the use of a regular expression in order to apply the same configuration to all processes matching the specified pattern condition. For example:
+
+```groovy
+process {
+    withLabel: 'hello|bye' {
+        cpus = 2
+        memory = 4.GB
+    }
+}
+```
+
+The above configuration snippet requests 2 cpus and 4 GB of memory for processes labeled as `hello` or `bye`.
+
+A process selector can be negated prefixing it with the special character `!`. For example:
+
+```groovy
+process {
+    withLabel: 'hello' { cpus = 2 }
+    withLabel: '!hello' { cpus = 4 }
+    withName: '!align.*' { queue = 'long' }
+}
+```
+
+The above configuration snippet sets 2 cpus for every process labeled as `hello` and 4 cpus to every process *not* labeled as `hello`. It also specifies the `long` queue for every process whose name does *not* start with `align`.
+
+### Selector priority
+
+Process configuration settings are applied to a process in the following order (from lowest to highest priority):
+
+1. Process configuration settings (without a selector)
+2. Process directives in the process definition
+3. `withLabel` selectors matching any of the process labels
+4. `withName` selectors matching the process name
+5. `withName` selectors matching the process included alias
+6. `withName` selectors matching the process fully qualified name
+
+For example:
+
+```groovy
+process {
+    cpus = 4
+    withLabel: hello { cpus = 8 }
+    withName: bye { cpus = 16 }
+    withName: 'aloha:bye' { cpus = 32 }
+}
+```
+
+With the above configuration:
+
+- All processes will use 4 cpus (unless otherwise specified in their process definition).
+- Processes annotated with the `hello` label will use 8 cpus.
+- Any process named `bye` (or imported as `bye`) will use 16 cpus.
+- Any process named `bye` (or imported as `bye`) invoked by a workflow named `aloha` will use 32 cpus.
+
+## Config profiles
+
+Configuration files can define one or more *profiles*. A profile is a set of configuration settings that can be selected during pipeline execution using the `-profile` command line option.
+
+Configuration profiles are defined in the `profiles` scope. For example:
+
+```groovy
+profiles {
+    standard {
+        process.executor = 'local'
+    }
+
+    cluster {
+        process.executor = 'sge'
+        process.queue = 'long'
+        process.memory = '10GB'
+    }
+
+    cloud {
+        process.executor = 'cirrus'
+        process.container = 'cbcrg/imagex'
+        docker.enabled = true
+    }
+}
+```
+
+The above configuration defines three profiles: `standard`, `cluster`, and `cloud`. Each profile provides a different configuration for a given execution environment. The `standard` profile is used by default when no profile is specified.
+
+Configuration profiles can be specified at runtime as a comma-separated list:
+
+```bash
+nextflow run main.nf -profile standard,cloud
+```
+
+Config profiles are applied in the order in which they were defined in the config file, regardless of the order they are specified on the command line.
+
+<AddedInVersion version="25.02.0-edge">
+When using the [strict config syntax][updating-config-syntax], profiles are applied in the order in which they are specified on the command line.
+</AddedInVersion>
+
+:::warning
+When defining a profile in the config file, avoid using both the dot and block syntax for the same scope. For example:
+
+```groovy
+profiles {
+    cluster {
+        process.memory = '2 GB'
+        process {
+            cpus = 2
+        }
+    }
+}
+```
+
+Due to a limitation of the legacy config parser, the first setting will be overwritten by the second:
+
+```console
+$ nextflow config -profile cluster
+process {
+   cpus = 2
+}
+```
+
+This limitation can be avoided by using the [strict config syntax][updating-config-syntax].
+:::
+
+## Workflow handlers
+
+<deprecatedInVersion version="25.10.0">
+Use a trace observer in a plugin to add custom workflow handlers to a pipeline via configuration.
+</deprecatedInVersion>
+
+You can define workflow event handlers in the config file:
+
+```groovy
+workflow.onComplete = {
+    // any workflow property can be used here
+    println "Pipeline complete"
+    println "Command line: $workflow.commandLine"
+}
+
+workflow.onError = {
+    println "Error: something went wrong"
+}
+```
+
+This approach is useful for handling workflow events without modifying the pipeline code. See [Workflow handlers][workflow-handlers] for more information.
+
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[config-options]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx
+[nxf-env-vars]: /nextflow_docs/nextflow_repo/docs/reference/env-vars.mdx#nextflow-settings
+[process-reference]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx
+[process-label]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#label
+[secrets-page]: /nextflow_docs/nextflow_repo/docs/secrets.mdx
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[updating-config-syntax]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx#configuration-syntax
+[workflow-handlers]: /nextflow_docs/nextflow_repo/docs/notifications.mdx#workflow-handlers
diff --git a/docs/container.mdx b/docs/container.mdx
new file mode 100644
index 0000000000..1d558b4812
--- /dev/null
+++ b/docs/container.mdx
@@ -0,0 +1,656 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Containers
+
+Nextflow supports a variety of container runtimes. Containerization allows you to write self-contained and truly reproducible computational pipelines, by packaging the binary dependencies of a script into a standard and portable format that can be executed on any platform that supports a container runtime. Furthermore, the same pipeline can be transparently executed with any of the supported container runtimes, depending on which runtimes are available in the target compute environment.
+
+:::note
+When creating a container image to use with Nextflow, make sure that Bash (3.x or later) and `ps` are installed in the image, along with other tools required for collecting metrics (see [Tasks][execution-report-tasks] for more information). Bash should be available on the path `/bin/bash` and it should be the container entrypoint.
+:::
+
+## Apptainer
+
+<AddedInVersion version="22.11.0-edge" />
+
+[Apptainer](https://apptainer.org) is an alternative container runtime to Docker and an open source fork of Singularity. The main advantages of Apptainer are that it can be used without root privileges and it doesn't require a separate daemon process. These, along with other features such as support for autofs mounts, makes Apptainer better suited to the requirements of HPC workloads. Apptainer is able to use existing Docker images and can pull from Docker registries.
+
+### Prerequisites
+
+You will need Apptainer installed on your execution environment e.g. your computer or a distributed cluster, depending on where you want to run your pipeline.
+
+### Images
+
+Apptainer makes use of a container image file, which physically contains the container. Refer to the [Apptainer documentation](https://apptainer.org/docs) to learn how to create Apptainer images.
+
+Apptainer allows paths that do not currently exist within the container to be created and mounted dynamically by specifying them on the command line. However this feature is only supported on hosts that support the [Overlay file system](https://en.wikipedia.org/wiki/OverlayFS) and is not enabled by default.
+
+:::note
+Nextflow expects that data paths are defined system wide, and your Apptainer images need to be created having the mount paths defined in the container file system.
+:::
+
+If your Apptainer installation support the "user bind control" feature, enable the Nextflow support for that by defining the `apptainer.autoMounts = true` setting in the Nextflow configuration file.
+
+### How it works
+
+The integration for Apptainer follows the same execution model implemented for Docker. You won't need to modify your Nextflow script in order to run it with Apptainer. Simply specify the Apptainer image file from where the containers are started by using the `-with-apptainer` command line option. For example:
+
+```bash
+nextflow run main.nf -with-apptainer [apptainer image file]
+```
+
+Every time your script launches a process execution, Nextflow will run it into an Apptainer container created by using the specified image. In practice Nextflow will automatically wrap your processes and launch them by running the `apptainer exec` command with the image you have provided.
+
+:::note
+An Apptainer image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
+:::
+
+If you want to avoid entering the Apptainer image as a command line parameter, you can define it in the Nextflow configuration file. For example you can add the following lines in the configuration file:
+
+```groovy
+process.container = '/path/to/apptainer.img'
+apptainer.enabled = true
+```
+
+In the above example replace `/path/to/apptainer.img` with any Apptainer image of your choice.
+
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
+
+:::note
+Unlike Docker, Nextflow does not automatically mount host paths in the container when using Apptainer. It expects that the paths are configured and mounted system wide by the Apptainer runtime. If your Apptainer installation allows user defined bind points. See [Apptainer][config-apptainer] to learn how to enable Nextflow auto mounts.
+:::
+
+:::warning
+When a process input is a *symbolic link* file, make sure the linked file is stored in a host folder that is accessible from a bind path defined in your Apptainer installation. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
+:::
+
+<ChangedInVersion version="23.07.0-edge">
+Nextflow no longer mounts the home directory when launching an Apptainer container. To re-enable the old behavior, set the environment variable `NXF_APPTAINER_HOME_MOUNT` to `true`.
+</ChangedInVersion>
+
+### Multiple containers
+
+It is possible to specify a different Apptainer image for each process definition in your pipeline script. For example, suppose you have two processes named `hello` and `bye`. You can specify two different Apptainer images in the configuration file as shown below:
+
+```groovy
+process {
+    withName:hello {
+        container = 'image_name_1'
+    }
+    withName:bye {
+        container = 'image_name_2'
+    }
+}
+apptainer {
+    enabled = true
+}
+```
+
+See [Process configuration][config-process] to learn more about processes configuration.
+
+### Apptainer & Docker Hub
+
+Nextflow is able to transparently pull remote container images stored in any Docker compatible registry.
+
+By default, when a container name is specified, Nextflow checks if an image file with that name exists in the local file system. If that image file exists, it's used to execute the container. If a matching file does not exist, Nextflow automatically tries to pull an image with the specified name from the container registry.
+
+If you want Nextflow to check only for local file images, prefix the container name with the `file://` pseudo-protocol. For example:
+
+```groovy
+process.container = 'file:///path/to/apptainer.img'
+apptainer.enabled = true
+```
+
+:::warning
+Use three `/` slashes to specify an **absolute** file path, otherwise the path will be interpreted as relative to the workflow launch directory.
+:::
+
+To pull images from Apptainer Hub or a third party Docker registry, prefix the image name with the `shub://`, `docker://` or `docker-daemon://` pseudo-protocol as required by Apptainer. For example:
+
+```groovy
+process.container = 'docker://quay.io/biocontainers/multiqc:1.3--py35_2'
+apptainer.enabled = true
+```
+
+You do not need to specify `docker://` to pull from a Docker repository. Nextflow will automatically prepend it to your image name when Apptainer is enabled. Additionally, the Docker engine will not work with containers specified as `docker://`.
+
+:::note
+This feature requires the `apptainer` tool to be installed where the workflow execution is launched (as opposed to the compute nodes).
+:::
+
+Nextflow caches Apptainer images in the `apptainer` directory, in the pipeline work directory, by default. However, it is recommended to provide a centralized cache directory using the `NXF_APPTAINER_CACHEDIR` environment variable or the `apptainer.cacheDir` setting in the Nextflow config file.
+
+Nextflow uses the library directory to determine the location of Apptainer containers. The library directory can be defined using the `apptainer.libraryDir` configuration setting or the `NXF_APPTAINER_LIBRARYDIR` environment variable. The configuration file option overrides the environment variable if both are set.
+
+Nextflow first checks the library directory when searching for the image. If the image is not found it then checks the cache directory. The main difference between the library directory and the cache directory is that the first is assumed to be a read-only container repository, while the latter is expected to be writable path where container images can be added for caching purposes.
+
+:::warning
+When using a compute cluster, the Apptainer cache directory must reside in a shared filesystem accessible to all compute nodes.
+:::
+
+:::danger
+When pulling Docker images, Apptainer may be unable to determine the container size if the image was stored using an old Docker format, resulting in a pipeline execution error. See Apptainer documentation for details.
+:::
+
+### Advanced settings
+
+Apptainer advanced configuration settings are described in[Apptainer][config-apptainer] section in the Nextflow configuration page.
+
+## Charliecloud
+
+<AddedInVersion version="20.12.0-edge" />
+
+<ChangedInVersion version="21.03.0-edge">
+Requires Charliecloud 0.22 to 0.27.
+</ChangedInVersion>
+
+<ChangedInVersion version="22.09.0-edge">
+Requires Charliecloud 0.28 or later.
+</ChangedInVersion>
+
+:::warning{title="Experimental: not recommended for production environments."}
+:::
+
+[Charliecloud](https://hpc.github.io/charliecloud) is an alternative container runtime to Docker, that is better suited for use in HPC environments. Its main advantage is that it can be used without root privileges, making use of user namespaces in the Linux kernel. Charliecloud is able to pull from Docker registries.
+
+### Prerequisites
+
+You will need Charliecloud installed in your execution environment e.g. on your computer or a distributed cluster, depending on where you want to run your pipeline.
+
+### How it works
+
+You won't need to modify your Nextflow script in order to run it with Charliecloud. Simply specify the docker image from where the containers are started by using the `-with-charliecloud` command line option. For example:
+
+```bash
+nextflow run main.nf -with-charliecloud [container]
+```
+
+Every time your script launches a process execution, Nextflow will run it into a charliecloud container created by using the specified container image. In practice Nextflow will automatically wrap your processes and run them by executing the `ch-run` command with the container you have provided.
+
+:::note
+A container image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
+:::
+
+If you want to avoid entering the Container image as a command line parameter, you can define it in the Nextflow configuration file. For example you can add the following lines in the configuration file:
+
+```groovy
+process.container = '/path/to/container'
+charliecloud.enabled = true
+```
+
+:::warning
+If an absolute path is provided, the container needs to be in the Charliecloud flat directory format. See below on compatibility with Docker registries.
+:::
+
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
+
+:::warning
+Nextflow automatically manages the file system mounts whenever a container is launched depending on the process input files. However, when a process input is a *symbolic link*, the linked file **must** be stored in the same folder where the symlink is located, or a sub-folder of it. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
+:::
+
+### Charliecloud & Docker Hub
+
+Nextflow is able to transparently pull remote container images stored in any Docker compatible registry and converts them to the Charliecloud compatible format.
+
+By default when a container name is specified, Nextflow checks if a container with that name exists in the local file system. If it exists, it's used to execute the container. If a matching file does not exist, Nextflow automatically tries to pull an image with the specified name from the Docker Hub.
+
+To pull images from a third party Docker registry simply provide the URL to the image. If no URL is provided, Docker Hub is assumed. For example this can be used to pull an image from quay.io and convert it automatically to the Charliecloud container format:
+
+```groovy
+process.container = 'https://quay.io/biocontainers/multiqc:1.3--py35_2'
+charliecloud.enabled = true
+```
+
+Whereas this would pull from Docker Hub:
+
+```groovy
+process.container = 'nextflow/examples:latest'
+charliecloud.enabled = true
+```
+
+### Multiple containers
+
+It is possible to specify a different Docker image for each process definition in your pipeline script. For example, suppose you have two processes named `hello` and `bye`. You can specify two different Docker images for them in the config file as shown below:
+
+```groovy
+process {
+    withName:hello {
+        container = 'image_name_1'
+    }
+    withName:bye {
+        container = 'image_name_2'
+    }
+}
+
+charliecloud {
+    enabled = true
+}
+```
+
+See [Process configuration][config-process] to learn more about processes configuration.
+
+After running your pipeline, you can easily query the container image that each process used with the following command:
+
+```bash
+nextflow log last -f name,container
+```
+
+### Advanced settings
+
+Charliecloud advanced configuration settings are described in the [Charliecloud][config-charliecloud] section in the Nextflow configuration page.
+
+## Docker
+
+[Docker](http://www.docker.io) is the industry standard container runtime.
+
+### Prerequisites
+
+You will need Docker installed on your execution environment e.g. your computer or a distributed cluster, depending on where you want to run your pipeline.
+
+If you are running Docker on Mac OSX make sure you are mounting your local `/Users` directory into the Docker VM as explained in this excellent tutorial: [How to use Docker on OSX](http://viget.com/extend/how-to-use-docker-on-os-x-the-missing-guide).
+
+### How it works
+
+You won't need to modify your Nextflow script in order to run it with Docker. Simply specify the Docker image from where the containers are started by using the `-with-docker` command line option. For example:
+
+```bash
+nextflow run main.nf -with-docker [docker image]
+```
+
+Every time your script launches a process execution, Nextflow will run it into a Docker container created by using the specified image. In practice Nextflow will automatically wrap your processes and run them by executing the `docker run` command with the image you have provided.
+
+:::note
+A Docker image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
+:::
+
+If you want to avoid entering the Docker image as a command line parameter, you can define it in the Nextflow configuration file. For example you can add the following lines in the configuration file:
+
+```groovy
+process.container = 'nextflow/examples:latest'
+docker.enabled = true
+```
+
+In the above example replace `nextflow/examples:latest` with any Docker image of your choice.
+
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
+
+:::warning
+Nextflow automatically manages the file system mounts whenever a container is launched depending on the process input files. However, when a process input is a *symbolic link*, the linked file **must** be stored in the same folder where the symlink is located, or a sub-folder of it. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
+:::
+
+### Multiple containers
+
+It is possible to specify a different Docker image for each process definition in your pipeline script. Suppose you have two processes named `hello` and `bye`. You can specify two different Docker images for them in the Nextflow script as shown below:
+
+```nextflow
+process hello {
+  container 'image_name_1'
+
+  script:
+  """
+  do this
+  """
+}
+
+process bye {
+  container 'image_name_2'
+
+  script:
+  """
+  do that
+  """
+}
+```
+
+Alternatively, the same containers definitions can be provided by using the configuration file as shown below:
+
+```groovy
+process {
+    withName:hello {
+        container = 'image_name_1'
+    }
+    withName:bye {
+        container = 'image_name_2'
+    }
+}
+
+docker {
+    enabled = true
+}
+```
+
+See [Process configuration][config-process] to learn more.
+
+### Advanced settings
+
+Docker advanced configuration settings are described in the [docker][config-docker] section in the Nextflow configuration page.
+
+## Podman
+
+<AddedInVersion version="20.01.0" />
+
+[Podman](http://www.podman.io) is a drop-in replacement for Docker that can run containers with or without root privileges.
+
+### Prerequisites
+
+You will need Podman installed on your execution environment e.g. your computer or a distributed cluster, depending on where you want to run your pipeline. Running in rootless mode requires appropriate OS configuration. Due to current Podman limits using cpuset for cpus and memory such is only possible using sudo.
+
+### How it works
+
+You won't need to modify your Nextflow script in order to run it with Podman. Simply specify the Podman image from where the containers are started by using the `-with-podman` command line option. For example:
+
+```bash
+nextflow run main.nf -with-podman [OCI container image]
+```
+
+Every time your script launches a process execution, Nextflow will run it into a Podman container created by using the specified image. In practice Nextflow will automatically wrap your processes and run them by executing the `podman run` command with the image you have provided.
+
+:::note
+An OCI container image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
+:::
+
+If you want to avoid entering the Podman image as a command line parameter, you can define it in the Nextflow configuration file. For example you can add the following lines in the configuration file:
+
+```groovy
+process.container = 'nextflow/examples:latest'
+podman.enabled = true
+```
+
+In the above example replace `nextflow/examples:latest` with any Podman image of your choice.
+
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
+
+:::warning
+Nextflow automatically manages the file system mounts whenever a container is launched depending on the process input files. However, when a process input is a *symbolic link*, the linked file **must** be stored in the same folder where the symlink is located, or a sub-folder of it. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
+:::
+
+### Multiple containers
+
+It is possible to specify a different container image for each process definition in your pipeline script. Let's suppose you have two processes named `hello` and `bye`. You can specify two different container images for them in the Nextflow script as shown below:
+
+```nextflow
+process hello {
+  container 'image_name_1'
+
+  script:
+  """
+  do this
+  """
+}
+
+process bye {
+  container 'image_name_2'
+
+  script:
+  """
+  do that
+  """
+}
+```
+
+Alternatively, the same containers definitions can be provided by using the configuration file as shown below:
+
+```groovy
+process {
+    withName:hello {
+        container = 'image_name_1'
+    }
+    withName:bye {
+        container = 'image_name_2'
+    }
+}
+
+podman {
+    enabled = true
+}
+```
+
+See[Process configuration][config-process] to learn more about processes configuration.
+
+### Advanced settings
+
+Podman advanced configuration settings are described in the [podman][config-podman] section in the Nextflow configuration page.
+
+## Sarus
+
+<AddedInVersion version="22.12.0-edge">
+Requires Sarus 1.5.1 or later.
+</AddedInVersion>
+
+[Sarus](https://sarus.readthedocs.io) is an alternative container runtime to Docker. Sarus works by converting Docker images to a common format that can then be distributed and launched on HPC systems. The user interface to Sarus enables a user to select an image from [Docker Hub](https://hub.docker.com/) and then submit jobs which run entirely within the container.
+
+### Prerequisites
+
+You need Sarus installed in your execution environment, i.e. your personal computer or a distributed cluster, depending on where you want to run your pipeline.
+
+### Images
+
+Sarus converts a docker image to Squashfs layers which are distributed and launched in the cluster. For more information on how to build Sarus images see the [official documentation](https://sarus.readthedocs.io/en/stable/user/user_guide.html#develop-the-docker-image).
+
+### How it works
+
+The integration for Sarus, at this time, requires you to set up the following parameters in your config file:
+
+```groovy
+process.container = "dockerhub_user/image_name:image_tag"
+sarus.enabled = true
+```
+
+and it will always try to search the Docker Hub registry for the images.
+
+:::note
+if you do not specify an image tag, the `latest` tag will be fetched by default.
+:::
+
+### Multiple containers
+
+It is possible to specify a different Sarus image for each process definition in your pipeline script. For example, suppose you have two processes named `hello` and `bye`. You can specify two different Sarus images specifying them in the configuration file as shown below:
+
+```groovy
+process {
+    withName:hello {
+        container = 'image_name_1'
+    }
+    withName:bye {
+        container = 'image_name_2'
+    }
+}
+
+sarus {
+    enabled = true
+}
+```
+
+See [Process configuration][config-process] to learn more about processes configuration.
+
+## Shifter
+
+[Shifter](https://docs.nersc.gov/programming/shifter/overview/) is an alternative container runtime to Docker. Shifter works by converting Docker images to a common format that can then be distributed and launched on HPC systems. The user interface to Shifter enables a user to select an image from [Docker Hub](https://hub.docker.com/) and then submit jobs which run entirely within the container.
+
+### Prerequisites
+
+You need Shifter and Shifter image gateway installed in your execution environment, i.e: your personal computer or the entry node of a distributed cluster. In the case of a distributed cluster, you should have Shifter installed on all of the compute nodes and the `shifterimg` command should also be available and Shifter properly setup to access the Image gateway, for more information see the [official documentation](https://github.com/NERSC/shifter/tree/master/doc).
+
+### Images
+
+Shifter converts a Docker image to squashfs layers which are distributed and launched in the cluster. For more information on how to build Shifter images see the [official documentation](https://docs.nersc.gov/programming/shifter/how-to-use/#building-shifter-images).
+
+### How it works
+
+The integration for Shifter requires you to set up the following parameters in your config file:
+
+```groovy
+process.container = "dockerhub_user/image_name:image_tag"
+shifter.enabled = true
+```
+
+Shifter will search the Docker Hub registry for the images. If you do not specify an image tag, the `latest` tag will be fetched by default.
+
+### Multiple containers
+
+It is possible to specify a different Shifter image for each process definition in your pipeline script. For example, suppose you have two processes named `hello` and `bye`. You can specify two different Shifter images specifying them in the configuration file as shown below:
+
+```groovy
+process {
+    withName:hello {
+        container = 'image_name_1'
+    }
+    withName:bye {
+        container = 'image_name_2'
+    }
+}
+
+shifter {
+    enabled = true
+}
+```
+
+See [Process configuration][config-process] to learn more about processes configuration.
+
+## Singularity
+
+[Singularity](http://singularity.lbl.gov/) is an alternative container runtime to Docker. The main advantages of Singularity are that it can be used without root privileges and it doesn't require a separate daemon process. These, along with other features such as support for autofs mounts, makes Singularity better suited to the requirements of HPC workloads. Singularity is able to use existing Docker images and can pull from Docker registries.
+
+### Prerequisites
+
+You will need Singularity installed on your execution environment e.g. your computer or a distributed cluster, depending on where you want to run your pipeline.
+
+### Images
+
+Singularity makes use of a container image file, which physically contains the container. Refer to the [Singularity documentation](https://www.sylabs.io/docs/) to learn how create Singularity images.
+
+Singularity allows paths that do not currently exist within the container to be created and mounted dynamically by specifying them on the command line. However this feature is only supported on hosts that support the [Overlay file system](https://en.wikipedia.org/wiki/OverlayFS) and is not enabled by default.
+
+:::note
+Nextflow expects that data paths are defined system wide, and your Singularity images need to be created having the mount paths defined in the container file system.
+:::
+
+If your Singularity installation support the "user bind control" feature, enable the Nextflow support for that by defining the `singularity.autoMounts = true` setting in the Nextflow configuration file.
+
+### How it works
+
+The integration for Singularity follows the same execution model implemented for Docker. You won't need to modify your Nextflow script in order to run it with Singularity. Simply specify the Singularity image file from where the containers are started by using the `-with-singularity` command line option. For example:
+
+```bash
+nextflow run main.nf -with-singularity [singularity image file]
+```
+
+Every time your script launches a process execution, Nextflow will run it into a Singularity container created by using the specified image. In practice Nextflow will automatically wrap your processes and launch them by running the `singularity exec` command with the image you have provided.
+
+:::note
+A Singularity image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
+:::
+
+If you want to avoid entering the Singularity image as a command line parameter, you can define it in the Nextflow configuration file. For example you can add the following lines in the configuration file:
+
+```groovy
+process.container = '/path/to/singularity.img'
+singularity.enabled = true
+```
+
+In the above example replace `/path/to/singularity.img` with any Singularity image of your choice.
+
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
+
+:::note
+Unlike Docker, Nextflow does not automatically mount host paths in the container when using Singularity. It expects that the paths are configured and mounted system wide by the Singularity runtime. If your Singularity installation allows user defined bind points, see [Singularity][config-singularity] to learn how to enable Nextflow auto mounts.
+:::
+
+:::warning
+When a process input is a *symbolic link* file, make sure the linked file is stored in a host folder that is accessible from a bind path defined in your Singularity installation. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
+:::
+
+<ChangedInVersion version="23.07.0-edge">
+Nextflow no longer mounts the home directory when launching a Singularity container. To re-enable the old behavior, set the environment variable `NXF_SINGULARITY_HOME_MOUNT` to `true`.
+</ChangedInVersion>
+
+<ChangedInVersion version="23.09.0-edge">
+Nextflow automatically mounts the required host paths in the container. To re-enable the old behavior, set the environment variable `NXF_SINGULARITY_AUTO_MOUNTS` to `false` or set `singularity.autoMounts=false` in the Nextflow configuration file.
+</ChangedInVersion>
+
+<ChangedInVersion version="23.09.0-edge">
+The execution command for Singularity/Apptainer containers can be set to `run` by means of the environment variable `NXF_SINGULARITY_RUN_COMMAND` (default command is `exec`).
+</ChangedInVersion>
+
+### Multiple containers
+
+It is possible to specify a different Singularity image for each process definition in your pipeline script. For example, suppose you have two processes named `hello` and `bye`. You can specify two different Singularity images specifying them in the configuration file as shown below:
+
+```groovy
+process {
+    withName:hello {
+        container = 'image_name_1'
+    }
+    withName:bye {
+        container = 'image_name_2'
+    }
+}
+
+singularity {
+    enabled = true
+}
+```
+
+See [Process configuration][config-process] to learn more about processes configuration.
+
+### Singularity & Docker Hub
+
+*Requires Singularity 2.3 or later*
+
+Nextflow is able to transparently pull remote container images stored in the [Singularity-Hub](https://singularity-hub.org/), [Singularity Library](https://cloud.sylabs.io/library/), or any Docker compatible registry.
+
+By default when a container name is specified, Nextflow checks if an image file with that name exists in the local file system. If that image file exists, it's used to execute the container. If a matching file does not exist, Nextflow automatically tries to pull an image with the specified name from the Docker Hub.
+
+If you want Nextflow to check only for local file images, prefix the container name with the `file://` pseudo-protocol. For example:
+
+```groovy
+process.container = 'file:///path/to/singularity.img'
+singularity.enabled = true
+```
+
+:::warning
+Use three `/` slashes to specify an **absolute** file path, otherwise the path will be interpreted as relative to the workflow launch directory.
+:::
+
+To pull images from the Singularity Hub or a third party Docker registry simply prefix the image name with the `shub://`, `docker://` or `docker-daemon://` pseudo-protocol as required by the Singularity tool. For example:
+
+```groovy
+process.container = 'docker://quay.io/biocontainers/multiqc:1.3--py35_2'
+singularity.enabled = true
+```
+
+You do not need to specify `docker://` to pull from a Docker repository. Nextflow will automatically prepend it to your image name when Singularity is enabled. Additionally, the Docker engine will not work with containers specified as `docker://`.
+
+Nextflow supports the [Singularity Library](https://cloud.sylabs.io/library/) repository:
+
+```groovy
+process.container = 'library://library/default/alpine:3.8'
+```
+
+The `library://` pseudo-protocol allows you to import Singularity images from a local Docker installation instead of downloading them from a Docker registry. This feature requires the `singularity` tool to be installed where the workflow execution is launched (as opposed to the compute nodes).
+
+Nextflow caches Singularity images in the `singularity` directory, in the pipeline work directory, by default. However, it is recommended to provide a centralized cache directory using the `NXF_SINGULARITY_CACHEDIR` environment variable or the `singularity.cacheDir` setting in the Nextflow config file.
+
+Nextflow uses the library directory to determine the location of Singularity images. The library directory can be defined using the `singularity.libraryDir` configuration setting or the `NXF_SINGULARITY_LIBRARYDIR` environment variable. The configuration file option overrides the environment variable if both are set.
+
+Nextflow first checks the library directory when searching for the image. If the image is not found it then checks the cache directory. The main difference between the library directory and the cache directory is that the first is assumed to be a read-only container repository, while the latter is expected to be writable path where container images can be added for caching purposes.
+
+:::warning
+When using a compute cluster, the Singularity cache directory must reside in a shared filesystem accessible to all compute nodes.
+:::
+
+:::danger
+When pulling Docker images, Singularity may be unable to determine the container size if the image was stored using an old Docker format, resulting in a pipeline execution error. See Singularity documentation for details.
+:::
+
+### Advanced settings
+
+Singularity advanced configuration settings are described in the [singularity][config-singularity] section in the Nextflow configuration page.
+
+[execution-report-tasks]: /nextflow_docs/nextflow_repo/docs/reports.mdx#tasks
+[config-page]: /nextflow_docs/nextflow_repo/docs/config.mdx
+[config-apptainer]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#apptainer
+[config-process]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-configuration
+[config-charliecloud]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#charliecloud
+[config-docker]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#docker
+[config-podman]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#podman
+[config-singularity]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#singularity
diff --git a/docs/developer-env.md b/docs/developer-env.mdx
similarity index 77%
rename from docs/developer-env.md
rename to docs/developer-env.mdx
index 839297d839..dfc765f5a8 100644
--- a/docs/developer-env.md
+++ b/docs/developer-env.mdx
@@ -1,4 +1,5 @@
-(devenv-page)=
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
 
 # Environment setup
 
@@ -6,32 +7,29 @@ Setting up a Nextflow development environment is a prerequisite for creating, te
 
 <h3>Recommended tools</h3>
 
-- {ref}`devenv-vscode`: A versatile code editor that enhances your Nextflow development with features like syntax highlighting and debugging.
-- {ref}`devenv-extensions`: The VS Code marketplace offers a variety of extensions to enhance development. The {ref}`Nextflow extension <devenv-nextflow>` is specifically designed to enhance Nextflow development with diagnostics, hover hints, code navigation, code completion, and more.
-- {ref}`devenv-docker`: A containerization platform that ensures your Nextflow workflows run consistently across different environments by packaging dependencies into isolated containers.
-- {ref}`devenv-git`: A version control system that helps manage and track changes in your Nextflow projects, making collaboration and code management more efficient.
+- [VS Code][devenv-vscode]: A versatile code editor that enhances your Nextflow development with features like syntax highlighting and debugging.
+- [Extensions][devenv-extensions]: The VS Code marketplace offers a variety of extensions to enhance development. The [Nextflow extension][devenv-nextflow] is specifically designed to enhance Nextflow development with diagnostics, hover hints, code navigation, code completion, and more.
+- [Docker][devenv-docker]: A containerization platform that ensures your Nextflow workflows run consistently across different environments by packaging dependencies into isolated containers.
+- [Git][devenv-git]: A version control system that helps manage and track changes in your Nextflow projects, making collaboration, and code management more efficient.
 
 The sections below outline the steps for setting up these tools.
 
-:::{note}
-Nextflow must be installed separately. See {ref}`install-page` for Nextflow installation instructions.
+:::note
+Nextflow must be installed separately. See [Installation][install-page] for Nextflow installation instructions.
 :::
 
-:::{note}
-If you are using a Windows computer, first install and configure the Windows Subsystem for Linux (WSL). See {ref}`devenv-wsl` for installation instructions.
+:::note
+If you are using a Windows computer, first install and configure the Windows Subsystem for Linux (WSL). See [Windows Subsystem for Linux][devenv-wsl] for installation instructions.
 :::
 
-(devenv-vscode)=
-
 ## VS Code
 
 An Integrated Development Environment (IDE) provides a user-friendly interface for writing, editing, and managing code. Installing one is an essential step for setting up your environment. 
 
 Visual Studio Code (VS Code) is a popular lightweight IDE known for its versatility and extensibility. It offers features like syntax highlighting, intelligent code completion, and integrated debugging tools for various programming languages. VS Code supports Windows, macOS, and Linux, and is a good choice for both new and experienced Nextflow developers.
 
-````{tabs}
-
-```{group-tab} Windows
+<Tabs>
+<TabItem value="Windows" label="Windows" default>
 
 To install VS Code on Windows:
 
@@ -39,9 +37,8 @@ To install VS Code on Windows:
 1. Download VS Code for Windows.
 1. Double-click the installer executable (`.exe`) file and follow the setup steps.
 
-```
-
-```{group-tab} macOS
+</TabItem>
+<TabItem value="macOS" label="macOS" default>
 
 To install VS Code on macOS:
 
@@ -49,9 +46,8 @@ To install VS Code on macOS:
 1. Download VS Code for macOS.
 1. Drag the `Visual Studio Code.app` application to the Applications folder to add it to the macOS Launchpad.
 
-```
-
-```{group-tab} Linux
+</TabItem>
+<TabItem value="Linux" label="Linux" default>
 
 To install VS Code on Linux Debian/Ubuntu distributions:
 
@@ -61,25 +57,20 @@ To install VS Code on Linux Debian/Ubuntu distributions:
 1. Navigate to the folder where you downloaded VS Code.
 1. Run `sudo apt install ./<file>.deb`, replacing `<file>` with the full file name.
    
-   :::{note}
+   :::note
    If you're using an older Linux distribution, run `sudo dpkg -i <file>.deb` to install VS Code and `sudo apt-get install -f` to install dependencies.
    :::
    
 See [Linux installation](https://code.visualstudio.com/docs/setup/linux#_installation) for information about installing VS Code on other distributions.
 
-```
-
-````
-
-(devenv-extensions)=
+</TabItem>
+</Tabs>
 
 ## Extensions
 
 Extensions are a key feature of IDEs and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. Popular VS Code extensions for Nextflow developers are listed below:
 
-(devenv-nextflow)=
-
-**Nextflow**
+### Nextflow
 
 The VS Code [Nextflow extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) adds Nextflow language support to the editor. The Nextflow extension enhances development with:
 
@@ -92,31 +83,28 @@ The VS Code [Nextflow extension](https://marketplace.visualstudio.com/items?item
 - Parameter schemas
 - DAG previews
 
-See {ref}`vscode-page` for more information about the Nextflow extension features and how it enforces the Nextflow syntax.
+See [VS Code][vscode-page] for more information about the Nextflow extension features and how it enforces the Nextflow syntax.
 
-**nf-core**
+### nf-core
 
 [nf-core](https://nf-co.re/) is a community effort to collect a curated set of analysis pipelines built using Nextflow. The [nf-core extension pack](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) adds a selection of tools that support development. For example, it includes [Code Spell Checker](https://marketplace.visualstudio.com/items?itemName=streetsidesoftware.code-spell-checker), [Prettier](https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode), [Todo Tree](https://marketplace.visualstudio.com/items?itemName=Gruntfuggly.todo-tree), and [Markdown Extended](https://marketplace.visualstudio.com/items?itemName=jebbs.markdown-extended).
 
 See the [nf-core extension pack](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) for more information about the included tools.
 
-(devenv-remote)=
-
-**Remote development**
+### Remote development
 
 The [Remote Development extension pack](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) enables you to run WSL, SSH, or a development container for editing and debugging with the full set of VS Code features.
 
 The pack includes the [Remote - SSH](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh), [Remote - Tunnels](https://marketplace.visualstudio.com/items?itemName=ms-vscode.remote-server), [Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers), and [WSL](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-wsl) extensions. See [Remote Development](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) for more information about the tools included in the remote development extension pack.
 
-:::{note}
+:::note
 The Remote Development extension pack is required if you are developing using remote servers, Windows Subsystem for Linux, or Development Containers.
 :::
 
 Installing VS Code extensions requires just a few clicks in the Extensions Marketplace. 
 
-````{tabs}
-
-```{group-tab} Windows
+<Tabs>
+<TabItem value="Windows" label="Windows" default>
 
 To install a VS Code extension on Windows:
 
@@ -125,9 +113,8 @@ To install a VS Code extension on Windows:
 1. Search for the extension.
 1. Select **Install**.
 
-```
-
-```{group-tab} macOS
+</TabItem>
+<TabItem value="macOS" label="macOS" default>
 
 To install a VS Code extension on macOS:
 
@@ -136,9 +123,8 @@ To install a VS Code extension on macOS:
 1. Search for the extension.
 1. Select **Install**.
 
-```
-
-```{group-tab} Linux
+</TabItem>
+<TabItem value="Linux" label="Linux" default>
 
 To install a VS Code extension on Linux Debian/Ubuntu distributions:
 
@@ -147,11 +133,8 @@ To install a VS Code extension on Linux Debian/Ubuntu distributions:
 1. Search for the extension.
 1. Select **Install**.
 
-```
-
-````
-
-(devenv-docker)=
+</TabItem>
+</Tabs>
 
 ## Docker
 
@@ -159,9 +142,8 @@ Docker is an open-source platform that simplifies application development, deplo
 
 Docker Desktop provides a Graphical User Interface (GUI) for managing Docker containers. Installing Docker Desktop is a straightforward process that allows you to create, deploy, and manage applications within containers.
 
-````{tabs}
-
-```{group-tab} Windows
+<Tabs>
+<TabItem value="Windows" label="Windows" default>
 
 To install Docker Desktop on Windows:
 
@@ -170,7 +152,7 @@ To install Docker Desktop on Windows:
 1. Double-click Docker Desktop `Installer.exe` to run the installer. By default, Docker Desktop is installed at `C:\Program Files\Docker\Docker`.
 1. Depending on your choice of backend, select the **Use WSL 2 instead of Hyper-V** option on the Configuration page.
 
-    :::{note}
+    :::note
     You won't be able to select which backend to use if your system only supports one of the two options.
     :::
 
@@ -179,15 +161,14 @@ To install Docker Desktop on Windows:
 1. Start Docker Desktop.
 1. Review the Docker Subscription Service Agreement and select **Accept** to continue.
 
-    :::{note}
+    :::note
     Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop.
     :::
 
 1. Docker Desktop starts after you accept the terms.
 
-```
-
-```{group-tab} macOS
+</TabItem>
+<TabItem value="macOS" label="macOS" default>
 
 To install Docker Desktop on macOS:
 
@@ -198,20 +179,20 @@ To install Docker Desktop on macOS:
 1. Double-click **Docker.app** in the **Applications** folder to start Docker.
 1. Review the Docker Subscription Service Agreement and select **Accept** to continue.
 
-    :::{note}
+    :::note
     Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop.
     :::
     
 1. From the installation window, select **Use recommended settings (Requires password)**.
 
-    :::{note} The **recommended settings** allow Docker Desktop to automatically set the necessary configuration settings. Advanced settings allow you to set the location of the Docker CLI tools either in the system or user directory, enable the default Docker socket, and enable privileged port mapping. See [Settings](https://docs.docker.com/desktop/settings/#advanced), for more information and how to set the location of the Docker CLI tools.
+    :::note
+    The **recommended settings** allow Docker Desktop to automatically set the necessary configuration settings. Advanced settings allow you to set the location of the Docker CLI tools either in the system or user directory, enable the default Docker socket, and enable privileged port mapping. See [Settings](https://docs.docker.com/desktop/settings/#advanced), for more information and how to set the location of the Docker CLI tools.
     :::
 
 1. Select **Finish**. If you have applied any of the previous configurations that require a password, enter your password to confirm your choice.
 
-```
-
-```{group-tab} Linux
+</TabItem>
+<TabItem value="Linux" label="Linux" default>
 
 To install Docker Desktop on Linux Debian/Ubuntu distributions:
 
@@ -219,7 +200,7 @@ To install Docker Desktop on Linux Debian/Ubuntu distributions:
 1. Download the latest Debian/Ubuntu (`.deb`) distribution.
 1. In your terminal, run `sudo apt-get install ./docker-desktop-amd64.deb`
 
-    :::{note}
+    :::note
     By default, Docker Desktop is installed at `/opt/docker-desktop`.
     :::
 
@@ -227,17 +208,14 @@ To install Docker Desktop on Linux Debian/Ubuntu distributions:
 1. Review the Docker Subscription Service Agreement and select **Accept** to continue.
 1. From the installation window, select **Use recommended settings (Requires password)**. Docker Desktop starts after you accept the terms.
 
-    :::{note}
+    :::note
     Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop.
     :::
 
-```
-
-````
+</TabItem>
+</Tabs>
 
-Nextflow supports multiple container technologies (e.g., Singularity and Podman) so you can choose the one that best fits your needs. See {ref}`container-page` for more information about other supported container engines.
-
-(devenv-git)=
+Nextflow supports multiple container technologies (e.g., Singularity and Podman) so you can choose the one that best fits your needs. See [Containers][containers-page] for more information about other supported container engines.
 
 ## Git
 
@@ -245,9 +223,8 @@ Git provides powerful version control that helps track code changes. Git operate
 
 Nextflow seamlessly integrates with Git for source code management providers to manage pipelines as version-controlled Git repositories.
 
-````{tabs}
-
-```{group-tab} Windows
+<Tabs>
+<TabItem value="Windows" label="Windows" default>
 
 Git is already installed on most WSL distributions. You can check if it is already installed by running `git version`.
 
@@ -258,17 +235,16 @@ To install the latest stable Git version on Linux Debian/Ubuntu distributions:
 
 See [git-scm documentation](https://git-scm.com/downloads/linux) for more information about installing Git on other Linux distributions.
 
-```
-
-```{group-tab} macOS
+</TabItem>
+<TabItem value="macOS" label="macOS" default>
 
 To install Git on macOS with [Homebrew](https://docs.brew.sh/):
 
 1. Open a terminal window and run `brew install git`.
 
-   :::{note}
-   You must have Homebrew installed. See [Homebrew installation](https://docs.brew.sh/Installation) for instructions.
-   :::
+    :::note
+    You must have Homebrew installed. See [Homebrew installation](https://docs.brew.sh/Installation) for instructions.
+    :::
 
 1. Once complete, run `git version` to verify Git was installed.
 
@@ -279,9 +255,8 @@ To install Git on macOS with [Xcode](https://developer.apple.com/xcode/):
 1. Select **Install**.
 1. Once complete, open a new terminal window and run `git version` to verify Git was installed.
 
-```
-
-```{group-tab} Linux
+</TabItem>
+<TabItem value="Linux" label="Linux" default>
 
 Git is already installed on most Linux Debian/Ubuntu distributions.
 
@@ -292,11 +267,8 @@ To install the latest stable Git version on Linux Debian/Ubuntu distributions:
 
 See [git-scm documentation](https://git-scm.com/downloads/linux) for more information about installing Git on other Linux distributions.
 
-```
-
-````
-
-(devenv-wsl)=
+</TabItem>
+</Tabs>
 
 ## Windows Subsystem for Linux
 
@@ -309,15 +281,25 @@ To enable WSL on Windows using Powershell or Windows Command Prompt:
 1. Right-click and select **Run as administrator** to use PowerShell or Windows Command Prompt in administrator mode.
 1. Run `wsl --install`.
 
-    :::{note}
+    :::note
     This command will enable the features necessary to run WSL and install the Ubuntu distribution.
     :::
 
 1. When prompted, restart Windows.
 1. After restarting Windows, open the Ubuntu distribution and create a new Linux **User Name** and **Password** when prompted.
 
-    :::{note}
+    :::note
     The **User Name** and **Password** is specific to each Linux distribution that you install and has no bearing on your Windows user name.
     :::
 
 See [Set up a WSL development environment](https://learn.microsoft.com/en-us/windows/wsl/setup/environment) for more about installing WSL.
+
+[containers-page]: /nextflow_docs/nextflow_repo/docs/container.mdx
+[devenv-docker]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#docker
+[devenv-extensions]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#extensions
+[devenv-git]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#git
+[devenv-nextflow]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#nextflow
+[devenv-vscode]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#vs-code
+[devenv-wsl]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#windows-subsystem-for-linux
+[install-page]: /nextflow_docs/nextflow_repo/docs/install.mdx
+[vscode-page]: /nextflow_docs/nextflow_repo/docs/vscode.mdx
\ No newline at end of file
diff --git a/docs/developer/config-scopes.md b/docs/developer/config-scopes.mdx
similarity index 98%
rename from docs/developer/config-scopes.md
rename to docs/developer/config-scopes.mdx
index 4f2fc9b603..2db1354bf5 100644
--- a/docs/developer/config-scopes.md
+++ b/docs/developer/config-scopes.mdx
@@ -1,5 +1,3 @@
-(config-scopes-page)=
-
 # Configuration scopes
 
 This page provides guidance on defining configuration scopes in the Nextflow runtime.
@@ -161,7 +159,7 @@ The scope classes themselves can be used to construct domain objects on-demand f
 new ExecutorConfig( Global.session.config.executor as Map ?: Collections.emptyMap() )
 ```
 
-:::{note}
+:::note
 In practice, it is better to avoid the use of `Global` and provide an instance of `Session` to the client class instead.
 :::
 
@@ -171,6 +169,8 @@ Config scope classes can be converted into a config spec with the `SpecNode` cla
 
 ### Documentation
 
-The config spec described above can be rendered to Markdown using the `MarkdownRenderer` class. It produces a Markdown document approximating the {ref}`config-options` page.
+The config spec described above can be rendered to Markdown using the `MarkdownRenderer` class. It produces a Markdown document approximating the [Configuration options][config-options] page.
 
 This approach to docs generation is not yet complete, and has not been incorporated into the build process yet. However, it can be used to check for discrepancies between the source code and docs when making changes. The documentation should match the `@Description` annotations as closely as possible, but may contain additional details such as version notes and extra paragraphs.
+
+[config-options]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx
diff --git a/docs/developer/diagram.md b/docs/developer/diagram.md
deleted file mode 100644
index 90300113c2..0000000000
--- a/docs/developer/diagram.md
+++ /dev/null
@@ -1,10 +0,0 @@
-(diagram-page)=
-
-# Workflow Diagram
-
-The following diagram is a high-level overview of the Nextflow source code in a similar style as the {ref}`workflow diagram <workflow-diagram>` visualization for Nextflow pipelines. Each node and subgraph is a class. Arrows depict the flow of data and/or communication between classes.
-
-In general, nodes with sharp corners are "record" classes that simply hold information, while nodes with rounded edges are "function" classes that transform some input into an output. Subgraphs are either long-running classes, i.e. "places where things happen", or one of the other two types for which it was useful to expand and show internal details.
-
-```{mermaid} diagrams/overview.mmd
-```
diff --git a/docs/developer/diagram.mdx b/docs/developer/diagram.mdx
new file mode 100644
index 0000000000..edf4a3a93e
--- /dev/null
+++ b/docs/developer/diagram.mdx
@@ -0,0 +1,80 @@
+# Workflow diagram
+
+The following diagram is a high-level overview of the Nextflow source code in a similar style as the [workflow diagram][workflow-diagram] visualization for Nextflow pipelines. Each node and subgraph is a class. Arrows depict the flow of data and/or communication between classes.
+
+In general, nodes with sharp corners are "record" classes that simply hold information, while nodes with rounded edges are "function" classes that transform some input into an output. Subgraphs are either long-running classes, i.e. "places where things happen", or one of the other two types for which it was useful to expand and show internal details.
+
+```mermaid
+flowchart TB
+  subgraph Launcher
+    subgraph CmdRun
+      subgraph AssetManager
+        ScriptFile
+      end
+      subgraph ConfigBuilder
+        ConfigParser([ConfigParser])
+        ConfigBase([ConfigBase])
+      end
+      subgraph ScriptRunner
+        subgraph Session
+          ConfigMap
+          DAG
+          ExecutorFactory([ExecutorFactory])
+          subgraph TaskProcessor
+            TaskRun
+          end
+          subgraph Executor
+            subgraph TaskMonitor
+              TaskHandler
+            end
+            TaskBean
+            BashWrapperBuilder([BashWrapperBuilder])
+          end
+          TraceRecord
+          CacheFactory([CacheFactory])
+          CacheDB
+          TraceObserver([TraceObserver])
+        end
+        ScriptParser([ScriptParser])
+        BaseScript([BaseScript])
+        subgraph ScriptMeta
+          WorkflowDef([WorkflowDef])
+          ProcessDef([ProcessDef])
+          FunctionDef([FunctionDef])
+        end
+        IncludeDef([IncludeDef])
+        OpCall([OpCall])
+      end
+      ConfigParser --> ConfigBase
+      ConfigBase --> ConfigMap
+      ScriptFile --> ScriptParser
+      ScriptParser --> BaseScript
+      BaseScript --> WorkflowDef
+      BaseScript --> ProcessDef
+      BaseScript --> FunctionDef
+      BaseScript --> IncludeDef
+      IncludeDef --> ScriptParser
+      WorkflowDef --> OpCall
+      OpCall --> DAG
+      ProcessDef --> DAG
+      DAG --> TaskRun
+      TaskRun --> DAG
+      ExecutorFactory --> Executor
+      ConfigMap --> Executor
+      ProcessDef --> TaskProcessor
+      ConfigMap --> TaskProcessor
+      TaskRun --> TaskHandler
+      TaskRun --> TaskBean
+      TaskBean --> BashWrapperBuilder
+      BashWrapperBuilder --> TaskHandler
+      CacheFactory --> CacheDB
+      TaskHandler --> CacheDB
+      TaskHandler --> TraceRecord
+      TraceRecord --> CacheDB
+      TaskHandler --> TraceObserver
+    end
+  end
+```
+
+[nextflow-diagram]: /nextflow_docs/nextflow_repo/docs/reports.mdx#workflow-diagram
+```
diff --git a/docs/developer/index.mdx b/docs/developer/index.mdx
new file mode 100644
index 0000000000..4af5d2624c
--- /dev/null
+++ b/docs/developer/index.mdx
@@ -0,0 +1,183 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Overview
+
+This section provides a high-level overview of the Nextflow source code for users who want to understand or contribute to it. Rather than a comprehensive API documentation, these docs simply provide a conceptual map to help you understand the key concepts of the Nextflow implementation, and to quickly find code sections of interest for further investigation.
+
+Before you dive into code, be sure to check out the [CONTRIBUTING.md](https://github.com/nextflow-io/nextflow/blob/master/CONTRIBUTING.md) for Nextflow to learn about the many ways to contribute to the project.
+
+## IntelliJ IDEA
+
+The suggested development environment is [IntelliJ IDEA](https://www.jetbrains.com/idea/download/). Nextflow development with IntelliJ IDEA requires a recent version of the IDE (2019.1.2 or later).
+
+After installing IntelliJ IDEA, use the following steps to use it with Nextflow:
+
+1. Clone the Nextflow repository to a directory in your computer.
+
+2. Open IntelliJ IDEA and go to **File > New > Project from Existing Sources...**.
+
+3. Select the Nextflow project root directory in your computer and click **OK**.
+
+4. Select **Import project from external model > Gradle** and click **Finish**.
+
+5. After the import process completes, select **File > Project Structure...**.
+
+6. Select **Project**, and make sure that the **SDK** field contains Java 11 (or later).
+
+7. Go to **File > Settings > Editor > Code Style > Groovy > Imports** and apply the following settings:
+
+   * Use single class import
+   * Class count to use import with '*': `99`
+   * Names count to use static import with '*': `99`
+   * Imports layout:
+      * `import java.*`
+      * `import javax.*`
+      * *blank line*
+      * all other imports
+      * all other static imports
+
+New files must include the appropriate license header boilerplate and the author name(s) and contact email(s) ([see for example](https://github.com/nextflow-io/nextflow/blob/e8945e8b6fc355d3f2eec793d8f288515db2f409/modules/nextflow/src/main/groovy/nextflow/Const.groovy#L1-L15)).
+
+## Groovy
+
+Nextflow is written in [Groovy](http://groovy-lang.org/), which is itself a programming language based on [Java](https://www.java.com/). Groovy is designed to be highly interoperable with Java -- Groovy programs compile to Java bytecode, and nearly any Java program is also a valid Groovy program. However, Groovy adds several language features (e.g. closures, list and map literals, optional typing, optional semicolons, meta-programming) and standard libraries (e.g. JSON and XML parsing) that greatly improve the overall experience of developing for the Java virtual machine.
+
+Recommended resources for Groovy, from most reference-complete to most user-friendly, are listed below:
+
+- [Groovy documentation](http://groovy-lang.org/documentation.html)
+- [Groovy in Action](https://www.manning.com/books/groovy-in-action-second-edition)
+- [Groovy: The Awesome Parts](https://www.slideshare.net/paulk_asert/awesome-groovy)
+- [Groovy cheat sheet](http://www.cheat-sheets.org/saved-copy/rc015-groovy_online.pdf)
+
+## Software Dependencies
+
+Nextflow depends on a variety of libraries and frameworks, the most prominent of which are listed below:
+
+- [AWS SDK for Java 1.x](https://aws.amazon.com/sdk-for-java/): AWS integration
+- [Azure SDK for Java](https://learn.microsoft.com/en-us/azure/developer/java/sdk/): Azure integration
+- [Google Cloud Client Libraries for Java](https://cloud.google.com/java/docs/reference): Google Cloud integration
+- [GPars](http://gpars.org/1.2.1/guide/guide/dataflow.html): dataflow concurrency
+- [Gradle](https://gradle.org/): build automation
+- [JCommander](https://jcommander.org/): command line interface
+- [JGit](https://www.eclipse.org/jgit/): Git integration
+- [Kryo](https://github.com/EsotericSoftware/kryo): serialization
+- [LevelDB](https://mvnrepository.com/artifact/org.iq80.leveldb/leveldb): key-value store for the cache database
+- [Logback](https://logback.qos.ch/): application logging
+- [PF4J](https://pf4j.org/): plugin extensions
+- [Spock](https://spockframework.org/): unit testing framework
+
+Any other integrations are likely implemented using a CLI (e.g. Conda, Docker, HPC schedulers) or REST API (e.g. Kubernetes).
+
+## Class Diagrams
+
+Each package has a class diagram, abridged and annotated for relevance and ease of use.
+
+Each node is a class. Fields are selectively documented in order to show only the core data structures and the classes that "own" them. Methods are not explicitly documented, but they are mentioned in certain links where appropriate. Links are selectively documented in order to show only the most important classes and relationships.
+
+Links between classes denote one of the following relationships:
+
+- Inheritance (`A <|-- B`): `B` is a subclass of `A`
+- Composition (`A --* B`): `A` contains `B`
+- Instantiation (`A --> B : f`): `A` creates instance(s) of `B` at runtime via `A::f()`
+
+See [packages-page][packages-page] for the list of Nextflow packages.
+
+```warning
+Class diagrams are manually curated, so they might not always reflect the latest version of the source code.
+```
+
+## Building from source
+
+If you are interested in modifying the source code, you only need Java 11 or later to build Nextflow from source. Nextflow uses the [Gradle](http://www.gradle.org/) build automation system, but you do not need to install Gradle to build Nextflow. In other words, if you can run Nextflow, then you can probably build it too!
+
+To build locally from a branch (useful for testing PRs):
+
+```bash
+git clone -b <branch> git@github.com:nextflow-io/nextflow.git
+cd nextflow
+make compile
+```
+
+The build system will automatically download all of the necessary dependencies on the first run, which may take several minutes.
+
+Once complete, you can run your local build of Nextflow using the `launch.sh` script in place of the `nextflow` command:
+
+```bash
+./launch.sh run <script> ...
+```
+
+Alternatively, you can build a self-contained executable with the following command:
+
+```bash
+make pack
+```
+
+It will create a binary in the `build/releases` directory which can be used in place of `nextflow`. This approach is useful when testing a pipeline that uses third-party plugins, which is not supported by `launch.sh`.
+
+## Testing
+
+To run the unit tests:
+
+```bash
+# run all tests
+make test
+
+# run individual test
+make test module=<nextflow|plugins:nf-amazon|...> class=<package>.<class>.<method>
+
+# refer to the Makefile for all build rules
+```
+
+When a test fails, it will give you a report that you can open in your browser to view the reason for each failed test. The **Standard output** tab is particularly useful as it shows the console output of each test.
+
+To run the integration tests:
+
+```bash
+cd tests/checks
+./qrun.sh
+```
+
+To run a specific integration test:
+
+```bash
+cd tests/checks
+./qrun.sh <FOLDER>
+```
+
+To test the documentation snippets:
+
+```bash
+cd docs/snippets
+./test.sh
+```
+
+Refer to the [build.yml](https://github.com/nextflow-io/nextflow/tree/master/.github/workflows/build.yml) configuration to see how to run other end-to-end tests locally.
+
+## Debugging
+
+### Groovy REPL
+
+The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java on the [Installation][install-requirements] page.
+
+:::note
+If you are using WSL, you must also install an X server for Windows, such as [VcXsrv](https://sourceforge.net/projects/vcxsrv/) or [Xming](http://www.straightrunning.com/XmingNotes/), in order to use these commands.
+:::
+
+### IntelliJ IDEA
+
+<AddedInVersion version="23.09.0-edge" />
+
+You can perform limited breakpoint debugging on a Nextflow script using IntelliJ IDEA.
+
+1. Set a breakpoint in your Nextflow script by clicking on a line number.
+
+2. Run `nextflow -remote-debug run <script>`
+
+3. Select the **Run / Debug Configurations** dropdown, select **Edit Configurations...**, and create a new configuration of type **Remote JVM Debug**. Set the port that appeared in the terminal when you launched your Nextflow script. Click **OK**.
+
+4. Select the green bug icon to begin the remote debug session. The Debug window will appear and allow you to step through and inspect your script as it runs.
+
+Note that this approach can only be used to debug the *script* execution, which does not include the *pipeline* execution.
+
+[install-requirements]: /nextflow_docs/nextflow_repo/docs/install.mdx#requirements
+[packages-page]: /nextflow_docs/nextflow_repo/docs/developer/packages.mdx
\ No newline at end of file
diff --git a/docs/developer/nextflow.ast.md b/docs/developer/nextflow.ast.mdx
similarity index 95%
rename from docs/developer/nextflow.ast.md
rename to docs/developer/nextflow.ast.mdx
index 159b23a112..b6d65dd338 100644
--- a/docs/developer/nextflow.ast.md
+++ b/docs/developer/nextflow.ast.mdx
@@ -5,12 +5,19 @@ The `nextflow.ast` package implements the Nextflow language extensions as AST tr
 
 ## Class Diagram
 
-```{mermaid} diagrams/nextflow.ast.mmd
+```mermaid
+classDiagram
+    %%
+    %% nextflow.ast
+    %%
+    ScriptParser --> NextflowDSLImpl : parse
+    ScriptParser --> NextflowXformImpl : parse
+    ScriptParser --> OpXformImpl : parse
 ```
 
-```{note}
+:::note
 Some classes may be excluded from the above diagram for brevity.
-```
+:::
 
 ## Notes
 
@@ -23,7 +30,7 @@ You can see the effect of Nextflow's AST transforms by using the Nextflow consol
 3. Execute the script
 4. Go to **Script** > **Inspect AST**
 
-Here is the example from {ref}`your-first-script`:
+Here is an example:
 
 ```nextflow
 params.str = 'Hello world!'
diff --git a/docs/developer/nextflow.cache.md b/docs/developer/nextflow.cache.mdx
similarity index 68%
rename from docs/developer/nextflow.cache.md
rename to docs/developer/nextflow.cache.mdx
index eb96603937..48ac59c33c 100644
--- a/docs/developer/nextflow.cache.md
+++ b/docs/developer/nextflow.cache.mdx
@@ -5,12 +5,34 @@ The `nextflow.cache` package implements the cache database of previously execute
 
 ## Class Diagram
 
-```{mermaid} diagrams/nextflow.cache.mmd
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cache
+    %%
+    Session --* CacheDB
+
+    CacheDB --* CacheStore
+
+    CacheStore <|-- DefaultCacheStore
+    CacheStore <|-- CloudCacheStore
+
+    class DefaultCacheStore {
+        uniqueId : UUID
+        runName : String
+        baseDir : Path
+    }
+
+    class CloudCacheStore {
+        uniqueId : UUID
+        runName : String
+        basePath : Path
+    }
 ```
 
-```{note}
+:::note
 Some classes may be excluded from the above diagram for brevity.
-```
+:::
 
 ## Notes
 
diff --git a/docs/developer/nextflow.cli.md b/docs/developer/nextflow.cli.md
deleted file mode 100644
index 8a93b5c76c..0000000000
--- a/docs/developer/nextflow.cli.md
+++ /dev/null
@@ -1,17 +0,0 @@
-
-# `nextflow.cli`
-
-The `nextflow.cli` package implements the command line interface.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.cli.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-The `Launcher` class is the entrypoint for Nextflow. It uses [JCommander](https://jcommander.org/) to parse the command-line arguments. Additionally, there is a class for each subcommand which implements the application logic of that command. By far the most complex command is `CmdRun`.
diff --git a/docs/developer/nextflow.cli.mdx b/docs/developer/nextflow.cli.mdx
new file mode 100644
index 0000000000..e3ac6387df
--- /dev/null
+++ b/docs/developer/nextflow.cli.mdx
@@ -0,0 +1,46 @@
+
+# `nextflow.cli`
+
+The `nextflow.cli` package implements the command line interface.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cli
+    %%
+    class Launcher {
+        cliOptions : CliOptions
+        command : CmdBase
+    } 
+    Launcher --* CliOptions
+    Launcher --* CmdBase
+
+    %% CmdBase <|-- CmdClean
+    %% CmdBase <|-- CmdClone
+    %% CmdBase <|-- CmdConfig
+    CmdBase <|-- CmdConsole
+    %% CmdBase <|-- CmdDrop
+    %% CmdBase <|-- CmdFs
+    CmdBase <|-- CmdHelp
+    CmdBase <|-- CmdInfo
+    %% CmdBase <|-- CmdKubeRun
+    %% CmdBase <|-- CmdList
+    %% CmdBase <|-- CmdLog
+    %% CmdBase <|-- CmdNode
+    %% CmdBase <|-- CmdPlugin
+    %% CmdBase <|-- CmdPull
+    CmdBase <|-- CmdRun
+    %% CmdBase <|-- CmdSecret
+    %% CmdBase <|-- CmdSelfUpdate
+    %% CmdBase <|-- CmdView
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The `Launcher` class is the entrypoint for Nextflow. It uses [JCommander](https://jcommander.org/) to parse the command-line arguments. Additionally, there is a class for each subcommand which implements the application logic of that command. By far the most complex command is `CmdRun`.
diff --git a/docs/developer/nextflow.cloud.aws.md b/docs/developer/nextflow.cloud.aws.md
deleted file mode 100644
index 30195218b2..0000000000
--- a/docs/developer/nextflow.cloud.aws.md
+++ /dev/null
@@ -1,13 +0,0 @@
-
-# `nextflow.cloud.aws`
-
-The `nextflow.cloud.aws` package implements the AWS Batch executor.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.cloud.aws.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagrams for brevity.
-```
diff --git a/docs/developer/nextflow.cloud.aws.mdx b/docs/developer/nextflow.cloud.aws.mdx
new file mode 100644
index 0000000000..89ef9cd43b
--- /dev/null
+++ b/docs/developer/nextflow.cloud.aws.mdx
@@ -0,0 +1,35 @@
+
+# `nextflow.cloud.aws`
+
+The `nextflow.cloud.aws` package implements the AWS Batch executor.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cloud.aws
+    %%
+    Executor <|-- AwsBatchExecutor
+    TaskHandler <|-- AwsBatchTaskHandler
+    BashWrapperBuilder <|-- AwsBatchScriptLauncher
+
+    AwsBatchExecutor --* AwsOptions
+    AwsOptions --* AwsConfig
+    AwsConfig --* AwsBatchConfig
+    AwsConfig --* AwsS3Config
+
+    AwsBatchExecutor --> ParallelPollingMonitor : init
+    AwsBatchExecutor --> AwsBatchTaskHandler : submit
+    AwsBatchTaskHandler --> AwsBatchScriptLauncher : submit
+
+    %% TaskPollingMonitor <|-- ParallelPollingMonitor
+
+    SimpleFileCopyStrategy <|-- AwsBatchFileCopyStrategy
+    AwsBatchScriptLauncher --* AwsBatchFileCopyStrategy
+
+```
+
+:::note
+Some classes may be excluded from the above diagrams for brevity.
+:::
diff --git a/docs/developer/nextflow.cloud.aws.nio.md b/docs/developer/nextflow.cloud.aws.nio.md
deleted file mode 100644
index 78bf60525f..0000000000
--- a/docs/developer/nextflow.cloud.aws.nio.md
+++ /dev/null
@@ -1,17 +0,0 @@
-
-# `nextflow.cloud.aws.nio`
-
-The `nextflow.cloud.aws.nio` package implements the S3 filesystem.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.cloud.aws.nio.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagrams for brevity.
-```
-
-## Notes
-
-The S3 filesystem translates Java Path API calls into S3 API calls, which allows Nextflow to interact with S3 objects through the same interface for local files.
diff --git a/docs/developer/nextflow.cloud.aws.nio.mdx b/docs/developer/nextflow.cloud.aws.nio.mdx
new file mode 100644
index 0000000000..a33d4f22c5
--- /dev/null
+++ b/docs/developer/nextflow.cloud.aws.nio.mdx
@@ -0,0 +1,51 @@
+
+# `nextflow.cloud.aws.nio`
+
+The `nextflow.cloud.aws.nio` package implements the S3 filesystem.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cloud.aws.nio
+    %%
+    FileSystemProvider <|-- S3FileSystemProvider
+
+    S3FileSystemProvider --> S3FileSystem : newFileSystem
+
+    class S3FileSystem {
+        client : S3Client
+        endpoint : String
+    }
+    S3FileSystem --* S3Client
+
+    class S3Client {
+        client : AmazonS3
+        cannedAcl : CannedAccessControlList
+        kmsKeyId : String
+        storageEncryption : SSEAlgorithm
+        transferManager : TransferManager
+        transferPool : ExecutorService
+        uploadChunkSize : Long
+        uploadMaxThreads : Integer
+    }
+
+    Path <|-- S3Path
+
+    class S3Path {
+        bucket : String
+        parts : List~String~
+        fileSystem : S3FileSystem
+    }
+    S3Path --* S3FileSystem
+
+```
+
+:::note
+Some classes may be excluded from the above diagrams for brevity.
+:::
+
+## Notes
+
+The S3 filesystem translates Java Path API calls into S3 API calls, which allows Nextflow to interact with S3 objects through the same interface for local files.
diff --git a/docs/developer/nextflow.cloud.azure.md b/docs/developer/nextflow.cloud.azure.md
deleted file mode 100644
index 649e243cc0..0000000000
--- a/docs/developer/nextflow.cloud.azure.md
+++ /dev/null
@@ -1,13 +0,0 @@
-
-# `nextflow.cloud.azure`
-
-The `nextflow.cloud.azure` package implements the Azure Batch executor.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.cloud.azure.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagrams for brevity.
-```
diff --git a/docs/developer/nextflow.cloud.azure.mdx b/docs/developer/nextflow.cloud.azure.mdx
new file mode 100644
index 0000000000..4e21dec1cc
--- /dev/null
+++ b/docs/developer/nextflow.cloud.azure.mdx
@@ -0,0 +1,31 @@
+
+# `nextflow.cloud.azure`
+
+The `nextflow.cloud.azure` package implements the Azure Batch executor.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cloud.azure
+    %%
+    Executor <|-- AzBatchExecutor
+    TaskHandler <|-- AzBatchTaskHandler
+    BashWrapperBuilder <|-- AzBatchScriptLauncher
+
+    AzBatchExecutor --* AzConfig
+    AzBatchExecutor --> AzBatchService : register
+
+    AzBatchExecutor --> TaskPollingMonitor : init
+    AzBatchExecutor --> AzBatchTaskHandler : submit
+    AzBatchTaskHandler --> AzBatchScriptLauncher : submit
+
+    SimpleFileCopyStrategy <|-- AzFileCopyStrategy
+    AzBatchScriptLauncher --* AzFileCopyStrategy
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
diff --git a/docs/developer/nextflow.cloud.google.md b/docs/developer/nextflow.cloud.google.md
deleted file mode 100644
index bf793fb6ce..0000000000
--- a/docs/developer/nextflow.cloud.google.md
+++ /dev/null
@@ -1,13 +0,0 @@
-
-# `nextflow.cloud.google`
-
-The `nextflow.cloud.google` package implements the Google Batch executor.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.cloud.google.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagrams for brevity.
-```
diff --git a/docs/developer/nextflow.cloud.google.mdx b/docs/developer/nextflow.cloud.google.mdx
new file mode 100644
index 0000000000..305b261320
--- /dev/null
+++ b/docs/developer/nextflow.cloud.google.mdx
@@ -0,0 +1,27 @@
+
+# `nextflow.cloud.google`
+
+The `nextflow.cloud.google` package implements the Google Batch executor.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cloud.google
+    %%
+    Executor <|-- GoogleBatchExecutor
+    TaskHandler <|-- GoogleBatchTaskHandler
+    BashWrapperBuilder <|-- GoogleBatchScriptLauncher
+
+    GoogleBatchExecutor --* BatchConfig
+
+    GoogleBatchExecutor --> TaskPollingMonitor : init
+    GoogleBatchExecutor --> GoogleBatchTaskHandler : submit
+    GoogleBatchTaskHandler --> GoogleBatchScriptLauncher : submit
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
diff --git a/docs/developer/nextflow.config.md b/docs/developer/nextflow.config.mdx
similarity index 77%
rename from docs/developer/nextflow.config.md
rename to docs/developer/nextflow.config.mdx
index e4db3ed87a..a43f475381 100644
--- a/docs/developer/nextflow.config.md
+++ b/docs/developer/nextflow.config.mdx
@@ -5,12 +5,20 @@ The `nextflow.config` package contains the implementation of the Nextflow config
 
 ## Class Diagram
 
-```{mermaid} diagrams/nextflow.config.mmd
+```mermaid
+classDiagram
+    %%
+    %% nextflow.config
+    %%
+    Session --* ConfigMap
+    CmdRun --> ConfigBuilder : run
+    ConfigBuilder --> ConfigMap : build
+
 ```
 
-```{note}
+:::note
 Some classes may be excluded from the above diagram for brevity.
-```
+:::
 
 ## Notes
 
diff --git a/docs/developer/nextflow.container.md b/docs/developer/nextflow.container.mdx
similarity index 58%
rename from docs/developer/nextflow.container.md
rename to docs/developer/nextflow.container.mdx
index facdf75f7b..a406a62bcc 100644
--- a/docs/developer/nextflow.container.md
+++ b/docs/developer/nextflow.container.mdx
@@ -5,12 +5,29 @@ The `nextflow.container` package implements the integration with container runti
 
 ## Class Diagram
 
-```{mermaid} diagrams/nextflow.container.mmd
+```mermaid
+classDiagram
+    %%
+    %% nextflow.container
+    %%
+    direction LR
+
+    BashWrapperBuilder --> ContainerBuilder : build
+
+    ContainerBuilder <|-- CharliecloudBuilder
+    ContainerBuilder <|-- DockerBuilder
+    ContainerBuilder <|-- PodmanBuilder
+    ContainerBuilder <|-- ShifterBuilder
+    ContainerBuilder <|-- SingularityBuilder
+    ContainerBuilder <|-- UdockerBuilder
+
+    SingularityBuilder <|-- ApptainerBuilder
+
 ```
 
-```{note}
+:::note
 Some classes may be excluded from the above diagram for brevity.
-```
+:::
 
 ## Notes
 
diff --git a/docs/developer/nextflow.dag.md b/docs/developer/nextflow.dag.md
deleted file mode 100644
index b08328c32a..0000000000
--- a/docs/developer/nextflow.dag.md
+++ /dev/null
@@ -1,19 +0,0 @@
-
-# `nextflow.dag`
-
-The `nextflow.dag` package implements the workflow DAG and renderers for several diagram formats.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.dag.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-The workflow DAG defines the network of processes, channels, and operators that comprise a workflow. It is produced by the execution of the Nextflow script. See [nextflow.script](nextflow.script.md) for more details.
-
-Implementations of the `DagRenderer` interface define how to render the workflow DAG to a particular diagram format. See {ref}`workflow-diagram` for more details.
diff --git a/docs/developer/nextflow.dag.mdx b/docs/developer/nextflow.dag.mdx
new file mode 100644
index 0000000000..16c09b70d0
--- /dev/null
+++ b/docs/developer/nextflow.dag.mdx
@@ -0,0 +1,55 @@
+
+# `nextflow.dag`
+
+The `nextflow.dag` package implements the workflow DAG and renderers for several diagram formats.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.dag
+    %%
+    Session --* DAG
+
+    class DAG {
+        vertices : List~Vertex~
+        edges : List~Edge~
+    }
+    DAG "1" --* "*" Vertex
+    DAG "1" --* "*" Edge
+
+    class Vertex {
+        label : String
+        type : Type
+        operators : List~DataflowProcessor~
+        process : TaskProcessor
+    }
+
+    class Edge {
+        channel : Object
+        from : Vertex
+        to : Vertex
+        label : String
+    }
+
+    %% DagRenderer <|-- CytoscapeHtmlRenderer
+    %% DagRenderer <|-- CytoscapeJsRenderer
+    %% DagRenderer <|-- DotRenderer
+    %% DagRenderer <|-- GexfRenderer
+    %% DagRenderer <|-- GraphvizRenderer
+    %% DagRenderer <|-- MermaidRenderer
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The workflow DAG defines the network of processes, channels, and operators that comprise a workflow. It is produced by the execution of the Nextflow script. See [nextflow.script][nextflow-script] for more details.
+
+Implementations of the `DagRenderer` interface define how to render the workflow DAG to a particular diagram format. See [Workflow diagram][workflow-diagram] for more details.
+
+[nextflow-script]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.script.mdx
+[workflow-diagram]: /nextflow_docs/nextflow_repo/docs/reports.mdx#workflow-diagram
diff --git a/docs/developer/nextflow.executor.md b/docs/developer/nextflow.executor.md
deleted file mode 100644
index 8be432393e..0000000000
--- a/docs/developer/nextflow.executor.md
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# `nextflow.executor`
-
-The `nextflow.executor` package defines the executor interface and implements several built-in executors.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.executor.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-The `Executor` class is the base class for all Nextflow executors. The main purpose of an `Executor` is to submit tasks to an underlying compute environment, such as an HPC scheduler or cloud batch executor. It uses a `TaskMonitor` to manage the lifecycle of all tasks and a `TaskHandler` to manage each individual task. Most executors use the same polling monitor, but each executor implements its own task handler to customize it for a particular compute environment. See [nextflow.processor](nextflow.processor.md) for more details about these classes.
-
-The built-in executors include the local executor (`LocalExecutor`) and the various grid executors (SLURM, PBS, LSF, etc), all of which extend `AbstractGridExecutor`. The `LocalExecutor` implements both "script" tasks (processes with a `script` or `shell` block) and "native" tasks (processes with an `exec` block).
-
-The `BashWrapperBuilder` is used by executors to generate the wrapper script (`.command.run`) for a task, from a template script called `command-run.txt`, as well as the task configuration and the execution environment.
diff --git a/docs/developer/nextflow.executor.mdx b/docs/developer/nextflow.executor.mdx
new file mode 100644
index 0000000000..daf0e63085
--- /dev/null
+++ b/docs/developer/nextflow.executor.mdx
@@ -0,0 +1,90 @@
+
+# `nextflow.executor`
+
+The `nextflow.executor` package defines the executor interface and implements several built-in executors.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.executor
+    %%
+    ExecutorFactory --> Executor : getExecutor
+
+    class Executor {
+        name : String
+        monitor : TaskMonitor
+    }
+    Executor --* TaskMonitor
+    Executor --> TaskHandler : submit
+
+    TaskMonitor <|-- TaskPollingMonitor
+
+    class TaskPollingMonitor {
+        capacity : int
+        submitRateLimit : RateLimiter
+        pollIntervalMillis : long
+        dumpInterval : Duration
+    }
+
+    TaskPollingMonitor <|-- LocalPollingMonitor
+
+    class LocalPollingMonitor {
+        maxCpus : int
+        maxMemory : long
+    }
+
+    Executor <|-- AbstractGridExecutor
+    Executor <|-- LocalExecutor
+    %% Executor <|-- NopeExecutor
+    %% AbstractGridExecutor <|-- CondorExecutor
+    %% AbstractGridExecutor <|-- HyperQueueExecutor
+    %% AbstractGridExecutor <|-- LsfExecutor
+    %% AbstractGridExecutor <|-- MoabExecutor
+    %% AbstractGridExecutor <|-- NqsiiExecutor
+    %% AbstractGridExecutor <|-- OarExecutor
+    %% AbstractGridExecutor <|-- PbsExecutor
+    %% AbstractGridExecutor <|-- SgeExecutor
+    %% AbstractGridExecutor <|-- SlurmExecutor
+    %% PbsExecutor <|-- PbsProExecutor
+    %% SgeExecutor <|-- CrgExecutor
+
+    %% TaskHandler <|-- CachedTaskHandler
+    TaskHandler <|-- GridTaskHandler
+    TaskHandler <|-- LocalTaskHandler
+    TaskHandler <|-- NativeTaskHandler
+    %% TaskHandler <|-- NopeTaskHandler
+    %% TaskHandler <|-- StoredTaskHandler
+
+    class BashWrapperBuilder {
+        bean : TaskBean
+        copyStrategy : ScriptFileCopyStrategy
+    }
+    BashWrapperBuilder --* TaskBean
+    BashWrapperBuilder --* ScriptFileCopyStrategy
+
+    ScriptFileCopyStrategy <|-- SimpleFileCopyStrategy
+
+    class SimpleFileCopyStrategy {
+        stageinMode : String
+        stageoutMode : String
+        targetDir : Path
+        workDir : Path
+    }
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The `Executor` class is the base class for all Nextflow executors. The main purpose of an `Executor` is to submit tasks to an underlying compute environment, such as an HPC scheduler or cloud batch executor. It uses a `TaskMonitor` to manage the lifecycle of all tasks and a `TaskHandler` to manage each individual task. Most executors use the same polling monitor, but each executor implements its own task handler to customize it for a particular compute environment.
+See [nextflow.processor][nextflow.processor] for more details about these classes.
+
+The built-in executors include the local executor (`LocalExecutor`) and the various grid executors (SLURM, PBS, LSF, etc), all of which extend `AbstractGridExecutor`. The `LocalExecutor` implements both "script" tasks (processes with a `script` or `shell` block) and "native" tasks (processes with an `exec` block).
+
+The `BashWrapperBuilder` is used by executors to generate the wrapper script (`.command.run`) for a task, from a template script called `command-run.txt`, as well as the task configuration and the execution environment.
+
+[nextflow.processor]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.processor.mdx
\ No newline at end of file
diff --git a/docs/developer/nextflow.extension.md b/docs/developer/nextflow.extension.md
deleted file mode 100644
index 7bafc14a81..0000000000
--- a/docs/developer/nextflow.extension.md
+++ /dev/null
@@ -1,19 +0,0 @@
-
-# `nextflow.extension`
-
-The `nextflow.extension` package implements the channel operators and other extension methods.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.extension.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-Operators are implemented using the [GPars](http://gpars.org/1.2.1/guide/guide/dataflow.html) dataflow library. In general, an operator consumes one or more `DataflowReadChannel`s and produces one or more `DataflowWriteChannel`s. See {ref}`operator-page` for details about each operator.
-
-Other notable classes include `Bolts` and `FilesEx`, which implement various extension methods used throughout the Nextflow codebase. If you see a method that doesn't appear to be implemented by the calling object, it may be implemented in one of these extension classes.
diff --git a/docs/developer/nextflow.extension.mdx b/docs/developer/nextflow.extension.mdx
new file mode 100644
index 0000000000..6c3eef9837
--- /dev/null
+++ b/docs/developer/nextflow.extension.mdx
@@ -0,0 +1,52 @@
+
+# `nextflow.extension`
+
+The `nextflow.extension` package implements the channel operators and other extension methods.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.extension
+    %%
+    direction LR
+
+    ChannelEx --> DumpOp : dump
+    Nextflow --> GroupKey : groupKey
+
+    OperatorImpl --> BranchOp : branch
+    OperatorImpl --> BufferOp : buffer
+    OperatorImpl --> CollectFileOp : collectFile
+    OperatorImpl --> CollectOp : collect
+    OperatorImpl --> CombineOp : combine
+    OperatorImpl --> ConcatOp : concat
+    OperatorImpl --> CrossOp : cross
+    OperatorImpl --> GroupTupleOp : groupTuple
+    OperatorImpl --> JoinOp : join
+    OperatorImpl --> MapOp : map
+    OperatorImpl --> MergeOp : merge
+    OperatorImpl --> MixOp : mix
+    OperatorImpl --> MultiMapOp : multiMap
+    OperatorImpl --> RandomSampleOp : randomSample
+    OperatorImpl --> SplitOp : splitCsv, splitFasta, splitFastq, splitText
+    OperatorImpl --> TakeOp : take
+    OperatorImpl --> ToListOp : toList, toSortedList
+    OperatorImpl --> TransposeOp : transpose
+    OperatorImpl --> UntilOp : until
+
+    WorkflowBinding --> OpCall : invokeMethod
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+Operators are implemented using the [GPars](http://gpars.org/1.2.1/guide/guide/dataflow.html) dataflow library. In general, an operator consumes one or more `DataflowReadChannel`s and produces one or more `DataflowWriteChannel`s. See [Operators][operator-page] for details about each operator.
+
+Other notable classes include `Bolts` and `FilesEx`, which implement various extension methods used throughout the Nextflow codebase. If you see a method that doesn't appear to be implemented by the calling object, it may be implemented in one of these extension classes.
+
+[operator-page]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx
\ No newline at end of file
diff --git a/docs/developer/nextflow.k8s.md b/docs/developer/nextflow.k8s.md
deleted file mode 100644
index 1f51e0dac5..0000000000
--- a/docs/developer/nextflow.k8s.md
+++ /dev/null
@@ -1,17 +0,0 @@
-
-# `nextflow.k8s`
-
-The `nextflow.k8s` package implements the Kubernetes executor and the `kuberun` command.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.k8s.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-The Kubernetes integration uses the K8s HTTP API to interact with K8s clusters, and relies on the `kubectl` command and `~/.kube/config` file for authentication.
diff --git a/docs/developer/nextflow.k8s.mdx b/docs/developer/nextflow.k8s.mdx
new file mode 100644
index 0000000000..fd7532e5f9
--- /dev/null
+++ b/docs/developer/nextflow.k8s.mdx
@@ -0,0 +1,74 @@
+
+# `nextflow.k8s`
+
+The `nextflow.k8s` package implements the Kubernetes executor and the `kuberun` command.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.k8s
+    %%
+    Executor <|-- K8sExecutor
+    TaskHandler <|-- K8sTaskHandler
+    BashWrapperBuilder <|-- K8sWrapperBuilder
+
+    K8sExecutor --> TaskPollingMonitor : init
+    K8sExecutor --> K8sTaskHandler : submit
+    K8sExecutor --* K8sClient
+    K8sTaskHandler --> K8sWrapperBuilder : submit
+
+    CmdKubeRun --> K8sDriverLauncher : run
+
+    class K8sDriverLauncher {
+        args : List~String~
+        cmd : CmdKubeRun
+        config : ConfigObject
+        configMapName : String
+        headCpus : int
+        headImage : String
+        headMemory : String
+        headPreScript : String
+        paramsFile : String
+        pipelineName : String
+        runName : String
+    }
+    K8sDriverLauncher --* K8sClient
+    K8sDriverLauncher --* K8sConfig
+
+    K8sClient --* ClientConfig
+    %% ConfigDiscovery --> ClientConfig : discover
+
+    class K8sConfig {
+        target : Map
+        podOptions : PodOptions
+    }
+    K8sConfig --* PodOptions
+
+    class PodOptions {
+        affinity : Map
+        annotations : Map
+        automountServiceAccountToken : boolean
+        configMaps : Collection~PodMountConfig~
+        envVars : Collection~PodEnv~
+        imagePullPolicy : String
+        imagePullSecret : String
+        labels : Map
+        nodeSelector : PodNodeSelector
+        priorityClassName : String
+        privileged : Boolean
+        secrets : Collection~PodMountSecret~
+        securityContext : PodSecurityContext
+        tolerations : List~Map~
+        volumeClaims : Collection~PodVolumeClaim~
+    }
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The Kubernetes integration uses the K8s HTTP API to interact with K8s clusters, and relies on the `kubectl` command and `~/.kube/config` file for authentication.
diff --git a/docs/developer/nextflow.md b/docs/developer/nextflow.md
deleted file mode 100644
index 61f66828f5..0000000000
--- a/docs/developer/nextflow.md
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# `nextflow`
-
-The `nextflow` package contains various top-level classes.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-The `Nextflow` class implements several methods that are exposed to Nextflow scripts. See {ref}`stdlib-namespaces-global` for details.
-
-The `Channel` class implements the channel factory methods, and it is exposed directly to Nextflow scripts. See {ref}`dataflow-page` for details.
-
-The `Session` class is the top-level representation of a Nextflow run, or "session". See [nextflow.script](nextflow.script.md) for more details about how a `Session` is created.
diff --git a/docs/developer/nextflow.mdx b/docs/developer/nextflow.mdx
new file mode 100644
index 0000000000..d5351fcbd3
--- /dev/null
+++ b/docs/developer/nextflow.mdx
@@ -0,0 +1,47 @@
+
+# `nextflow`
+
+The `nextflow` package contains various top-level classes.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow
+    %%
+    class Nextflow
+    class Channel
+    class Session {
+        baseDir : Path
+        binding : ScriptBinding
+        cache : CacheDB
+        commandLine : String
+        commitId : String
+        config : Map
+        configFiles : List~Path~
+        dag : DAG
+        profile : String
+        runName : String
+        script : BaseScript
+        uniqueId : UUID
+        workDir : Path
+    }
+
+```
+
+```note
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The `Nextflow` class implements several methods that are exposed to Nextflow scripts. See [Global namespace][stdlib-namespaces-global] for details.
+
+The `Channel` class implements the channel factory methods, and it is exposed directly to Nextflow scripts. See [Dataflow][channel-page] for details.
+
+The `Session` class is the top-level representation of a Nextflow run, or "session". See [nextflow.script][nextflow-script] for more details about how a `Session` is created.
+
+[dataflow-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[nextflow-script]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.script.mdx
+[stdlib-namespaces-global]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-namespaces.mdx#global-namespace
\ No newline at end of file
diff --git a/docs/developer/nextflow.plugin.md b/docs/developer/nextflow.plugin.mdx
similarity index 71%
rename from docs/developer/nextflow.plugin.md
rename to docs/developer/nextflow.plugin.mdx
index e95fd307bc..d5786c175c 100644
--- a/docs/developer/nextflow.plugin.md
+++ b/docs/developer/nextflow.plugin.mdx
@@ -5,12 +5,26 @@ The `nextflow.plugin` package implements the plugin manager.
 
 ## Class Diagram
 
-```{mermaid} diagrams/nextflow.plugin.mmd
+```mermaid
+classDiagram
+    %%
+    %% nextflow.plugin
+    %%
+    CmdRun --> Plugins : run
+
+    Plugins --> PluginsFacade : init
+
+    PluginsFacade "1" --> "*" PluginSpec : load
+
+    class PluginSpec {
+        id : String
+        version : String
+    }
 ```
 
-```{note}
+:::note
 Some classes may be excluded from the above diagram for brevity.
-```
+:::
 
 ## Notes
 
diff --git a/docs/developer/nextflow.processor.md b/docs/developer/nextflow.processor.mdx
similarity index 52%
rename from docs/developer/nextflow.processor.md
rename to docs/developer/nextflow.processor.mdx
index ec5e2fa0fa..f718d1f591 100644
--- a/docs/developer/nextflow.processor.md
+++ b/docs/developer/nextflow.processor.mdx
@@ -5,19 +5,65 @@ The `nextflow.processor` package implements the execution and monitoring of task
 
 ## Class Diagram
 
-```{mermaid} diagrams/nextflow.processor.mmd
+```mermaid
+classDiagram
+    %%
+    %% nextflow.processor
+    %%
+    %% ProcessDef --> TaskProcessor : run
+
+    class TaskProcessor {
+        config : ProcessConfig
+        executor : Executor
+        id : int
+        name : String
+        operator : DataflowProcessor
+        taskBody : BodyDef
+    }
+    TaskProcessor --> TaskRun : invokeTask
+    TaskProcessor --> PublishDir : finalizeTask
+
+    class TaskRun {
+        config : TaskConfig
+        context : TaskContext
+        hash : HashCode
+        id : TaskId
+        index : int
+        inputs : Map
+        name : String
+        outputs : Map
+        runType : RunType
+        type : ScriptType
+        workDir : Path
+    }
+    TaskRun --* TaskConfig
+    TaskRun --* TaskContext
+    TaskRun --> TaskBean : toTaskBean
+
+    class TaskConfig {
+        target : Map
+        binding : Map
+    }
+
+    class TaskContext {
+        holder : Map
+        script : Script
+        name : String
+    }
 ```
 
-```{note}
+:::note
 Some classes may be excluded from the above diagram for brevity.
-```
+:::
 
 ## Notes
 
-While the [`executor`](nextflow.executor.md) package defines how tasks are submitted to a particular execution backend (such as an HPC scheduler), the `processor` package defines how tasks are created and executed. As such, these packages work closely together, and in fact several components of the `Executor` interface, specifically the `TaskHandler` and `TaskMonitor`, are defined in this package.
+While the [`executor`][nextflow-executor] package defines how tasks are submitted to a particular execution backend (such as an HPC scheduler), the `processor` package defines how tasks are created and executed. As such, these packages work closely together, and in fact several components of the `Executor` interface, specifically the `TaskHandler` and `TaskMonitor`, are defined in this package.
 
 The `TaskProcessor` is by far the largest and most complex class in this package. It implements both the dataflow operator for a given process as well as the task execution logic. In other words, it defines the mapping from an abstract process definition with input and output channels into concrete task executions.
 
 A `TaskRun` represents a particular task execution. There is also `TaskBean`, which is a serializable representation of a task. Legends say that `TaskBean` was originally created to support a "daemon" mode in which Nextflow would run on both the head node and the worker nodes, so the Nextflow "head" would need to send tasks to the Nextflow "workers". This daemon mode was never completed, but echoes of it remain (see `CmdNode`, `DaemonLauncher`, and the `nf-ignite` plugin).
 
 When a `TaskProcessor` receives a set of input values, it creates a `TaskRun` and submits it to an `Executor`, which in turn submits the task to a underlying execution backend. The executor's `TaskMonitor` then monitors the status of the task, and when it is completed, returns it to the task processor for finalization. If the task completed successfully, the task processor collects the task outputs and emits them on the corresponding output channels. If the task failed, the task processor will retry it if possible, or else return a task error to the workflow run.
+
+[nextflow-executor]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.executor.mdx
\ No newline at end of file
diff --git a/docs/developer/nextflow.scm.md b/docs/developer/nextflow.scm.md
deleted file mode 100644
index ee7a4e0146..0000000000
--- a/docs/developer/nextflow.scm.md
+++ /dev/null
@@ -1,17 +0,0 @@
-
-# `nextflow.scm`
-
-The `nextflow.scm` package defines the Git provider interface and implements several built-in Git providers.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.scm.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-The `RepositoryProvider` class is the base class for all Git providers. It defines how to authenticate with the provider, clone a Git repository, inspect branches and tags, etc.
diff --git a/docs/developer/nextflow.scm.mdx b/docs/developer/nextflow.scm.mdx
new file mode 100644
index 0000000000..ea647d2e8f
--- /dev/null
+++ b/docs/developer/nextflow.scm.mdx
@@ -0,0 +1,43 @@
+
+# `nextflow.scm`
+
+The `nextflow.scm` package defines the Git provider interface and implements several built-in Git providers.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.scm
+    %%
+    direction LR
+
+    CmdRun --> AssetManager : run
+
+    class AssetManager {
+        project : String
+        localPath : File
+        mainScript : String
+        repositoryProvider : RepositoryProvider
+        hub : String
+        providerConfigs : List~ProviderConfig~
+    }
+    AssetManager --* RepositoryProvider
+    AssetManager "1" --* "*" ProviderConfig
+
+    RepositoryProvider <|-- AzureRepositoryProvider
+    RepositoryProvider <|-- BitbucketRepositoryProvider
+    RepositoryProvider <|-- BitbucketServerRepositoryProvider
+    RepositoryProvider <|-- GiteaRepositoryProvider
+    RepositoryProvider <|-- GithubRepositoryProvider
+    RepositoryProvider <|-- GitlabRepositoryProvider
+    RepositoryProvider <|-- LocalRepositoryProvider
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The `RepositoryProvider` class is the base class for all Git providers. It defines how to authenticate with the provider, clone a Git repository, inspect branches and tags, etc.
diff --git a/docs/developer/nextflow.script.md b/docs/developer/nextflow.script.md
deleted file mode 100644
index 7c76f1c2bd..0000000000
--- a/docs/developer/nextflow.script.md
+++ /dev/null
@@ -1,21 +0,0 @@
-
-# `nextflow.script`
-
-The `nextflow.script` package implements the parsing and execution of Nextflow scripts.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.script.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-The execution of a Nextflow pipeline occurs in two phases. In the first phase, Nextflow parses and runs the script (using the language extensions in [nextflow.ast](nextflow.ast.md) and [nextflow.extension](nextflow.extension.md)), which produces the workflow DAG. In the second phase, Nextflow executes the workflow.
-
-```{note}
-In DSL1, there was no separation between workflow construction and execution -- dataflow operators were executed as soon as they were constructed. DSL2 introduced lazy execution in order to separate process definition from execution, and thereby facilitate subworkflows and modules.
-```
diff --git a/docs/developer/nextflow.script.mdx b/docs/developer/nextflow.script.mdx
new file mode 100644
index 0000000000..0cb9e3bced
--- /dev/null
+++ b/docs/developer/nextflow.script.mdx
@@ -0,0 +1,154 @@
+
+# `nextflow.script`
+
+The `nextflow.script` package implements the parsing and execution of Nextflow scripts.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.script
+    %%
+    CmdRun --> ScriptRunner : run
+
+    class ScriptRunner {
+        scriptFile : ScriptFile
+        session : Session
+    }
+    ScriptRunner --* ScriptFile
+    ScriptRunner --> ScriptParser : execute
+    ScriptParser --> BaseScript : parse
+
+    class ScriptFile {
+        source : Path
+        main : Path
+        repository : String
+        revisionInfo : AssetManager.RevisionInfo
+        localPath : Path
+        projectName : String
+    }
+
+    class BaseScript {
+        meta : ScriptMeta
+        entryFlow : WorkflowDef
+    }
+    BaseScript --* ScriptBinding
+    BaseScript --* ScriptMeta
+    BaseScript --> IncludeDef : include
+
+    IncludeDef --> ScriptParser : load0
+
+    class ScriptBinding {
+        scriptPath : Path
+        args : List~String~
+        params : ParamsMap
+        configEnv : Map
+        entryName : String
+    }
+
+    class ScriptMeta {
+        scriptPath : Path
+        definitions : Map
+        imports : Map
+        module : boolean
+    }
+    ScriptMeta "1" --* "*" ComponentDef : definitions
+    ScriptMeta "1" --* "*" ComponentDef : imports
+
+    ComponentDef <|-- FunctionDef
+    ComponentDef <|-- ProcessDef
+    ComponentDef <|-- WorkflowDef
+
+    class FunctionDef {
+        target : Object
+        name : String
+        alias : String
+    }
+
+    class ProcessDef {
+        processName : String
+        simpleName : String
+        baseName : String
+        rawBody : Closure~BodyDef~
+    }
+    ProcessDef --* ProcessConfig
+    ProcessDef --* BodyDef
+    ProcessDef --* ChannelOut
+
+    class WorkflowDef {
+        name : String
+        body : BodyDef
+        declaredInputs : List~String~
+        declaredOutputs : List~String~
+        variableNames : Set~String~
+    }
+    WorkflowDef --* BodyDef
+    WorkflowDef --* WorkflowBinding
+    WorkflowDef --* ChannelOut
+
+    class ProcessConfig {
+        configProperties : Map
+        inputs : InputsList
+        outputs : OutputsList
+    }
+    ProcessConfig --* InputsList
+    ProcessConfig --* OutputsList
+
+    class BodyDef {
+        closure : Closure
+        source : String
+        type : ScriptType
+        isShell : boolean
+    }
+
+    class ChannelOut {
+        target : List~DataflowWriteChannel~
+        channels : Map
+    }
+
+    class WorkflowBinding {
+        vars : Map
+    }
+
+    class InputsList {
+        target : List~InParam~
+    }
+    InputsList "1" --* "*" InParam
+
+    class OutputsList {
+        target : List~OutParam~
+    }
+    OutputsList "1" --* "*" OutParam
+
+    %% InParam <|-- BaseInParam
+    %% BaseInParam <|-- EachInParam
+    %% BaseInParam <|-- EnvInParam
+    %% BaseInParam <|-- FileInParam
+    %% BaseInParam <|-- StdInParam
+    %% BaseInParam <|-- TupleInParam
+    %% BaseInParam <|-- ValueInParam
+
+    %% OutParam <|-- BaseOutParam
+    %% BaseOutParam <|-- EachOutParam
+    %% BaseOutParam <|-- EnvOutParam
+    %% BaseOutParam <|-- FileOutParam
+    %% BaseOutParam <|-- StdOutParam
+    %% BaseOutParam <|-- TupleOutParam
+    %% BaseOutParam <|-- ValueOutParam
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The execution of a Nextflow pipeline occurs in two phases. In the first phase, Nextflow parses and runs the script (using the language extensions in [nextflow.ast][nextflow-ast] and [nextflow.extension][nextflow-extension]), which produces the workflow DAG. In the second phase, Nextflow executes the workflow.
+
+:::note
+In DSL1, there was no separation between workflow construction and execution -- dataflow operators were executed as soon as they were constructed. DSL2 introduced lazy execution in order to separate process definition from execution, and thereby facilitate subworkflows and modules.
+:::
+
+[nextflow-ast]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.ast.mdx
+[nextflow-extension]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.extension.mdx
diff --git a/docs/developer/nextflow.secret.md b/docs/developer/nextflow.secret.md
deleted file mode 100644
index db7b84f1a8..0000000000
--- a/docs/developer/nextflow.secret.md
+++ /dev/null
@@ -1,17 +0,0 @@
-
-# `nextflow.secret`
-
-The `nextflow.secret` package defines the secrets provider interface and implements the built-in local secrets store.
-
-## Class Diagram
-
-```{mermaid} diagrams/nextflow.secret.mmd
-```
-
-```{note}
-Some classes may be excluded from the above diagram for brevity.
-```
-
-## Notes
-
-The default secrets provider simply stores key-value pairs in a local JSON file.
diff --git a/docs/developer/nextflow.secret.mdx b/docs/developer/nextflow.secret.mdx
new file mode 100644
index 0000000000..84f88682b3
--- /dev/null
+++ b/docs/developer/nextflow.secret.mdx
@@ -0,0 +1,30 @@
+
+# `nextflow.secret`
+
+The `nextflow.secret` package defines the secrets provider interface and implements the built-in local secrets store.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.secret
+    %%
+    ConfigBuilder --> SecretsLoader : build
+    BaseScript --> SecretsLoader : run
+    BashWrapperBuilder --> SecretsLoader : build
+
+    SecretsLoader --> SecretsProvider : load
+    SecretsProvider --> Secret : getSecret
+    SecretsProvider <|-- LocalSecretsProvider
+    Secret <|-- SecretImpl
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The default secrets provider simply stores key-value pairs in a local JSON file.
diff --git a/docs/developer/nextflow.trace.md b/docs/developer/nextflow.trace.mdx
similarity index 65%
rename from docs/developer/nextflow.trace.md
rename to docs/developer/nextflow.trace.mdx
index 8e86092c6e..86ad076303 100644
--- a/docs/developer/nextflow.trace.md
+++ b/docs/developer/nextflow.trace.mdx
@@ -5,12 +5,25 @@ The `nextflow.trace` package defines the trace observer interface and implements
 
 ## Class Diagram
 
-```{mermaid} diagrams/nextflow.trace.mmd
+```mermaid
+classDiagram
+    %%
+    %% nextflow.trace
+    %%
+    Session --> TraceObserverFactory : init
+
+    TraceObserverFactory "1" --> "*" TraceObserver : create
+    TraceObserver <|-- AnsiLogObserver
+    TraceObserver <|-- GraphObserver
+    TraceObserver <|-- ReportObserver
+    TraceObserver <|-- TimelineObserver
+    TraceObserver <|-- TraceFileObserver
+    TraceObserver <|-- WorkflowStatsObserver
 ```
 
-```{note}
+:::note
 Some classes may be excluded from the above diagram for brevity.
-```
+:::
 
 ## Notes
 
diff --git a/docs/developer/packages.md b/docs/developer/packages.md
deleted file mode 100644
index 364d61960b..0000000000
--- a/docs/developer/packages.md
+++ /dev/null
@@ -1,12 +0,0 @@
-(packages-page)=
-
-# Packages
-
-The following subpages correspond to packages in the Nextflow source code:
-
-```{toctree}
-:glob:
-:maxdepth: 1
-
-nextflow*
-```
diff --git a/docs/developer/packages.mdx b/docs/developer/packages.mdx
new file mode 100644
index 0000000000..6cf3ed167c
--- /dev/null
+++ b/docs/developer/packages.mdx
@@ -0,0 +1,7 @@
+import DocCardList from "@theme/DocCardList";
+
+# Packages
+
+The following pages correspond to packages in the Nextflow source code.
+
+<DocCardList />
diff --git a/docs/executor.mdx b/docs/executor.mdx
new file mode 100644
index 0000000000..1c007f2156
--- /dev/null
+++ b/docs/executor.mdx
@@ -0,0 +1,453 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Executors
+
+In the Nextflow framework architecture, the *executor* is the component that determines the system where a pipeline process is run and supervises its execution.
+
+The executor provides an abstraction between the pipeline processes and the underlying execution system. This allows you to write the pipeline functional logic independently from the actual processing platform.
+
+In other words, you can write your pipeline script once and have it running on your computer, a cluster resource manager, or the cloud — simply change the executor definition in the Nextflow configuration file.
+
+## AWS Batch
+
+Nextflow supports the [AWS Batch](https://aws.amazon.com/batch/) service that allows job submission in the cloud without having to spin out and manage a cluster of virtual machines. AWS Batch uses Docker containers to run tasks, which greatly simplifies pipeline deployment.
+
+The pipeline processes must specify the Docker image to use by defining the `container` directive, either in the pipeline script or the `nextflow.config` file.
+
+To enable this executor, set `process.executor = 'awsbatch'` in the `nextflow.config` file.
+
+The pipeline can be launched either on a local computer, or an EC2 instance. EC2 is suggested for heavy or long-running workloads. Additionally, an S3 bucket must be used as the pipeline work directory.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [accelerator][process-accelerator]
+- [arch][process-arch] (only when using Fargate platform type for AWS Batch)
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+- [cpus][process-cpus]
+- [disk][process-disk] (only when using Fargate platform type for AWS Batch)
+- [memory][process-memory]
+- [queue][process-queue]
+- [resourcelabels][process-resourcelabels]
+- [time][process-time]
+
+See [AWS Batch][aws-batch] for more information.
+
+## Azure Batch
+
+Nextflow supports the [Azure Batch](https://azure.microsoft.com/en-us/services/batch/) service that allows job submission in the cloud without having to spin out and manage a cluster of virtual machines. Azure Batch uses Docker containers to run tasks, which greatly simplifies pipeline deployment.
+
+The pipeline processes must specify the Docker image to use by defining the `container` directive, either in the pipeline script or the `nextflow.config` file.
+
+To enable this executor, set `process.executor = 'azurebatch'` in the `nextflow.config` file.
+
+The pipeline can be launched either on a local computer, or a cloud virtual machine. The cloud VM is suggested for heavy or long-running workloads. Additionally, an Azure Blob storage container must be used as the pipeline work directory.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [machineType][process-machinetype]
+- [memory][process-memory]
+- [queue][process-queue]
+- [resourcelabels][process-resourcelabels]
+- [time][process-time]
+
+See [Azure Batch][azure-batch] for more information.
+
+## Bridge
+
+<AddedInVersion version="22.09.1-edge" />
+
+[Bridge](https://github.com/cea-hpc/bridge) is an abstraction layer to ease batch system and resource manager usage in heterogeneous HPC environments.
+
+It is open source software that can be installed on top of existing classical job schedulers such as Slurm, LSF, or other schedulers. Bridge allows you to submit jobs, get information on running jobs, stop jobs, get information on the cluster system, etc.
+
+For more details on how to install the Bridge system, see the [documentation](https://github.com/cea-hpc/bridge).
+
+To enable the Bridge executor, set `process.executor = 'bridge'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
+
+## Flux Executor
+
+<AddedInVersion version="22.11.0-edge" />
+
+The `flux` executor allows you to run your pipeline script using the [Flux Framework](https://flux-framework.org).
+
+Nextflow submits each process to the cluster as a separate job using the `flux submit` command.
+
+To enable the Flux executor, set `process.executor = 'flux'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [queue][process-queue]
+- [time][process-time]
+
+:::note
+Flux does not support the `memory` directive.
+:::
+
+:::note
+By default, Flux will send all output to the `.command.log` file. To send this output to stdout and stderr instead, set `flux.terminalOutput = true` in your config file.
+:::
+
+## Google Cloud Batch
+
+<AddedInVersion version="22.07.1-edge" />
+
+[Google Cloud Batch](https://cloud.google.com/batch) is a managed computing service that allows the execution of containerized workloads in the Google Cloud Platform infrastructure.
+
+Nextflow provides built-in support for the Cloud Batch API, which allows the seamless deployment of Nextflow pipelines in the cloud, offloading the pipeline process executions.
+
+The pipeline processes must specify the Docker image to use by defining the `container` directive, either in the pipeline script or the `nextflow.config` file. Additionally, the pipeline work directory must be located in a Google Storage bucket.
+
+To enable this executor, set `process.executor = 'google-batch'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [accelerator][process-accelerator]
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [machineType][process-machinetype]
+- [memory][process-memory]
+- [resourcelabels][process-resourcelabels]
+- [time][process-time]
+
+See [Cloud Batch][google-batch]for further configuration details.
+
+## HTCondor
+
+:::warning{title="Experimental: may change in a future release"}  
+:::
+
+
+The `condor` executor allows you to run your pipeline script by using the [HTCondor](https://research.cs.wisc.edu/htcondor/) resource manager.
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `condor_submit` command.
+
+The pipeline must be launched from a node where the `condor_submit` command is available, which is typically the cluster login node.
+
+:::note
+The HTCondor executor for Nextflow does not currently support HTCondor's ability to transfer input/output data to the corresponding job's compute node. Therefore, the data must be made accessible to the compute nodes through a shared file system directory from where the Nextflow workflow is executed (or specified via the `-w` option).
+:::
+
+To enable the HTCondor executor, set `process.executor = 'condor'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [memory][process-memory]
+- [time][process-time]
+
+## HyperQueue
+
+<ChangedInVersion version="24.06.0-edge">
+HyperQueue 0.17.0 or later is required.
+</ChangedInVersion>
+
+<ChangedInVersion version="25.01.0-edge">
+HyperQueue 0.20.0 or later is required.
+</ChangedInVersion>
+
+The `hyperqueue` executor allows you to run your pipeline script by using the [HyperQueue](https://github.com/It4innovations/hyperqueue) job scheduler.
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `hq` command line tool.
+
+The pipeline must be launched from a node where the `hq` command is available, which is typically the cluster login node.
+
+To enable the HyperQueue executor, set `process.executor = 'hq'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [accelerator][process-accelerator]
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [time][process-time]
+
+## Kubernetes
+
+The `k8s` executor allows you to run a pipeline on a [Kubernetes](http://kubernetes.io/) cluster.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [accelerator][process-accelerator]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [memory][process-memory]
+- [pod][process-pod]
+- [resourcelabels][process-resourcelabels]
+- [time][process-time]
+
+See the [Kubernetes][k8s-page] page to learn how to set up a Kubernetes cluster to run Nextflow pipelines.
+
+## Local
+
+The `local` executor is used by default. It runs the pipeline processes on the computer where Nextflow is launched. The processes are parallelized by spawning multiple threads, taking advantage of the multi-core architecture of the CPU.
+
+The `local` executor is useful for developing and testing a pipeline script on your computer, before switching to a cluster or cloud environment with production data.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [time][process-time]
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+
+:::note
+While the `local` executor limits the number of concurrent tasks based on requested vs available resources, it does not enforce task resource requests. In other words, it is possible for a local task to use more CPUs and memory than it requested, in which case it may starve other tasks. An exception to this behavior is when using [Docker][container-docker] or [Podman][container-podman] containers, in which case the resource requests are enforced by the container runtime.
+:::
+
+The local executor supports two types of tasks:
+- Script tasks (processes with a `script` or `shell` block) - executed via a Bash wrapper
+- Native tasks (processes with an `exec` block) - executed directly in the JVM.
+
+## LSF
+
+The `lsf` executor allows you to run your pipeline script using a [Platform LSF](http://en.wikipedia.org/wiki/Platform_LSF) cluster.
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `bsub` command.
+
+The pipeline must be launched from a node where the `bsub` command is available, which is typically the cluster login node.
+
+To enable the LSF executor, set `process.executor = 'lsf'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
+
+:::note
+LSF supports both *per-core* and *per-job* memory limits. Nextflow assumes that LSF works in the *per-core* mode, thus it divides the requested [memory][process-memory] by the number of requested [cpus][process-cpus].
+
+When LSF is configured to work in the *per-job* memory limit mode, you must specify this limit with the `perJobMemLimit` option in the [`executor`][config-executor] scope of your Nextflow config file.
+
+See also the [Platform LSF documentation](https://www.ibm.com/support/knowledgecenter/SSETD4_9.1.3/lsf_config_ref/lsf.conf.lsb_job_memlimit.5.dita).
+:::
+
+## Moab
+
+:::warning{title="Experimental: may change in a future release"}
+:::
+
+The `moab` executor allows you to run your pipeline script using the [Moab](https://en.wikipedia.org/wiki/Moab_Cluster_Suite) resource manager by [Adaptive Computing](http://www.adaptivecomputing.com/).
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `msub` command provided by the resource manager.
+
+The pipeline must be launched from a node where the `msub` command is available, which is typically the cluster login node.
+
+To enable the `Moab` executor, set `process.executor = 'moab'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
+
+## NQSII
+
+The `nqsii` executor allows you to run your pipeline script using the [NQSII](https://www.rz.uni-kiel.de/en/our-portfolio/hiperf/nec-linux-cluster) resource manager.
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `qsub` command provided by the scheduler.
+
+The pipeline must be launched from a node where the `qsub` command is available, which is typically the cluster login node.
+
+To enable the NQSII executor, set `process.executor = 'nqsii'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
+
+## OAR
+
+The `oar` executor allows you to run your pipeline script using the [OAR](https://oar.imag.fr) resource manager.
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `oarsub` command.
+
+The pipeline must be launched from a node where the `oarsub` command is available, which is typically the cluster login node.
+
+To enable the OAR executor set `process.executor = 'oar'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
+
+When specifying `clusterOptions` as a string, multiple options must be separated by semicolons to ensure that the job script is formatted correctly:
+```groovy
+clusterOptions = '-t besteffort;--project myproject'
+```
+
+<AddedInVersion version="24.04.0" />
+
+The same behavior can now be achieved using a string list:
+```groovy
+clusterOptions = [ '-t besteffort', '--project myproject' ]
+```
+
+See [clusterOptions][process-clusteroptions] for details.
+
+## PBS/Torque
+
+The `pbs` executor allows you to run your pipeline script using a resource manager from the [PBS/Torque](http://en.wikipedia.org/wiki/Portable_Batch_System) family of batch schedulers.
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `qsub` command provided by the scheduler.
+
+The pipeline must be launched from a node where the `qsub` command is available, which is typically the cluster login node.
+
+To enable the PBS executor, set `process.executor = 'pbs'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
+
+## PBS Pro
+
+The `pbspro` executor allows you to run your pipeline script using the [PBS Pro](https://www.pbspro.org/) resource manager.
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `qsub` command provided by the scheduler.
+
+The pipeline must be launched from a node where the `qsub` command is available, which is typically the cluster login node.
+
+To enable the PBS Pro executor, set `process.executor = 'pbspro'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
+
+## SGE
+
+The `sge` executor allows you to run your pipeline script using a [Sun Grid Engine](http://en.wikipedia.org/wiki/Oracle_Grid_Engine) cluster or a compatible platform ([Open Grid Engine](http://gridscheduler.sourceforge.net/), [Univa Grid Engine](http://www.univa.com/products/grid-engine.php), etc).
+
+Nextflow manages each process as a separate grid job that is submitted to the cluster using the `qsub` command.
+
+The pipeline must be launched from a node where the `qsub` command is available, which is typically the cluster login node.
+
+To enable the SGE executor, set `process.executor = 'sge'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [penv][process-penv]
+- [queue][process-queue]
+- [time][process-time]
+
+## SLURM
+
+The `slurm` executor allows you to run your pipeline script using the [SLURM](https://slurm.schedmd.com/documentation.html) resource manager.
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `sbatch` command.
+
+The pipeline must be launched from a node where the `sbatch` command is available, which is typically the cluster login node.
+
+To enable the SLURM executor, set `process.executor = 'slurm'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
+
+:::note
+SLURM partitions can be specified with the `queue` directive.
+:::
+
+:::note
+Nextflow does not provide direct support for SLURM multi-clusters. If you need to submit workflow executions to a cluster other than the current one, specify it with the `SLURM_CLUSTERS` variable in the launch environment.
+:::
+
+<AddedInVersion version="23.07.0-edge">
+Some SLURM clusters require memory allocations to be specified with `--mem-per-cpu` instead of `--mem`. You can specify `executor.perCpuMemAllocation = true` in the Nextflow configuration to enable this behavior. Nextflow will automatically compute the memory per CPU for each task (by default 1 CPU is used).
+</AddedInVersion>
+
+## TCS
+
+The `tcs` executor allows you to run your pipeline script using a [Fujitsu Technical Computing Suite (TCS)](https://software.fujitsu.com/jp/manual/manualindex/p21000155e.html).
+
+Nextflow manages each process as a separate job that is submitted to the cluster using the `pjsub` command.
+
+The pipeline must be launched from a node where the `pjsub` command is available, which is typically the login node.
+
+To enable the TCS executor, set `process.executor = 'tcs'` in the `nextflow.config` file.
+
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- [clusterOptions][process-clusteroptions]
+- [time][process-time]
+
+:::note
+Use `clusterOptions` to specify system-dependent options such as queue (resource group), CPU, and node. These options vary across target systems and are not standardized.
+They correspond to `-L` options in the arguments of the `pjsub` command and should be configured according to the requirements of the specific cluster environment.
+
+For example:
+
+```groovy
+process {
+  executor = 'tcs'
+  time = '00:30:00'
+  clusterOptions = '-L rscgrp=a-batch -L vnode-core=4'
+}
+```
+:::
+
+[aws-batch]: /nextflow_docs/nextflow_repo/docs/aws.mdx#aws-batch
+[azure-batch]: /nextflow_docs/nextflow_repo/docs/azure.mdx#azure-batch
+[config-executor]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#executor
+[container-docker]: /nextflow_docs/nextflow_repo/docs/container.mdx#docker
+[container-podman]: /nextflow_docs/nextflow_repo/docs/container.mdx#podman
+[google-batch]: /nextflow_docs/nextflow_repo/docs/google.mdx#cloud-batch
+[k8s-page]: /nextflow_docs/nextflow_repo/docs/kubernetes.mdx
+[process-accelerator]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#accelerator
+[process-arch]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#arch
+[process-clusteroptions]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#clusteroptions
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-containeroptions]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#containeroptions
+[process-cpus]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cpus
+[process-disk]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#disk
+[process-machinetype]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#machinetype
+[process-memory]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#memory
+[process-penv]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#penv
+[process-pod]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#pod
+[process-queue]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#queue
+[process-resourcelabels]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#resourcelabels
+[process-time]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#time
\ No newline at end of file
diff --git a/docs/fusion.mdx b/docs/fusion.mdx
new file mode 100644
index 0000000000..e840afc30b
--- /dev/null
+++ b/docs/fusion.mdx
@@ -0,0 +1,33 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Fusion file system
+
+<AddedInVersion version="22.10.0" />
+
+<AddedInVersion version="23.02.0-edge" />
+
+Cloud object stores such as AWS S3 are scalable and cost-effective, but they don't present a POSIX (Portable Operating System Interface). This means containerized applications must copy data to and from cloud storage for every task — a slow and inefficient process.
+
+Fusion is a virtual, lightweight, distributed file system that bridges the gap between pipelines and cloud-native storage. Fusion enables seamless filesystem I/O to cloud object stores via a standard POSIX interface, resulting in simpler pipeline logic and faster, more efficient pipeline execution.
+
+See [Fusion file system](https://docs.seqera.io/fusion) for more information about Fusion features.
+
+:::note
+Fusion requires a license for use in Seqera Platform compute environments or directly in Nextflow. Fusion can be trialed at no cost. See the [Fusion licensing documentation](https://docs.seqera.io/fusion/licensing) for more information.
+:::
+
+## Get started
+
+Fusion integrates with Nextflow directly and does not require any installation or change in pipeline code. It only requires use of a container runtime or a container computing service, such as Kubernetes, AWS Batch, or Google Cloud Batch.
+
+To enable Fusion in your Nextflow pipeline, add the following to your `nextflow.config` file:
+
+```nextflow
+fusion.enabled = true
+wave.enabled = true
+tower.accessToken = '<PLATFORM_ACCESS_TOKEN>'
+```
+
+Replace `<PLATFORM_ACCESS_TOKEN>` with your Platform access token.
+
+See [Get started](https://docs.seqera.io/fusion/get-started) for more information and guides to get started with Fusion.
diff --git a/docs/git.mdx b/docs/git.mdx
new file mode 100644
index 0000000000..fb354387c7
--- /dev/null
+++ b/docs/git.mdx
@@ -0,0 +1,250 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Git
+
+## Git configuration
+
+The file `$HOME/.nextflow/scm` allows you to centralize the security credentials required to access private project repositories on Bitbucket, GitHub and GitLab source code management (SCM) platforms or to manage the configuration properties of private server installations (of the same platforms).
+
+The configuration properties for each Git provider are defined inside the `providers` section. Properties for the same provider are grouped with a common name and delimited with curly brackets. For example:
+
+```groovy
+providers {
+    <provider-name> {
+property = value
+// ...
+    }
+}
+```
+
+In the above template replace `<provider-name>` with one of the "default" servers (i.e. `bitbucket`, `github` or `gitlab`) or a custom identifier representing a private SCM server installation.
+
+The following configuration properties are supported for each provider configuration:
+
+##### `providers.<provider>.user`
+
+User name required to access private repositories on the SCM server.
+
+##### `providers.<provider>.token`
+
+*Required only for private Gitlab servers and supported for BitBucket*
+
+Private API access token.
+
+User password required to access private repositories on the SCM server.
+
+##### `providers.<provider>.token`
+
+*Required only for private Gitlab servers.*
+
+Private API access token.
+
+##### `providers.<provider>.platform`
+
+*Required only for private SCM servers.*
+
+Git provider name, either: `github`, `gitlab`, or `bitbucket`.
+
+##### `providers.<provider>.server`
+
+*Required only for private SCM servers.*
+
+SCM server name including the protocol prefix, e.g., `https://github.com`.
+
+##### `providers.<provider>.endpoint`
+
+*Required only for private SCM servers.*
+
+SCM API `endpoint` URL, e.g., `https://api.github.com` (default: the same as `providers.<provider>.server`).
+
+## Git providers
+
+### Bitbucket
+
+Create a `bitbucket` entry in the [SCM configuration file](#git-configuration) specifying your user name and either an API token or app password, as shown below:
+
+```groovy
+providers {
+    bitbucket {
+        user = 'me'
+        token = 'my-api-token'
+    }
+}
+```
+
+<AddedInVersion version="25.07.0-edge">
+API tokens are supported for BitBucket authentication. When both `token` and `password` are provided, the API token takes priority over the app password.
+</AddedInVersion>
+
+:::note
+API tokens are substitute passwords for a user account which you can use for scripts and integrating tools in order to avoid putting your real password into configuration files. Learn more about [app passwords](https://support.atlassian.com/bitbucket-cloud/docs/app-passwords/) and [API tokens](https://support.atlassian.com/bitbucket-cloud/docs/using-api-tokens/).
+:::
+
+### Bitbucket Server
+
+[Bitbucket Server](https://confluence.atlassian.com/bitbucketserver) is a self-hosted Git repository and management platform.
+
+:::note
+Bitbucket Servers use a different API from the [Bitbucket](https://bitbucket.org/) Cloud service. Make sure to use the right configuration whether you are using the cloud service or a self-hosted installation.
+:::
+
+To access your local Bitbucket Server, create an entry in the [SCM configuration file](#git-configuration) as shown below:
+
+```groovy
+providers {
+    mybitbucket {
+        platform = 'bitbucketserver'
+        server = 'https://your.bitbucket.host.com'
+        endpoint = 'https://your.bitbucket.host.com'
+        user = 'your-user'
+        password = 'your-password or your-token'
+    }
+}
+```
+
+### GitHub
+
+Create a `github` entry in the [SCM configuration file](#git-configuration) specifying your user name and access token as shown below:
+
+```groovy
+providers {
+    github {
+        user = 'your-user-name'
+        password = 'your-personal-access-token'
+    }
+}
+```
+
+GitHub requires the use of a personal access token (PAT) in place of a password when accessing APIs. Learn more about PAT and how to create it at [this link](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token).
+
+<AddedInVersion version="23.01.0-edge">
+Nextflow automatically uses the `GITHUB_TOKEN` environment variable to authenticate access to the GitHub repository if no credentials are provided via the `scm` file. This is useful especially when accessing pipeline code from a GitHub Action. Read more about the token authentication in the [GitHub documentation](https://docs.github.com/en/actions/security-guides/automatic-token-authentication).
+</AddedInVersion>
+
+### GitLab
+
+Create a `gitlab` entry in the [SCM configuration file](#git-configuration) specifying the user name, password and your API access token that can be found in your GitLab [account page](https://gitlab.com/profile/account) (sign in required). For example:
+
+```groovy
+providers {
+    gitlab {
+        user = 'me'
+        password = 'my-secret'
+        token = 'YgpR8m7viH_ZYnC8YSe8'
+    }
+}
+```
+
+:::tip
+The GitLab *token* string can be used as the `password` value in the above setting. When doing that the `token` field can be omitted.
+:::
+
+### Gitea
+
+[Gitea](https://gitea.io) is a Git repository server with GitHub-like GUI access. Since Gitea installation is quite easy, it is suitable for building a private development environment in your network. To access your Gitea server, you have to provide all the credential information below:
+
+```groovy
+providers {
+    mygitea {
+        server = 'http://your-domain.org/gitea'
+        endpoint = 'http://your-domain.org/gitea/api/v1'
+        platform = 'gitea'
+        user = 'your-user'
+        password = 'your-password'
+        token = 'your-api-token'
+    }
+}
+```
+
+See [Gitea documentation](https://docs.gitea.io/en-us/api-usage/) about how to enable API access on your server and how to issue a token.
+
+### Azure Repos
+
+Nextflow has built-in support for [Azure Repos](https://azure.microsoft.com/en-us/services/devops/repos/), a Git source code management service hosted in the Azure cloud. To access your Azure Repos with Nextflow provide the repository credentials using the configuration snippet shown below:
+
+```groovy
+providers {
+    azurerepos {
+        user = 'your-user-name'
+        password = 'your-personal-access-token'
+    }
+}
+```
+
+:::tip
+The Personal access token can be generated in the repository `Clone Repository` dialog.
+:::
+
+### AWS CodeCommit
+
+Nextflow supports [AWS CodeCommit](https://aws.amazon.com/codecommit/) as a Git provider to access and to share pipelines code.
+
+To access your project hosted on AWS CodeCommit with Nextflow provide the repository credentials using the configuration snippet shown below:
+
+```groovy
+providers {
+    my_aws_repo {
+        platform = 'codecommit'
+        user = '<AWS ACCESS KEY>'
+        password = '<AWS SECRET KEY>'
+    }
+}
+```
+
+In the above snippet replace `<AWS ACCESS KEY>` and `<AWS SECRET KEY>` with your AWS credentials, and `my_aws_repo` with a name of your choice.
+
+:::tip
+The `user` and `password` settings are optional. If omitted, the [AWS default credentials provider chain](https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/credentials.html) is used.
+:::
+
+Then the pipeline can be accessed with Nextflow as shown below:
+
+```bash
+nextflow run https://git-codecommit.eu-west-1.amazonaws.com/v1/repos/my-repo
+```
+
+In the above example replace `my-repo` with your own repository. Note also that AWS CodeCommit has different URLs depending on the region in which you are working.
+
+:::note
+The support for protocols other than HTTPS is not available at this time.
+:::
+
+## Private server configuration
+
+Nextflow is able to access repositories hosted on private Bitbucket, GitHub, GitLab and Gitea server installations.
+
+In order to use a private SCM installation you will need to set the server name and access credentials in your [SCM configuration file](#git-configuration) .
+
+If, for example, the host name of your private GitLab server is `gitlab.acme.org`, you will need to have in the `$HOME/.nextflow/scm` file a configuration like the following:
+
+```groovy
+providers {
+    mygit {
+        server = 'http://gitlab.acme.org'
+        platform = 'gitlab'
+        user = 'your-user'
+        password = 'your-password'
+        token = 'your-api-token'
+    }
+}
+```
+
+Then you will be able to run/pull a project with Nextflow using the following command line:
+
+```bash
+nextflow run acme/hello -hub mygit
+```
+
+Or, alternatively, using the Git clone URL:
+
+```bash
+nextflow run http://gitlab.acme.org/acme/hello.git
+```
+
+:::note
+You must also specify the server API endpoint URL if it differs from the server base URL. For example, for GitHub Enterprise V3, add `endpoint = 'https://git.your-domain.com/api/v3'`.
+:::
+
+:::warning
+When accessing a private SCM installation over `https` from a server that uses a custom SSL certificate, you may need to import the certificate into your local Java keystore. See [Import the Certificate as a Trusted Certificate](https://docs.oracle.com/javase/tutorial/security/toolsign/rstep2.html) for more information.
+:::
diff --git a/docs/google.mdx b/docs/google.mdx
new file mode 100644
index 0000000000..e7ecfd4839
--- /dev/null
+++ b/docs/google.mdx
@@ -0,0 +1,292 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Google Cloud
+
+## Credentials
+
+Credentials for submitting requests to the Google Cloud Batch API are picked up from your environment using [Application Default Credentials](https://github.com/googleapis/google-auth-library-java#google-auth-library-oauth2-http). Application Default Credentials are designed to use the credentials most natural to the environment in which a tool runs.
+
+The most common case will be to pick up your end-user Google credentials from your workstation. You can create these by running the following command and running through the authentication flow:
+
+```bash
+gcloud auth application-default login
+```
+
+This will write a credential file to your gcloud configuration directory that will be used for any tool you run on your workstation that picks up default credentials.
+
+The next most common case would be when running on a Compute Engine VM. In this case, Application Default Credentials will pick up the Compute Engine Service Account credentials for that VM.
+
+See the [Application Default Credentials](https://github.com/googleapis/google-auth-library-java#google-auth-library-oauth2-http) documentation for how to enable other use cases.
+
+Finally, the `GOOGLE_APPLICATION_CREDENTIALS` environment variable can be used to specify location of the Google credentials file.
+
+If you don't have it, the credentials file can be downloaded from the Google Cloud Console following these steps:
+
+- Open the [Google Cloud Console](https://console.cloud.google.com)
+- Go to APIs & Services → Credentials
+- Click on the *Create credentials* (blue) drop-down and choose *Service account key*, in the following page
+- Select an existing *Service account* or create a new one if needed
+- Select JSON as *Key type*
+- Click the *Create* button and download the JSON file giving a name of your choice e.g. `creds.json`.
+
+Then, define the following variable replacing the path in the example with the one of your credentials file just downloaded:
+
+```bash
+export GOOGLE_APPLICATION_CREDENTIALS="/path/your/file/creds.json"
+```
+
+See [Get started with Nextflow on Google Cloud Batch](https://www.nextflow.io/blog/2023/nextflow-with-gbatch.html) for more information on how to use Google Cloud Batch,
+including how to set the required roles for your service account.
+
+## Cloud Batch
+
+<AddedInVersion version="22.07.1-edge" />
+
+[Google Cloud Batch](https://cloud.google.com/batch) is a managed computing service that allows the execution of containerized workloads in the Google Cloud Platform infrastructure.
+
+Nextflow provides built-in support for Google Cloud Batch, allowing the seamless deployment of Nextflow pipelines in the cloud, in which tasks are offloaded to the Cloud Batch service.
+
+Read the [Google Cloud Batch executor][google-batch-executor] section to learn more about the `google-batch` executor in Nextflow.
+
+### Configuration
+
+Make sure to have defined in your environment the `GOOGLE_APPLICATION_CREDENTIALS` variable. See the [Credentials](#credentials) section for details.
+
+:::note
+Make sure your Google account is allowed to access the Google Cloud Batch service by checking the [APIs & Services](https://console.cloud.google.com/apis/dashboard) dashboard.
+:::
+
+Create or edit the file `nextflow.config` in your project root directory. The config must specify the following parameters:
+
+- Google Cloud Batch as Nextflow executor
+- The Docker container image(s) for pipeline tasks
+- The Google Cloud project ID and location
+
+Example:
+
+```groovy
+process {
+    executor = 'google-batch'
+    container = 'your/container:latest'
+}
+
+google {
+    project = 'your-project-id'
+    location = 'us-central1'
+}
+```
+
+Notes:
+
+- A container image must be specified to execute processes. You can use a different Docker image for each process using one or more [process selectors][config-process-selectors].
+- Make sure to specify the project ID, not the project name.
+- Make sure to specify a location where Google Batch is available. Refer to the [Google Batch documentation](https://cloud.google.com/batch/docs/get-started#locations) for region availability.
+
+Read the [Google configuration][config-google] section to learn more about advanced configuration options.
+
+### Process definition
+
+By default, the `cpus` and `memory` directives are used to find the cheapest machine type that is available at the current
+location and that fits the requested resources. If `memory` is not specified, 1 GB of memory is allocated per CPU.
+
+The `machineType` directive can be used to request a specific VM instance type. It can be any predefined Google Compute
+Platform [machine type](https://cloud.google.com/compute/docs/machine-types) or [custom machine type](https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type).
+
+```nextflow
+process my_task {
+    cpus 8
+    memory '40 GB'
+
+    script:
+    """
+    your_command --here
+    """
+}
+
+process other_task {
+    machineType 'n1-highmem-8'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+<AddedInVersion version="23.02.0-edge" />
+
+The `machineType` directive can also be a comma-separated list of patterns. The pattern can contain a `*` to match any
+number of characters and `?` to match any single character. Examples of valid patterns: `c2-*`, `m?-standard*`, `n*`.
+
+```nextflow
+process my_task {
+    cpus 8
+    memory '20 GB'
+    machineType 'n2-*,c2-*,m3-*'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+<AddedInVersion version="23.12.0-edge" />
+
+The `machineType` directive can also be an [Instance Template](https://cloud.google.com/compute/docs/instance-templates),
+specified as `template://<instance-template>`. For example:
+
+```nextflow
+process my_task {
+    cpus 8
+    memory '20 GB'
+    machineType 'template://my-template'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+:::note
+Using an instance template will overwrite the `accelerator` and `disk` directives, as well as the following Google Batch
+config options: `bootDiskImage`, `cpuPlatform`, `preemptible`, and `spot`.
+:::
+
+To use an instance template with GPUs, you must also set the `google.batch.installGpuDrivers` config option to `true`.
+
+To use an instance template with Fusion, the instance template must include a `local-ssd` disk named `fusion` with 375 GB.
+See the [Google Batch documentation](https://cloud.google.com/compute/docs/disks/local-ssd) for more details about local SSDs.
+
+<AddedInVersion version="23.06.0-edge" />
+
+The `disk` directive can be used to set the boot disk size or provision a disk for scratch storage. If the disk type is specified with the `type` option, a new disk will be mounted to the task VM at `/tmp` with the requested size and type. Otherwise, it will set the boot disk size, overriding the `google.batch.bootDiskSize` config option. See the [Google Batch documentation](https://cloud.google.com/compute/docs/disks) for more information about the available disk types.
+
+Examples:
+
+```nextflow
+// set the boot disk size
+disk 100.GB
+
+// mount a persistent disk at '/tmp'
+disk 100.GB, type: 'pd-standard'
+
+// mount a local SSD disk at '/tmp' (should be a multiple of 375 GB)
+disk 375.GB, type: 'local-ssd'
+```
+
+### Pipeline execution
+
+The pipeline can be launched either on a local computer or a cloud instance. Pipeline input data can be stored either locally or in a Google Storage bucket.
+
+The pipeline execution must specify a Google Storage bucket where the workflow's intermediate results are stored using the `-work-dir` command line options. For example:
+
+```bash
+nextflow run <script or project name> -work-dir gs://my-bucket/some/path
+```
+
+:::tip
+Any input data **not** stored in a Google Storage bucket will automatically be transferred to the pipeline work bucket. Use this feature with caution being careful to avoid unnecessary data transfers.
+:::
+
+:::warning
+The Google Storage path needs to contain at least sub-directory. Do not use only the bucket name e.g. `gs://my-bucket`.
+:::
+
+### Spot Instances
+
+Spot Instances are supported by adding the following setting in the Nextflow config file:
+
+```groovy
+google {
+    batch.spot = true
+}
+```
+
+<AddedInVersion version="23.11.0-edge" />
+
+Since this type of virtual machines can be retired by the provider before the job completion, it is advisable to add the following retry strategy to your config file to instruct Nextflow to automatically re-execute a job if the virtual machine was terminated preemptively:
+
+```groovy
+process {
+    errorStrategy = { task.exitStatus==50001 ? 'retry' : 'terminate' }
+    maxRetries = 5
+}
+```
+
+### Fusion file system
+
+<AddedInVersion version="23.02.0-edge" />
+
+The Google Batch executor supports the use of [Fusion][fusion-page]. Fusion allows the use of Google Cloud Storage as a virtual distributed file system, optimizing the data transfer and speeding up most job I/O operations.
+
+See [Google Cloud Batch](https://docs.seqera.io/fusion/guide/gcp-batch) for more information about configuring Fusion for Google Cloud Batch.
+
+### Supported directives
+
+Currently, the following Nextflow directives are supported by the Google Batch executor:
+
+- [accelerator][process-accelerator]
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [executor][process-executor]
+- [machineType][process-machinetype]
+- [memory][process-memory]
+- [time][process-time]
+
+### Hybrid execution
+
+Nextflow allows the use of multiple executors in the same workflow. This feature enables the deployment of hybrid workloads, in which some jobs are executed in the local computer or local computing cluster, and some jobs are offloaded to Google Cloud.
+
+To enable this feature, use one or more [process selectors][config-process-selectors] in your Nextflow configuration file to apply the Google Cloud executor to the subset of processes that you want to offload. For example:
+
+```groovy
+process {
+    withLabel: bigTask {
+        executor = 'google-batch'
+        container = 'my/image:tag'
+    }
+}
+
+google {
+    project = 'your-project-id'
+    location = 'us-central1' // for Google Batch
+}
+```
+
+Then launch the pipeline with the `-bucket-dir` option to specify a Google Storage path for the jobs computed with Google Cloud and, optionally, the `-work-dir` to specify the local storage for the jobs computed locally:
+
+```bash
+nextflow run <script or project name> -bucket-dir gs://my-bucket/some/path
+```
+
+:::warning
+The Google Storage path needs to contain at least one subdirectory (e.g. `gs://my-bucket/work` rather than `gs://my-bucket`).
+:::
+
+:::note
+Nextflow will automatically manage the transfer of input and output files between the local and cloud environments when using hybrid workloads.
+:::
+
+### Limitations
+
+- Compute resources in Google Cloud are subject to [resource quotas](https://cloud.google.com/compute/quotas), which may affect your ability to run pipelines at scale. You can request quota increases, and your quotas may automatically increase over time as you use the platform. In particular, GPU quotas are initially set to 0, so you must explicitly request a quota increase in order to use GPUs. You can initially request an increase to 1 GPU at a time, and after one billing cycle you may be able to increase it further.
+
+- Currently, it's not possible to specify a disk type different from the default one assigned by the service depending on the chosen instance type.
+
+[config-google]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#google
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[google-batch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#google-cloud-batch
+[process-accelerator]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#accelerator
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-containeroptions]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#containeroptions
+[process-cpus]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cpus
+[process-disk]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#disk
+[process-executor]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#executor
+[process-machinetype]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#machinetype
+[process-memory]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#memory
+[process-time]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#time
diff --git a/docs/guides/aws-java-sdk-v2.md b/docs/guides/aws-java-sdk-v2.mdx
similarity index 98%
rename from docs/guides/aws-java-sdk-v2.md
rename to docs/guides/aws-java-sdk-v2.mdx
index 1d924001dc..9c54761abd 100644
--- a/docs/guides/aws-java-sdk-v2.md
+++ b/docs/guides/aws-java-sdk-v2.mdx
@@ -1,5 +1,3 @@
-(aws-java-sdk-v2-page)=
-
 # AWS Java SDK v2
 
 AWS Java SDK v1 will reach end of life at the end of 2025. Starting in Nextflow 25.10, Nextflow uses AWS Java SDK v2 in the `nf-amazon` plugin.
diff --git a/docs/guides/gradle-plugin.mdx b/docs/guides/gradle-plugin.mdx
new file mode 100644
index 0000000000..e0a522a9c6
--- /dev/null
+++ b/docs/guides/gradle-plugin.mdx
@@ -0,0 +1,111 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Using the Nextflow Gradle plugin
+
+Nextflow provides a new `plugin create` command that simplifies the creation of Nextflow plugins. This command leverages the [nf-plugin-template](https://github.com/nextflow-io/nf-plugin-template) project, which uses the [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle) to streamline plugin development.
+
+The [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle) configures default dependencies needed for Nextflow integration and defines Gradle tasks for building, testing, and publishing Nextflow plugins. The Gradle plugin is versioned and published to the [Gradle Plugin Portal](https://plugins.gradle.org/), allowing developers to manage it like any other dependency. As the plugin ecosystem evolves, the Gradle plugin will enable easier maintenance and adoption of improvements. This page introduces [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle) and how to use it.
+
+:::note
+The Nextflow Gradle plugin and plugin registry are currently available as a public preview. See the [Migrating to the Nextflow plugin registry][plugin-page-migrate] for more information.
+:::
+
+## Creating a plugin
+
+<AddedInVersion version="25.04.0" />
+
+The best way to create a plugin with the Nextflow Gradle plugin is to use the `nextflow plugin create` sub-command and create a plugin project based on the [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/). See [Nextflow plugin template][dev-plugins-template] for more information about the Nextflow plugin template.
+
+To create Nextflow plugins with the Gradle plugin:
+
+1. Run `nextflow plugin create`.
+
+2. Follow the prompts to add your plugin name, organization name, and project path.
+
+3. Develop your plugin extension points. See [Extension points][dev-plugins-extension-points] for more information.
+
+4. Develop your tests. See [Testing a plugin][gradle-plugin-test] for more information.
+
+5. In the plugin root directory, run `make assemble`.
+
+## Installing a plugin
+
+Plugins can be installed locally without being published.
+
+To install plugins locally:
+
+1. In the plugin root directory, run `make install`.
+
+    :::note
+    Running `make install` will add your plugin to your `$HOME/.nextflow/plugins` directory.
+    :::
+
+2. Run your pipeline:
+
+    ```bash
+    nextflow run main.nf -plugins <PLUGIN_NAME>@<VERSION>
+    ```
+
+    Replace `<PLUGIN_NAME>@<VERSION>` with your plugin name and version.
+
+    :::note
+    Plugins can also be configured via Nextflow configuration files. See [Using plugins][using-plugins-page] for more information.
+    :::
+
+## Testing a plugin
+
+Testing your Nextflow plugin requires unit tests and end-to-end tests.
+
+<h3>Unit tests</h3>
+
+Unit tests are small, focused tests designed to verify the behavior of individual plugin components.
+
+To run unit tests:
+
+1. Develop your unit tests. See [MyObserverTest.groovy](https://github.com/nextflow-io/nf-plugin-template/blob/main/src/test/groovy/acme/plugin/MyObserverTest.groovy) in the [plugin template](https://github.com/nextflow-io/nf-plugin-template) for an example unit test.
+
+2. In the plugin root directory, run `make test`.
+
+<h3>End-to-end tests</h3>
+
+End-to-end tests are comprehensive tests that verify the behavior of an entire plugin as it would be used in Nextflow pipelines.
+
+End-to-end tests should be tailored to the needs of your plugin, but generally take the form of a small Nextflow pipeline. See the `validation` directory in the [plugin template](https://github.com/nextflow-io/nf-plugin-template) for an example end-to-end test.
+
+## Publishing a plugin
+
+The Nextflow Gradle plugin allows you to publish plugins to the [Nextflow plugin registry](https://registry.nextflow.io/) from the command line.
+
+To publish plugins to the [Nextflow plugin registry](https://registry.nextflow.io/):
+
+1. [Claim your plugin][plugin-registry-claim] in the registry.
+
+    :::{note}
+    You can claim a plugin even if it doesn't exist in the registry yet.
+    :::
+
+2. Create a file named `$HOME/.gradle/gradle.properties`, where `$HOME` is your home directory.
+
+3. Add your API key to the file:
+
+    ```
+    npr.apiKey=<API_KEY>
+    ```
+
+    Replace `<API_KEY>` with your plugin registry API key. See [Creating an access token][plugin-registry-access-token] for more information.
+
+4. Run `make release`.
+
+## Additional resources
+
+For additional Nextflow Gradle plugin configuration options, see the [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle) repository.
+
+[plugin-registry-claim]: /nextflow_docs/nextflow_repo/docs/plugins/plugin-registry.html#claiming-a-plugin
+[dev-plugins-extension-points]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#extension-points
+[dev-plugins-template]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#nextflow-plugin-template
+[gradle-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx
+[gradle-plugin-test]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#testing-a-plugin
+[plugin-page-migrate]: /nextflow_docs/nextflow_repo/docs/guides/migrate-plugin.mdx
+[plugin-registry-access-token]: /nextflow_docs/nextflow_repo/docs/plugins/plugin-registry.mdx#creating-an-access-token
+[plugin-registry-page]: /nextflow_docs/nextflow_repo/docs/plugins/plugin-registry.mdx
+[using-plugins-page]: /nextflow_docs/nextflow_repo/docs/plugins/using-plugins.mdx
diff --git a/docs/guides/migrate-plugin.md b/docs/guides/migrate-plugin.mdx
similarity index 86%
rename from docs/guides/migrate-plugin.md
rename to docs/guides/migrate-plugin.mdx
index a5bd94f241..dcf3cb142e 100644
--- a/docs/guides/migrate-plugin.md
+++ b/docs/guides/migrate-plugin.mdx
@@ -6,8 +6,6 @@ The [Nextflow plugin registry](https://registry.nextflow.io/) is a central repos
 
 Starting with Nextflow 25.04, the plugin registry can be used as a direct replacement for the legacy plugin index. This page describes the migration timeline, it's impact on users and developers, and how to migrate existing plugins.
 
-(migrate-plugin-timeline)=
-
 ## Migration timeline
 
 The migration timeline is tentative and subject to modification.
@@ -36,11 +34,11 @@ No immediate actions are required for plugin users. The plugin configuration has
 
 ## Impact on plugin developers
 
-Plugin developers will need to update their plugin to publish to the Nextflow plugin registry instead of the legacy plugin index. The best way to do this is to migrate to the {ref}`Nextflow Gradle plugin<gradle-plugin-page>`, which simplifies the development process and supports publishing to the plugin registry from the command line.
+Plugin developers will need to update their plugin to publish to the Nextflow plugin registry instead of the legacy plugin index. The best way to do this is to migrate to the [Nextflow Gradle plugin][gradle-plugin-page], which simplifies the development process and supports publishing to the plugin registry from the command line.
 
 ## Migrating to the Nextflow Gradle plugin
 
-To migrate an existing Nextflow plugin to the {ref}`Nextflow Gradle plugin<gradle-plugin-page>`:
+To migrate an existing Nextflow plugin to the [Nextflow Gradle plugin][gradle-plugin-page]:
 
 1. Remove the following files and folders:
     - `buildSrc/`
@@ -49,7 +47,7 @@ To migrate an existing Nextflow plugin to the {ref}`Nextflow Gradle plugin<gradl
 
 2. If your plugin has a `plugins` directory, move the `src` directory to the project root.
 
-    :::{note}
+    :::note
     Plugin sources should be in `src/main/groovy` or `src/main/java`.
     :::
 
@@ -130,12 +128,16 @@ To migrate an existing Nextflow plugin to the {ref}`Nextflow Gradle plugin<gradl
 
 7. In the plugin root directory, run `make assemble`.
 
-Alternatively, use the `nextflow plugin create` command to re-create your plugin with the plugin template and add your existing plugin code. See {ref}`dev-plugins-template` for more information about the plugin template.
+Alternatively, use the `nextflow plugin create` command to re-create your plugin with the plugin template and add your existing plugin code. See [Nextflow plugin template][dev-plugins-template] for more information about the plugin template.
 
 ## Publishing to the Nextflow plugin registry
 
-The Nextflow Gradle plugin supports publishing plugins from the command line. See {ref}`gradle-plugin-publish` for more information.
+The Nextflow Gradle plugin supports publishing plugins from the command line. See [Publishing a plugin][gradle-plugin-publish] for more information.
 
-:::{warning}
+:::warning
 Once you migrate to the Gradle plugin, you will no longer be able to publish to the legacy plugin index. See the [Migration timeline](#migration-timeline) for more information.
 :::
+
+[dev-plugins-template]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#nextflow-plugin-template
+[gradle-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx
+[gradle-plugin-publish]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#publishing-a-plugin
diff --git a/docs/guides/updating-spot-retries.md b/docs/guides/updating-spot-retries.mdx
similarity index 98%
rename from docs/guides/updating-spot-retries.md
rename to docs/guides/updating-spot-retries.mdx
index 23f9a81533..75b0802fd1 100644
--- a/docs/guides/updating-spot-retries.md
+++ b/docs/guides/updating-spot-retries.mdx
@@ -1,5 +1,3 @@
-(spot-retries-page)=
-
 # Spot Instance failures and retries
 
 This page describes changes in how Nextflow handles Spot Instance failures and retries on AWS and Google Cloud, the impact of those changes, and how to configure spot retry behavior for your pipelines. These changes apply to Nextflow 24.10 and later.
@@ -8,11 +6,11 @@ This page describes changes in how Nextflow handles Spot Instance failures and r
 
 Up to version 24.10, Nextflow would silently retry Spot Instance failures up to `5` times when using AWS Batch or Google Batch. These retries were controlled by cloud-specific configuration parameters (e.g., `aws.batch.maxSpotAttempts`) and happened in cloud infrastructure without explicit visibility to Nextflow.
 
-<h3>Before Nextflow 24.10</h3>
+### Before Nextflow 24.10
 
 By default, Nextflow would instruct AWS and Google to automatically retry jobs lost to Spot reclamation up to `5` times. Retries were handled by the cloud provider _within_ a Nextflow task. It was often unclear that tasks were restarted as there was no explicit message. Task runtimes and associated cloud costs were increased because they included the runtime of the reclaimed and retried tasks. Due to the high likelihood of reclamation before completion, long-running tasks running on Spot Instances frequently required retries, leading to inefficient allocation of resources and higher costs.
 
-<h3>After Nextflow 24.10</h3>
+### After Nextflow 24.10
 
 The default Spot reclamation retry setting changed to `0` on AWS and Google. By default, no _internal_ retries are attempted on these platforms. Spot reclamations lead to an immediate failure, exposed to Nextflow in the same way as other generic failures (for example, returning `exit code 1` on AWS). Nextflow treats these failures like any other job failure, unless a retry strategy is configured.
 
@@ -34,7 +32,7 @@ There are four possible actions.
 
 If you do not configure anything, you will observe more pipeline failures when Spot Instances are reclaimed. This approach provides clearer visibility into failures. Failed tasks can be re-run with the `-resume` option. However, frequent task reclamation may lead to a higher failure rate and each retry requires manual intervention.
 
-:::{note}
+:::note
 If you resume the pipeline using the resume option, it will pick up at the point the pipeline was interrupted and start with a retry of that task.
 :::
 
diff --git a/docs/index.md b/docs/index.md
deleted file mode 100644
index 0f2a41d082..0000000000
--- a/docs/index.md
+++ /dev/null
@@ -1,192 +0,0 @@
-
-# Nextflow
-
-*"Dataflow variables are spectacularly expressive in concurrent programming"*
-<br />[Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum](https://dl.acm.org/doi/abs/10.1145/72551.72552)
-
-[![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)](https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush)
-[![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)
-[![Nextflow Twitter](https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=58bd9f&&label=%40nextflow&style=popout)](https://twitter.com/nextflowio)
-[![Nextflow Publication](https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=58bd9f&style=popout)](https://www.nature.com/articles/nbt.3820)
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=58bd9f&style=popout)](http://bioconda.github.io/recipes/nextflow/README.html)
-[![Nextflow license](https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/blob/master/COPYING)
-
-Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It uses a dataflow programming model that simplifies writing parallel and distributed pipelines by allowing you to focus on data flow and computation. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, and cloud. Additionally, Nextflow supports a range of compute environments, software container runtimes, and package managers, allowing workflows to be executed in reproducible and isolated environments.
-
-## Get started
-
-To get started with Nextflow:
-
-1. See the Nextflow {ref}`overview <overview-page>` to learn key concepts.
-2. Download and {ref}`install <install-page>` Nextflow.
-3. Set up an {ref}`environment <devenv-page>` with the {ref}`Nextflow VS Code extension <devenv-nextflow>`.
-4. Run {ref}`your first script <your-first-script>`.
-
-To continue learning about Nextflow, visit the [Nextflow community training portal](https://training.nextflow.io/latest/) and find a training course that is right for you. Seqera, the company that develops Nextflow, also runs a variety of training events. See [Seqera Events](https://seqera.io/events/) for more information.
-
-## Community
-
-You can post questions in the [Nextflow community forum](https://community.seqera.io) or the [Nextflow Slack](https://www.nextflow.io/slack-invite.html). Bugs and feature requests should be reported as [GitHub issues](https://github.com/nextflow-io/nextflow/issues/new/choose).
-
-The Nextflow community is highly active with regular community meetings, events, a podcast, and more. You can view this material on the [Nextflow](https://www.youtube.com/@Nextflow) YouTube channel.
-
-The [nf-core](https://nf-co.re/) project is a community effort aggregating high-quality Nextflow workflows that can be used by everyone.
-
-## Contributing
-
-Contributions to Nextflow are welcome. See {ref}`Contributing <contributing-page>` for more details.
-
-## License
-
-Nextflow is released under the Apache 2.0 license. Nextflow is a [registered trademark](https://github.com/nextflow-io/trademark).
-
-## Citations
-
-If you use Nextflow in your work, please cite:
-
-P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nature Biotechnology 35, 316–319 (2017) doi:[10.1038/nbt.3820](http://www.nature.com/nbt/journal/v35/n4/full/nbt.3820.html)
-
-```{toctree}
-:hidden:
-:caption: Get started
-:maxdepth: 1
-
-overview
-install
-developer-env
-your-first-script
-```
-
-```{toctree}
-:hidden:
-:caption: Running pipelines
-:maxdepth: 1
-
-cli
-config
-executor
-cache-and-resume
-reports
-```
-
-```{toctree}
-:hidden:
-:caption: Developing pipelines
-:maxdepth: 1
-
-script
-working-with-files
-process
-process-typed
-channel
-workflow
-module
-notifications
-secrets
-sharing
-vscode
-```
-
-```{toctree}
-:hidden:
-:caption: Software dependencies
-:maxdepth: 1
-
-git
-container
-conda
-spack
-wave
-```
-
-```{toctree}
-:hidden:
-:caption: Compute & storage
-:maxdepth: 1
-
-aws
-amazons3
-azure
-google
-kubernetes
-fusion
-```
-
-```{toctree}
-:hidden:
-:caption: Plugins
-:maxdepth: 1
-
-plugins/plugins
-plugins/using-plugins
-plugins/developing-plugins
-plugins/plugin-registry
-```
-
-```{toctree}
-:hidden:
-:caption: Language Reference
-:maxdepth: 1
-
-reference/feature-flags
-reference/syntax
-reference/stdlib
-reference/process
-reference/channel
-reference/operator
-```
-
-```{toctree}
-:hidden:
-:caption: Runtime Reference
-:maxdepth: 1
-
-reference/cli
-reference/config
-reference/env-vars
-```
-
-```{toctree}
-:hidden:
-:caption: Updates
-:maxdepth: 1
-
-updating-nextflow
-strict-syntax
-migrations/index
-```
-
-```{toctree}
-:hidden:
-:caption: Contributing
-:maxdepth: 1
-
-developer/index
-developer/diagram
-developer/config-scopes
-developer/packages
-```
-
-```{toctree}
-:hidden:
-:caption: Tutorials
-:maxdepth: 1
-
-tutorials/rnaseq-nf
-tutorials/data-lineage
-tutorials/workflow-outputs
-tutorials/static-types
-tutorials/metrics
-tutorials/flux
-```
-
-```{toctree}
-:hidden:
-:caption: Guides
-:maxdepth: 1
-
-guides/aws-java-sdk-v2
-guides/gradle-plugin
-guides/migrate-plugin
-guides/updating-spot-retries
-```
diff --git a/docs/index.mdx b/docs/index.mdx
new file mode 100644
index 0000000000..054e96edaa
--- /dev/null
+++ b/docs/index.mdx
@@ -0,0 +1,70 @@
+
+# Nextflow
+
+*"Dataflow variables are spectacularly expressive in concurrent programming"*
+<br />[Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum](https://dl.acm.org/doi/abs/10.1145/72551.72552)
+
+<div style={{ display: "flex", flexWrap: "wrap", gap: "8px", alignItems: "center" }}>
+    <a href="https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush">
+        <img src="https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg" alt="Nextflow CI" />
+    </a>
+    <a href="https://github.com/nextflow-io/nextflow/releases/latest">
+        <img src="https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout" alt="Nextflow version" />
+    </a>
+    <a href="https://twitter.com/nextflowio">
+        <img src="https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=58bd9f&&label=%40nextflow&style=popout" alt="Nextflow Twitter" />
+    </a>
+    <a href="https://www.nature.com/articles/nbt.3820">
+        <img src="https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=58bd9f&style=popout" alt="Nextflow publication" />
+    </a>
+    <a href="http://bioconda.github.io/recipes/nextflow/README.html">
+        <img src="https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=58bd9f&style=popout" alt="install with bioconda" />
+    </a>
+    <a href="https://github.com/nextflow-io/nextflow/blob/master/COPYING">
+        <img src="https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout" alt="Nextflow license" />
+    </a>
+</div>
+
+<br />
+
+Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It uses a dataflow programming model that simplifies writing parallel and distributed pipelines by allowing you to focus on data flow and computation. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, and cloud. Additionally, Nextflow supports a range of compute environments, software container runtimes, and package managers, allowing workflows to be executed in reproducible and isolated environments.
+
+## Get started
+
+To get started with Nextflow:
+
+1. See the Nextflow [overview][overview-page] to learn key concepts
+2. Download and [install][install-page] Nextflow
+3. Set up an [environment][devenv-page] with the [Nextflow VS Code extension][devenv-nextflow]
+4. Run [your first script][your-first-script]
+
+To continue learning about Nextflow, visit the [Nextflow community training portal](https://training.nextflow.io/latest/) and find a training course that is right for you. Seqera, the company that develops Nextflow, also runs a variety of training events. See [Seqera Events](https://seqera.io/events/) for more information.
+
+## Community
+
+You can post questions in the [Nextflow community forum](https://community.seqera.io) or the [Nextflow Slack](https://www.nextflow.io/slack-invite.html). Bugs and feature requests should be reported as [GitHub issues](https://github.com/nextflow-io/nextflow/issues/new/choose).
+
+The Nextflow community is highly active with regular community meetings, events, a podcast, and more. You can view this material on the [Nextflow](https://www.youtube.com/@Nextflow) YouTube channel.
+
+The [nf-core](https://nf-co.re/) project is a community effort aggregating high-quality Nextflow workflows that can be used by everyone.
+
+## Contributing
+
+Contributions to Nextflow are welcome. See [Contributing][contributing-page] for more details.
+
+## License
+
+Nextflow is released under the Apache 2.0 license. Nextflow is a [registered trademark](https://github.com/nextflow-io/trademark).
+
+## Citations
+
+If you use Nextflow in your work, please cite:
+
+P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nature Biotechnology 35, 316–319 (2017) doi:[10.1038/nbt.3820](http://www.nature.com/nbt/journal/v35/n4/full/nbt.3820.html)
+
+[contributing-page]: /nextflow_docs/nextflow_repo/docs/developer/index.mdx
+[overview-page]: /nextflow_docs/nextflow_repo/docs/overview.mdx
+[install-page]: /nextflow_docs/nextflow_repo/docs/install.mdx
+[devenv-page]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx
+[devenv-nextflow]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#nextflow
+[your-first-script]: /nextflow_docs/nextflow_repo/docs/your-first-script.mdx
diff --git a/docs/install.mdx b/docs/install.mdx
new file mode 100644
index 0000000000..681b4101fa
--- /dev/null
+++ b/docs/install.mdx
@@ -0,0 +1,161 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Installation
+
+Nextflow can be used on any POSIX-compatible system (Linux, macOS, etc), and on Windows through [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux). This page describes how to install Nextflow.
+
+:::note
+New versions of Nextflow are released regularly. See [Updating Nextflow][updating-nextflow] for more information about Nextflow release cadence, how to update Nextflow, and how select your version of Nextflow.
+:::
+
+## Requirements
+
+Nextflow requires Bash 3.2 (or later) and [Java 17 (or later, up to 25)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. To see which version of Java you have, run the following command:
+
+```bash
+java -version
+```
+
+<DeprecatedInVersion version="24.11.0-edge">
+Support for Java versions prior to 17 was dropped.
+</DeprecatedInVersion>
+
+If you don't have a compatible version of Java installed, it is recommended that you install it through [SDKMAN!](https://sdkman.io/), and that you use the latest Long-Term-Support (LTS) version of Temurin. See [Which version of JDK should I use?](https://whichjdk.com/) for more information about different versions of Java.
+
+To install Java with SDKMAN:
+
+1. [Install SDKMAN](https://sdkman.io/install):
+
+    ```bash
+    curl -s https://get.sdkman.io | bash
+    ```
+
+2. Open a new terminal.
+
+3. Install Java:
+
+    ```bash
+    sdk install java 17.0.10-tem
+    ```
+
+4. Confirm that Java is installed correctly:
+
+    ```bash
+    java -version
+    ```
+
+## Install Nextflow
+
+Nextflow is distributed as an easy to use self-installing package. It is also distributed via Conda and as a standalone distribution.
+
+### Self-install
+
+In order to make the installation process as simple as possible, Nextflow is distributed as a self-installing package.
+
+To install Nextflow with the self-installing package:
+
+1. Download Nextflow:
+
+    ```bash
+    curl -s https://get.nextflow.io | bash
+    ```
+
+    :::tip
+    Set `export CAPSULE_LOG=none` to make the installation logs less verbose.
+    :::
+
+2. Make Nextflow executable:
+
+    ```bash
+    chmod +x nextflow
+    ```
+
+3. Move Nextflow into an executable path. For example:
+
+    ```bash
+    mkdir -p $HOME/.local/bin/
+    mv nextflow $HOME/.local/bin/
+    ```
+
+    :::tip
+    Ensure the directory `$HOME/.local/bin/` is included in your `PATH` variable. Temporarily add this directory to `PATH` by setting `export PATH="$PATH:$HOME/.local/bin"`. Add the directory to `PATH` permanently by adding the export command to your shell configuration file, such as `~/.bashrc` or `~/.zshrc`. Alternatively, move the `nextflow` executable to a directory already in your `PATH`.
+    :::
+
+    :::warning
+    Nextflow updates its executable during the self-install process, therefore the update can fail if the executable is placed in a directory with restricted permissions.
+    :::
+
+4. Confirm Nextflow is installed correctly:
+
+    ```bash
+    nextflow info
+    ```
+
+### Conda
+
+To install Nextflow with Conda:
+
+1. Create an environment with Nextflow:
+
+    ```bash
+    conda create --name nf-env bioconda::nextflow
+    ```
+
+2. Activate the environment:
+
+    ```bash
+    source activate nf-env
+    ```
+
+3. Confirm Nextflow is installed correctly:
+
+    ```bash
+    nextflow info
+    ```
+
+:::warning
+Installing Nextflow via Conda may lead to outdated versions, dependency conflicts, and Java compatibility issues. Using the self-installing package is recommended for a more reliable and up-to-date installation.
+:::
+
+### Standalone distribution
+
+The Nextflow standalone distribution (i.e., the `dist` release) is a self-contained `nextflow` executable that can run without needing to download core dependencies at runtime. This distribution is useful for offline environments as well as building and testing Nextflow locally.
+
+To use the standalone distribution:
+
+1. Download the standalone distribution from Assets section of the [GitHub releases page](https://github.com/nextflow-io/nextflow/releases).
+
+2. Grant execution permissions to the downloaded file. For example:
+
+    ```bash
+    chmod +x nextflow-24.10.1-dist
+    ```
+
+3. Use it as a drop-in replacement for `nextflow` command. For example:
+
+    ```bash
+    ./nextflow-24.10.1-dist run info
+    ```
+
+:::note
+The standalone distribution will still download core and third-party plugins as needed at runtime.
+:::
+
+## Seqera Platform
+
+You can launch workflows directly from [Seqera Platform](https://seqera.io/platform/) without installing Nextflow locally.
+
+Launching from Seqera provides you with:
+
+- User-friendly launch interfaces.
+- Automated cloud infrastructure creation.
+- Organizational user management.
+- Advanced analytics with resource optimization.
+
+Seqera Cloud Basic is free for small teams. Researchers at qualifying academic institutions can apply for free access to Seqera Cloud Pro.
+See the [Seqera Platform documentation](https://docs.seqera.io/platform) for tutorials to get started.
+
+If you have installed Nextflow locally, you can use the [`nextflow auth`][cli-auth] command to authenticate with Seqera and automatically configure workflow monitoring.
+
+[cli-auth]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#cli-auth
+[updating-nextflow]: /nextflow_docs/nextflow_repo/docs/updating-nextflow.mdx
diff --git a/docs/kubernetes.mdx b/docs/kubernetes.mdx
new file mode 100644
index 0000000000..5aa199dbc2
--- /dev/null
+++ b/docs/kubernetes.mdx
@@ -0,0 +1,137 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Kubernetes
+
+[Kubernetes](https://kubernetes.io/) is a cloud-native open-source system for deployment, scaling, and management of containerized applications.
+
+It provides clustering and file system abstractions that allows the execution of containerized workloads across different cloud platforms and on-premises installations.
+
+The built-in support for Kubernetes provided by Nextflow streamlines the execution of containerized workflows in Kubernetes clusters.
+
+## Concepts
+
+Kubernetes main abstraction is the `pod`. A `pod` defines the (desired) state of one or more containers i.e. required computing resources, storage, network configuration.
+
+Kubernetes abstracts also the storage provisioning through the definition of one more persistent volumes that allow containers to access to the underlying storage systems in a transparent and portable manner.
+
+When using the `k8s` executor Nextflow deploys the workflow execution as a Kubernetes pod. This pod orchestrates the workflow execution and submits a separate pod execution for each job that need to be carried out by the workflow application.
+
+
+![Nextflow k8s](_static/nextflow-k8s-min.png)
+
+## Requirements
+
+At least a [Persistent Volume](https://kubernetes.io/docs/concepts/storage/persistent-volumes/#persistent-volumes) with `ReadWriteMany` access mode has to be defined in the Kubernetes cluster (check the supported storage systems at [this link](https://kubernetes.io/docs/concepts/storage/persistent-volumes/#access-modes)).
+
+Such volume needs to be accessible through a [Persistent Volume Claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/#persistentvolumeclaims), which will be used by Nextflow to run the application and store the scratch data and the pipeline final result.
+
+The workflow application has to be containerized using the usual Nextflow [container][process-container] directive.
+
+:::tip
+When using [Wave][wave-page] and [Fusion][fusion-page] there is no need to use a shared file system and configure a persistent volume claim for the deployment of Nextflow pipeline with Kubernetes. You can ignore this requirement when using the Fusion file system. See the [Fusion][fusion-page] for further information.
+:::
+
+## Execution
+
+The workflow execution needs to be submitted from a computer able to connect to the Kubernetes cluster.
+
+Nextflow uses the Kubernetes configuration file available at the path `$HOME/.kube/config` or the file specified by the environment variable `KUBECONFIG`.
+
+You can verify such configuration with the following command:
+
+```console
+$ kubectl cluster-info
+Kubernetes master is running at https://your-host:6443
+KubeDNS is running at https://your-host:6443/api/v1/namespaces/kube-system/services/kube-dns:dns/proxy
+```
+
+### Launch with `kuberun`
+
+:::warning
+The `kuberun` is considered an obsolete approach for the deployment of Nextflow pipeline with Kubernetes and is no longer maintained. For a better alternative, consider using [Launch with Fusion](#launch-with-fusion).
+:::
+
+To deploy and launch the workflow execution use the Nextflow command `kuberun` as shown below:
+
+```bash
+nextflow kuberun <pipeline-name> -v vol-claim:/mount/path
+```
+
+This command will create and execute a pod running the nextflow orchestrator for the specified workflow. In the above example replace `<pipeline-name>` with an existing nextflow project or the absolute path of a workflow already deployed in the Kubernetes cluster.
+
+The `-v` command line option is required to specify the volume claim name and mount path to use for the workflow execution. In the above example replace `vol-claim` with the name of an existing persistent volume claim and `/mount/path` with the path where the volume is required to be mount in the container. Volume claims can also be specified in the Nextflow configuration file. See [k8s][config-k8s>] for details.
+
+Once the pod execution starts, the application in the foreground prints the console output produced by the running workflow pod.
+
+### Interactive login
+
+For debugging purpose it's possible to execute a Nextflow pod and launch an interactive shell using the following command:
+
+```bash
+nextflow kuberun login -v vol-claim:/mount/path
+```
+
+This command creates a pod, sets up the volume claim(s), configures the Nextflow environment and finally launches a Bash login session.
+
+:::warning
+The pod is automatically destroyed once the shell session terminates. Do not use it to launch long-running workflows in the background.
+:::
+
+### Launch with Fusion
+
+<AddedInVersion version="22.10.0" />
+
+The use of [Fusion][fusion-page] allows deploying a Nextflow pipeline to a remote (or local) cluster without the need to use a shared file system and configure a persistent volume claim for the deployment of Nextflow pipeline with Kubernetes.
+
+This also makes unnecessary the use of the special `kuberun` command for the pipeline execution.
+
+See [Amazon EKS](https://docs.seqera.io/fusion/guide/aws-eks) for a guide to set up Fusion in Amazon EKS compute environments and [Google Kubernetes Engine (GKE)](https://docs.seqera.io/fusion/guide/gcp-gke) for a guide to set up Fusion in GKE compute environments.
+
+### Running in a pod
+
+Nextflow can be executed directly from a pod running in a Kubernetes cluster. In these cases you will need to use the plain Nextflow `run` command and specify the `k8s` executor and the required persistent volume claim in the `nextflow.config` file as shown below:
+
+```groovy
+process {
+    executor = 'k8s'
+}
+
+k8s {
+    storageClaimName = 'vol-claim'
+    storageMountPath = '/mount/path'
+    storageSubPath = '/my-data'
+}
+```
+
+In the above snippet replace `vol-claim` with the name of an existing persistent volume claim and replace `/mount/path` with the actual desired mount path (default: `/workspace`) and `storageSubPath` with the directory in the volume to be mounted (default: `/`).
+
+:::warning
+The running pod must have been created with the same persistent volume claim name and mount as the one specified in your Nextflow configuration file. Note also that the `run` command does not support the `-v` option.
+:::
+
+:::tip
+It is also possible to mount multiple volumes using the `pod` directive, for example:
+
+```groovy
+k8s.pod = [ [volumeClaim: "other-pvc", mountPath: "/other" ]]
+```
+:::
+
+## Pod settings
+
+The process [pod][process-pod] directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the [Kubernetes][k8s-executor] executor. See the [pod][process-pod] directive for more details.
+
+## Limitations
+
+The `kuberun` command does not allow the execution of local Nextflow scripts. It is only intended as a convenient way to test the deployment of pipelines to a Kubernetes cluster.
+
+## Advanced configuration
+
+See [k8s][config-k8s] and [Kubernetes][k8s-executor] to learn more about advanced configuration options.
+
+[config-k8s]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#k8s
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[k8s-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#kubernetes
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-pod]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#pod
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
\ No newline at end of file
diff --git a/docs/migrations/24-04.md b/docs/migrations/24-04.mdx
similarity index 66%
rename from docs/migrations/24-04.md
rename to docs/migrations/24-04.mdx
index 4322faf0e2..9f9776d45a 100644
--- a/docs/migrations/24-04.md
+++ b/docs/migrations/24-04.mdx
@@ -1,48 +1,44 @@
-(migrating-24-04-page)=
-
 # Migrating to 24.04
 
 [Nextflow 24.04](https://github.com/nextflow-io/nextflow/releases/tag/v24.04.0) was released on May 20, 2024.
 
 ## New features
 
-<h3>Topic channels (first preview)</h3>
+### Topic channels (first preview)
 
 A topic channel is a channel that can receive values from multiple sources, based on a matching name or *topic*.
 
 Topic channels are particularly useful for collecting metadata from various points in a pipeline without writing all of the channel logic that is normally required (e.g., using the `mix` operator).
 
-See {ref}`channel-topic` for details.
+See [topic][channel-topic] for details.
 
-<h3>Process <code>eval</code> outputs</h3>
+### Process `eval` outputs
 
 A process `eval` output is a new type of process output that captures the standard output of an arbitrary shell command.
 
 This output type is a simpler way to capture command outputs, such as the version of a command-line tool, instead of using a `path` or `env` output.
 
-See {ref}`process-out-eval` for details.
+See [Eval output (`eval`)][process-out-eval] for details.
 
-<h3>Resource limits</h3>
+### Resource limits
 
 The `resourceLimits` process directive allows you to define global limits on the resources requested by individual tasks.
 
-This directive is useful for ensuring that a task's resource requirements never exceed system-wide limits. It is especially important for preventing tasks from becoming unschedulable when using {ref}`retry with dynamic resources <dynamic-task-resources>`.
+This directive is useful for ensuring that a task's resource requirements never exceed system-wide limits. It is especially important for preventing tasks from becoming unschedulable when using retry with [dynamic resources][dynamic-task-resources].
 
-See {ref}`process-resourcelimits` for details.
+See [resourceLimits][process-resourcelimits] for details.
 
-<h3>Job arrays</h3>
+### Job arrays
 
 The `array` directive allows a process to submit jobs as *job arrays*, a feature used by many batch schedulers to submit many similar jobs in an efficient manner.
 
-:::{tip}
+:::tip
 On Google Batch, the `array` directive can be used in conjunction with the `cpus`, `memory`, and `machineType` directives to pack multiple tasks onto the same VM.
 :::
 
-See {ref}`process-array` for details.
-
-(workflow-outputs-first-preview)=
+See [array][process-array] for details.
 
-<h3>Workflow outputs (first preview)</h3>
+### Workflow outputs (first preview)
 
 Workflow outputs are a new way to publish outputs at the workflow level:
 
@@ -67,45 +63,45 @@ output {
 
 This syntax allows you to publish channels in a workflow, instead of publishing file patterns in a process using `publishDir`.
 
-See {ref}`workflow-output-def` for details.
+See [Workflow outputs][workflow-output-def] for details.
 
 ## Enhancements
 
-<h3>Colored logs</h3>
+### Colored logs
 
 Nextflow's console output now features colored logs and improved organization to highlight the most important information about a pipeline while it's running.
 
-<h3>AWS Fargate</h3>
+### AWS Fargate
 
-Nextflow now supports AWS Fargate for the AWS Batch executor. See {ref}`aws-fargate` for details.
+Nextflow now supports AWS Fargate for the AWS Batch executor. See [AWS Fargate][aws-fargate] for details.
 
-<h3>OCI auto-pull mode for Singularity and Apptainer</h3>
+### OCI auto-pull mode for Singularity and Apptainer
 
 The `singularity.ociAutoPull` (`apptainer.ociAutoPull`) config option enables OCI auto-pull mode for Singularity (Apptainer). When enabled, this setting allows Singularity (Apptainer) to download and convert Docker images during task execution rather than on the Nextflow head node.
 
-See {ref}`config-singularity` and {ref}`config-apptainer` for details.
+See [singularity][config-singularity] and [apptainer][config-apptainer] for details.
 
-<h3>Improved publish error handling</h3>
+### Improved publish error handling
 
 The publishing logic used by `publishDir` and workflow outputs will automatically retry failed publish operations with exponential backoff, providing better resilience against transient errors. The retry behavior can be controlled using the `nextflow.publish.retryPolicy.*` config settings.
 
 Additionally, the `failOnError` option of the `publishDir` directive is now `true` by default. This means that, by default, publish errors (after retries) will cause the pipeline to fail. To restore the previous behavior, set `failOnError` to `false` for each `publishDir` directive.
 
-:::{note}
-The `nextflow.publish` config settings have since been moved to `workflow.output`. See {ref}`config-workflow` for details.
+:::note
+The `nextflow.publish` config settings have since been moved to `workflow.output`. See [workflow][config-workflow] for details.
 :::
 
-<h3>GA4GH TES 1.1</h3>
+### GA4GH TES 1.1
 
 The TES executor has been updated to be compliant with version 1.1 of the [TES API specification](https://ga4gh.github.io/task-execution-schemas/docs/). Notable improvements include support for directory outputs, glob outputs, and the `bin` directory.
 
-:::{note}
+:::note
 The `nf-ga4gh` plugin has since been moved into its own repository, [nextflow-io/nf-ga4gh](https://github.com/nextflow-io/nf-ga4gh). Refer to this repository for documentation and the latest updates on GA4GH integrations for Nextflow.
 :::
 
 ## Breaking changes
 
-- Support for {ref}`Glacier auto-retrieval <config-aws>` was removed. Consider using the AWS CLI to restore Glacier objects before or at the beginning of your pipeline.
+- Support for [Glacier auto-retrieval][config-aws] was removed. Consider using the AWS CLI to restore Glacier objects before or at the beginning of your pipeline.
 
 - The `seqera` and `defaults` channels were removed from the list of default conda channels used by Wave. They can be restored with the following setting:
 
@@ -125,12 +121,26 @@ The `nf-ga4gh` plugin has since been moved into its own repository, [nextflow-io
 - New environment variable: `NXF_CLOUDINFO_ENABLED`
 - New environment variable: `NXF_CACHE_DIR`
 - New plugin extension point: `TaskTipProvider`
-- New `pod` directive option: `schedulerName` 
-- New `pod` directive option: `ttlSecondsAfterFinished` 
+- New `pod` directive option: `schedulerName`
+- New `pod` directive option: `ttlSecondsAfterFinished`
 - New workflow metadata: `workflow.fusion.enabled`
 - New workflow metadata: `workflow.fusion.version`
 - New workflow metadata: `workflow.preview`
 - New workflow metadata: `workflow.wave.enabled`
-- Support Google Batch {ref}`instance templates <google-batch-process>`
-- Support the use of {ref}`secrets in the pipeline script <secrets-pipeline-script>`
+- Support Google Batch [instance templates][google-batch-process]
+- Support the use of [secrets in the pipeline script][secrets-pipeline-script]
 - Upgrade to Groovy 4
+
+[aws-fargate]: /nextflow_docs/nextflow_repo/docs/aws.mdx#aws-fargate
+[config-aws]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#aws
+[config-apptainer]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#apptainer
+[config-singularity]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#singularity
+[channel-topic]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#topic
+[config-workflow]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#workflow
+[dynamic-task-resources]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-task-resources
+[google-batch-process]: /nextflow_docs/nextflow_repo/docs/google.mdx#process-definition
+[process-array]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#array
+[process-out-eval]: /nextflow_docs/nextflow_repo/docs/process.mdx#eval-output-eval
+[process-resourcelimits]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#resourcelimits
+[secrets-pipeline-script]: /nextflow_docs/nextflow_repo/docs/secrets.mdx#pipeline-script
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
diff --git a/docs/migrations/24-10.md b/docs/migrations/24-10.mdx
similarity index 57%
rename from docs/migrations/24-10.md
rename to docs/migrations/24-10.mdx
index 9d6fe18c5f..bfb9e337ec 100644
--- a/docs/migrations/24-10.md
+++ b/docs/migrations/24-10.mdx
@@ -1,21 +1,18 @@
-
 # Migrating to 24.10
 
 [Nextflow 24.10](https://github.com/nextflow-io/nextflow/releases/tag/v24.10.0) was released on October 27, 2024.
 
 ## New features
 
-<h3>Language server</h3>
-
-The [Nextflow language server](https://github.com/nextflow-io/language-server) implements the Language Server Protocol (LSP) for Nextflow scripts and config files. It can be integrated with any editor that functions as an LSP client, and is used by the official [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow). See {ref}`vscode-page` for details.
+### Language server
 
-The language server parses scripts and config files according to the {ref}`Nextflow language specification <syntax-page>`, which is more strict than the Nextflow CLI. See {ref}`strict-syntax-page` for details.
+The [Nextflow language server](https://github.com/nextflow-io/language-server) implements the Language Server Protocol (LSP) for Nextflow scripts and config files. It can be integrated with any editor that functions as an LSP client, and is used by the official [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow). See [VS Code integration][vscode-page] for details.
 
-(workflow-outputs-second-preview)=
+The language server parses scripts and config files according to the [Nextflow language specification][syntax-page], which is more strict than the Nextflow CLI. See [Preparing for strict syntax][strict-syntax-page] for details.
 
-<h3>Workflow outputs (second preview)</h3>
+### Workflow outputs (second preview)
 
-The second preview of workflow outputs introduces the following breaking changes from the {ref}`previous version <workflow-outputs-first-preview>`:
+The second preview of workflow outputs introduces the following breaking changes from the [previous version][workflow-outputs-first-preview]:
 
 - The `publish:` section within processes has been removed. Channels should now be published only from workflows, ideally the entry workflow.
 
@@ -25,33 +22,33 @@ The second preview of workflow outputs introduces the following breaking changes
 
 - Target names cannot begin or end with a slash (`/`).
 
-See {ref}`workflow-output-def` to learn more about the workflow output definition.
+See [Workflow outputs][workflow-output-def] to learn more about the workflow output definition.
 
 ## Enhancements
 
-<h3>Azure Managed Identities</h3>
+### Azure Managed Identities
 
-Nextflow now supports managed identities for the Azure Batch executor. See {ref}`azure-managed-identities` for details.
+Nextflow now supports managed identities for the Azure Batch executor. See [Managed identities][azure-managed-identities] for details.
 
-<h3>Task previous execution trace</h3>
+### Task previous execution trace
 
-The `task` variable in the process definition has two new properties, `task.previousTrace` and `task.previousException`, which allows a task to access the runtime metadata of the previous attempt. See {ref}`task-previous-execution-trace` for details.
+The `task` variable in the process definition has two new properties, `task.previousTrace` and `task.previousException`, which allows a task to access the runtime metadata of the previous attempt. See [Dynamic task resources with previous execution trace][task-previous-execution-trace] for details.
 
 ## Breaking changes
 
-- The `all` release of Nextflow has been replaced with the `dist` release, which includes fewer core plugins by default and supports third-party plugins. See {ref}`install-standalone` for details.
+- The `all` release of Nextflow has been replaced with the `dist` release, which includes fewer core plugins by default and supports third-party plugins. See [Standalone distribution][install-standalone] for details.
 
 - The `nf-ga4gh` plugin has been moved into its own repository, [nextflow-io/nf-ga4gh](https://github.com/nextflow-io/nf-ga4gh). To continue using the TES executor, you must explicitly declare the `nf-ga4gh` plugin in your Nextflow configuration. Refer to the plugin repository for documentation and updates on GA4GH integrations.
 
-- The {ref}`hyperqueue-executor` executor now requires HyperQueue 0.17.0 or later.
+- The [HyperQueue][hyperqueue-executor] executor now requires HyperQueue 0.17.0 or later.
 
 - The use of [Grape](https://docs.groovy-lang.org/latest/html/documentation/grape.html) dependencies with the `@Grab` annotation is no longer supported. Code that requires third-party libraries should be migrated to a plugin.
 
-- Automatic spot retries for AWS Batch and Google Batch have been disabled by default. See {ref}`spot-retries-page` for details.
+- Automatic spot retries for AWS Batch and Google Batch have been disabled by default. See [Spot Instance failures and retries][spot-retries-page] for details.
 
 ## Deprecations
 
-- The use of `addParams` and `params` clauses in include declarations is deprecated. See {ref}`module-params` for details.
+- The use of `addParams` and `params` clauses in include declarations is deprecated. See [Module parameters][module-params] for details.
 
 ## Miscellaneous
 
@@ -64,3 +61,16 @@ The `task` variable in the process definition has two new properties, `task.prev
 - New config option: `wave.scan.allowedLevels`
 - New config option: `workflow.failOnIgnore`
 - Rename `nextflow.publish.retryPolicy` config scope to `workflow.output.retryPolicy`
+
+
+[azure-managed-identities]: /nextflow_docs/nextflow_repo/docs/azure.mdx#managed-identities
+[hyperqueue-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#hyperqueue
+[install-standalone]: /nextflow_docs/nextflow_repo/docs/install.mdx#standalone-distribution
+[module-params]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-parameters
+[spot-retries-page]: /nextflow_docs/nextflow_repo/docs/guides/updating-spot-retries.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[task-previous-execution-trace]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-task-resources-with-previous-execution-trace
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-outputs-first-preview]: /nextflow_docs/nextflow_repo/docs/migrations/24-04.mdx#workflow-outputs-first-preview
+[vscode-page]: /nextflow_docs/nextflow_repo/docs/vscode.mdx
diff --git a/docs/migrations/25-04.md b/docs/migrations/25-04.mdx
similarity index 52%
rename from docs/migrations/25-04.md
rename to docs/migrations/25-04.mdx
index 720ca77011..2ddceda137 100644
--- a/docs/migrations/25-04.md
+++ b/docs/migrations/25-04.mdx
@@ -1,26 +1,22 @@
-(migrating-25-04-page)=
-
 # Migrating to 25.04
 
 [Nextflow 25.04](https://github.com/nextflow-io/nextflow/releases/tag/v25.04.0) was released on May 8, 2025.
 
 ## New features
 
-<h3>Strict syntax</h3>
-
-The *strict syntax* is a strict parser for Nextflow DSL2 that implements the {ref}`Nextflow language specification <syntax-page>`. Originally introduced by the [Nextflow language server](https://github.com/nextflow-io/language-server) alongside Nextflow 24.10, the strict syntax is now available in the Nextflow CLI.
+### Strict syntax
 
-The strict syntax is disabled by default. It can be enabled by setting the environment variable `NXF_SYNTAX_PARSER=v2`. See {ref}`strict-syntax-page` for details.
+The *strict syntax* is a strict parser for Nextflow DSL2 that implements the [Nextflow language specification][syntax-page]. Originally introduced by the [Nextflow language server](https://github.com/nextflow-io/language-server) alongside Nextflow 24.10, the strict syntax is now available in the Nextflow CLI.
 
-<h3>Linting and formatting</h3>
+The strict syntax is disabled by default. It can be enabled by setting the environment variable `NXF_SYNTAX_PARSER=v2`. See [strict syntax][strict-syntax-page] for details.
 
-The `nextflow lint` command checks Nextflow scripts and config files for errors using the {ref}`strict syntax <strict-syntax-page>`. It can also format Nextflow files using the same formatter as the Nextflow language server. See {ref}`cli-lint` for details.
+### Linting and formatting
 
-(workflow-outputs-third-preview)=
+The `nextflow lint` command checks Nextflow scripts and config files for errors using the [strict syntax][strict-syntax-page]. It can also format Nextflow files using the same formatter as the Nextflow language server. See [lint][cli-lint] for details.
 
-<h3>Workflow outputs (third preview)</h3>
+### Workflow outputs (third preview)
 
-The third preview of workflow outputs introduces the following breaking changes from the {ref}`previous version <workflow-outputs-second-preview>`:
+The third preview of workflow outputs introduces the following breaking changes from the [previous version][workflow-outputs-second-preview]:
 
 - The `publish:` section can only be specified in the entry workflow.
 
@@ -28,33 +24,33 @@ The third preview of workflow outputs introduces the following breaking changes
 
 - By default, output files are published to the base output directory, rather than a subdirectory corresponding to the output name.
 
-- The syntax for dynamic publish paths has changed. Instead of defining a closure that returns a closure with the `path` directive, the outer closure should use the `>>` operator to publish individual files. See {ref}`workflow-publishing-files` for details.
+- The syntax for dynamic publish paths has changed. Instead of defining a closure that returns a closure with the `path` directive, the outer closure should use the `>>` operator to publish individual files. See [Publishing files][workflow-publishing-files] for details.
 
 - The `mapper` index directive has been removed. Use a `map` operator in the workflow body instead.
 
-See {ref}`migrating-workflow-outputs` to get started.
+See [Workflow outputs][workflow-output-def] to get started.
 
-<h3>Topic channels (out of preview)</h3>
+### Topic channels (out of preview)
 
-{ref}`Topic channels <channel-topic>`, introduced in Nextflow 24.04 as a preview feature, have been brought out of preview, which means that they can be used without the `nextflow.preview.topic` feature flag.
+[Topic channels][channel-topic], introduced in Nextflow 24.04 as a preview feature, have been brought out of preview, which means that they can be used without the `nextflow.preview.topic` feature flag.
 
-<h3>Data lineage</h3>
+### Data lineage
 
 This release introduces built-in provenance tracking, also known as *data lineage*. When `lineage.enabled` is set to `true` in your configuration, Nextflow will record every workflow run, task execution, output file, and the links between them.
 
-You can explore this lineage from the command line using the {ref}`cli-lineage` command. Additionally, you can refer to files in the lineage store from a Nextflow script using the `lid://` path prefix as well as the {ref}`channel-from-lineage` channel factory.
+You can explore this lineage from the command line using the [lineage][cli-lineage] command. Additionally, you can refer to files in the lineage store from a Nextflow script using the `lid://` path prefix as well as the [fromLineage][channel-from-lineage] channel factory.
 
-See {ref}`data-lineage-page` to get started.
+See the [Data lineage][data-lineage-page] guide to get started.
 
 <h3>Simplified plugin development</h3>
 
 The `nextflow plugin create` sub-command creates the scaffold for a Nextflow plugin using the official [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/). It is simpler and easier to maintain than the previous plugin boilerplate.
 
-See the {ref}`gradle-plugin-page` guide for details.
+See the [Using the Nextflow Gradle plugin][gradle-plugin-page] guide for details.
 
 ## Enhancements
 
-<h3>Improved <code>inspect</code> command</h3>
+### Improved `inspect` command
 
 Previously, the `nextflow inspect` command included all processes that were invoked in a preview run. Now, the `inspect` command includes all processes that are *included* by the entry workflow (directly or indirectly), which has several benefits:
 
@@ -64,15 +60,15 @@ Previously, the `nextflow inspect` command included all processes that were invo
 
 - It can be run as `nextflow inspect <PIPELINE>`, without specifying any parameters or config profiles.
 
-See {ref}`cli-inspect` to learn more about the `inspect` command.
+See [inspect][cli-inspect] to learn more about the `inspect` command.
 
-<h3>Plugin version ranges</h3>
+### Plugin version ranges
 
 When specifying a plugin, the plugin version can now be prefixed with `~` to pin the major and minor version while allowing the latest patch release. This syntax makes it possible to pin the plugin version while automatically using new patch releases.
 
-See {ref}`plugins-page` for details.
+See [Plugins][plugins-page] for details.
 
-<h3>Improved publish error handling</h3>
+### Improved publish error handling
 
 Nextflow will terminate the run if the thread pool responsible for publishing files takes too long. Previously, this timeout was reported as a warning. Now, it is reported as an error.
 
@@ -84,13 +80,13 @@ workflow.output.ignoreErrors = true
 
 ## Breaking changes
 
-- Nextflow now requires Java 17 or newer. See {ref}`install-requirements` for instructions to install Java 17.
+- Nextflow now requires Java 17 or newer. See [Requirements][install-requirements] for instructions to install Java 17.
 
-- The {ref}`hyperqueue-executor` executor now requires HyperQueue 0.20.0 or later.
+- The [HyperQueue][hyperqueue-executor] executor now requires HyperQueue 0.20.0 or later.
 
 ## Deprecations
 
-- The process `shell` section has been deprecated. See {ref}`process-shell` for details.
+- The process `shell` section has been deprecated. See [Shell][process-shell] for details.
 
 - Nextflow will report a warning if it encounters a process `shell` directive that contains newlines. This warning will become an error in a future release.
 
@@ -108,3 +104,20 @@ workflow.output.ignoreErrors = true
 - New plugin extension point: `TraceObserverFactoryV2`
 - New standard library function: `env()`
 - Support `disk` directive for Azure Batch
+
+[channel-from-lineage]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#fromlineage
+[channel-topic]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#topic
+[cli-inspect]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#inspect
+[cli-lineage]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lineage
+[cli-lint]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lint
+[data-lineage-page]: /nextflow_docs/nextflow_repo/docs/tutorials/data-lineage.mdx
+[gradle-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx
+[hyperqueue-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#hyperqueue
+[install-requirements]: /nextflow_docs/nextflow_repo/docs/install.mdx#requirements
+[plugins-page]: /nextflow_docs/nextflow_repo/docs/plugins/plugins.mdx
+[process-shell]: /nextflow_docs/nextflow_repo/docs/process.mdx#shell
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[workflow-outputs-second-preview]: /nextflow_docs/nextflow_repo/docs/migrations/24-10.mdx#workflow-outputs-second-preview
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-publishing-files]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#publishing-files
diff --git a/docs/migrations/25-10.md b/docs/migrations/25-10.mdx
similarity index 65%
rename from docs/migrations/25-10.md
rename to docs/migrations/25-10.mdx
index 643266d26e..0b85ca7026 100644
--- a/docs/migrations/25-10.md
+++ b/docs/migrations/25-10.mdx
@@ -27,13 +27,13 @@ workflow {
 
 This syntax allows you to declare all parameters in one place with explicit type annotations, and it allows Nextflow to validate parameters at runtime.
 
-See {ref}`workflow-params-def` for details.
+See [Parameters][workflow-params-def] for details.
 
 (workflow-outputs-final)=
 
 <h3>Workflow outputs (out of preview)</h3>
 
-{ref}`Workflow outputs <workflow-output-def>`, introduced in Nextflow 24.04 as a preview feature, have been brought out of preview and can now be used without the `nextflow.preview.output` feature flag.
+[Workflow outputs][workflow-output-def], introduced in Nextflow 24.04 as a preview feature, have been brought out of preview and can now be used without the `nextflow.preview.output` feature flag.
 
 The final version adds the ability to specify a type annotation for each output declaration:
 
@@ -56,7 +56,7 @@ output {
 }
 ```
 
-See {ref}`migrating-workflow-outputs` to get started.
+See [Migrating to workflow outputs][migrating-workflow-outputs] to get started.
 
 <h3>Type annotations</h3>
 
@@ -107,7 +107,7 @@ The following declarations can be annotated with types:
 - Closure parameters
 - Workflow outputs (the `output` block)
 
-Type annotations can refer to any of the {ref}`standard types <stdlib-types>`.
+Type annotations can refer to any of the [standard types][stdlib-types].
 
 Some types use *generic type parameters* to work with different data types in a type-safe way. For example:
 
@@ -120,7 +120,7 @@ The following examples show types with type parameters:
 // List<E> where E is String
 def sequences: List<String> = ['ATCG', 'GCTA', 'TTAG']
 
-// List<E> where E is Path  
+// List<E> where E is Path
 def fastqs: List<Path> = [file('sample1.fastq'), file('sample2.fastq')]
 
 // Map<K,V> where K is String and V is Integer
@@ -136,13 +136,13 @@ Type annotations can be appended with `?` to denote values can be `null`:
 def x_opt: String? = null
 ```
 
-In the type system, queue channels are represented as `Channel`, while value channels are represented as `Value`. To make the terminology clearer and more concise, queue channels are now called *dataflow channels* (or simply *channels*), and value channels are now called *dataflow values*. See {ref}`dataflow-page` for more information.
+In the type system, queue channels are represented as `Channel`, while value channels are represented as `Value`. To make the terminology clearer and more concise, queue channels are now called *dataflow channels* (or simply *channels*), and value channels are now called *dataflow values*. See [Dataflow][dataflow-page] for more information.
 
-:::{note}
-Nextflow supports Groovy-style type annotations using the `<type> <name>` syntax, but this approach is deprecated in {ref}`strict syntax <strict-syntax-page>`. While Groovy-style annotations remain valid for functions and local variables, the language server and `nextflow lint` automatically convert them to Nextflow-style annotations during code formatting.
+:::note
+Nextflow supports Groovy-style type annotations using the `<type> <name>` syntax, but this approach is deprecated in [strict syntax][strict-syntax-page]. While Groovy-style annotations remain valid for functions and local variables, the language server and `nextflow lint` automatically convert them to Nextflow-style annotations during code formatting.
 :::
 
-See {ref}`migrating-static-types` for details.
+See [Migrating to static types][migrating-static-types] for details.
 
 <h3>Auth and Launch commands</h3>
 
@@ -162,7 +162,7 @@ nextflow auth config
 nextflow launch nextflow-io/hello
 ```
 
-See {ref}`cli-auth` and {ref}`cli-launch` for details.
+See [CLI Auth][cli-auth] and [CLI Launch][cli-launch] for details.
 
 ## Enhancements
 
@@ -176,8 +176,8 @@ The legacy plugin index can still be used by setting the `NXF_PLUGINS_REGISTRY_U
 export NXF_PLUGINS_REGISTRY_URL="https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json"
 ```
 
-:::{note}
-Plugin developers will not be able to submit PRs to the legacy plugin index once the plugin registry is generally available. Plugins should be updated to publish to the Nextflow plugin registry using the {ref}`Nextflow Gradle plugin <gradle-plugin-page>` instead. See {ref}`plugin-registry-page` for details.
+:::note
+Plugin developers will not be able to submit PRs to the legacy plugin index once the plugin registry is generally available. Plugins should be updated to publish to the Nextflow plugin registry using the [Nextflow Gradle plugin][gradle-plugin-page] instead. See [plugin registry][plugin-registry-page] for details.
 :::
 
 <h3>New syntax for workflow handlers</h3>
@@ -197,11 +197,11 @@ workflow {
 }
 ```
 
-This syntax is simpler and easier to use with the {ref}`strict syntax <strict-syntax-page>`. See {ref}`workflow-handlers` for details.
+This syntax is simpler and easier to use with the [strict syntax][strict-syntax-page]. See [Workflow handlers][workflow-handlers] for details.
 
 <h3>Simpler syntax for dynamic directives</h3>
 
-The {ref}`strict syntax <strict-syntax-page>` allows dynamic process directives to be specified without a closure:
+The [strict syntax][strict-syntax-page] allows dynamic process directives to be specified without a closure:
 
 ```nextflow
 process hello {
@@ -219,7 +219,7 @@ process hello {
 
 Dynamic process settings in configuration files must still be specified with closures.
 
-See {ref}`dynamic-directives` for details.
+See [Dynamic directives][dynamic-directives] for details.
 
 <h3>Configurable date formatting</h3>
 
@@ -244,17 +244,17 @@ This feature addresses previous inconsistencies in timestamp representations.
 
 - The `google-lifesciences` executor is no longer supported because the Google Cloud Life Sciences API was discontinued in July 2025. Use the `google-batch` executor instead.
 
-- The AWS Java SDK used by Nextflow was upgraded from v1 to v2, which introduced some breaking changes to the `aws.client` config options. See {ref}`the guide <aws-java-sdk-v2-page>` for details.
+- The AWS Java SDK used by Nextflow was upgraded from v1 to v2, which introduced some breaking changes to the `aws.client` config options. See [AWS Java SDK v2][aws-java-sdk-v2-page] for details.
 
-- The `nextflow.config.schema` package was renamed to `nextflow.config.spec`. Plugin developers that define custom {ref}`configuration scopes <dev-plugins-extension-points-config>` will need to update their imports accordingly.
+- The `nextflow.config.schema` package was renamed to `nextflow.config.spec`. Plugin developers that define custom [configuration scopes][dev-plugins-extension-points-config] will need to update their imports accordingly.
 
 ## Deprecations
 
-- The legacy type detection of CLI parameters is disabled when using the strict syntax (`NXF_SYNTAX_PARSER=v2`). {ref}`Legacy parameters <workflow-params-legacy>` in the strict syntax should not rely on legacy type detection. Alternatively, use the new `params` block to convert CLI parameters based on their type annotations. Legacy type detection can be disabled globally by setting the environment variable `NXF_DISABLE_PARAMS_TYPE_DETECTION=true`.
+- The use of workflow handlers in the configuration file has been deprecated. You should define workflow handlers in the pipeline script or a plugin instead. See [Workflow handlers][config-workflow-handlers] for details.
 
-- The use of workflow handlers in the configuration file has been deprecated. You should define workflow handlers in the pipeline script or a plugin instead. See {ref}`config-workflow-handlers` for details.
+- The legacy type detection of CLI parameters is disabled when using the strict syntax (`NXF_SYNTAX_PARSER=v2`). [Legacy parameters][workflow-params-legacy] in the strict syntax should not rely on legacy type detection. Alternatively, use the new `params` block to convert CLI parameters based on their type annotations. Legacy type detection can be disabled globally by setting the environment variable `NXF_DISABLE_PARAMS_TYPE_DETECTION=true`.
 
-- The `nextflow.enable.configProcessNamesValidation` feature flag is deprecated. It was originally introduced to suppress false warnings for process selectors targeting conditional processes. The {ref}`strict syntax <strict-syntax-page>` now validates process selectors without producing false warnings.
+- The `nextflow.enable.configProcessNamesValidation` feature flag is deprecated. It was originally introduced to suppress false warnings for process selectors targeting conditional processes. The [strict syntax][strict-syntax-page] now validates process selectors without producing false warnings.
 
 ## Miscellaneous
 
@@ -262,3 +262,21 @@ This feature addresses previous inconsistencies in timestamp representations.
 - New config options: `wave.build.compression.*`
 - New executor: Fujitsu Technical Computing Suite (`tcs`)
 - Support Java 25
+
+[aws-java-sdk-v2-page]: /nextflow_docs/nextflow_repo/docs/guides/aws-java-sdk-v2.mdx
+[cli-auth]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#auth
+[cli-launch]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#launch
+[config-workflow-handlers]: /nextflow_docs/nextflow_repo/docs/config.mdx#workflow-handlers
+[dataflow-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[dev-plugins-extension-points-config]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#dev-plugins-extension-points-config
+[dynamic-directives]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-directives
+[gradle-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx
+[migrating-workflow-outputs]: /nextflow_docs/nextflow_repo/docs/tutorials/workflow-outputs.mdx#migrating-workflow-outputs
+[migrating-static-types]: /nextflow_docs/nextflow_repo/docs/tutorials/static-types.mdx
+[plugin-registry-page]: /nextflow_docs/nextflow_repo/docs/plugins/plugin-registry.mdx
+[stdlib-types]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-params-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#parameters
+[workflow-params-legacy]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#legacy-parameters
+[workflow-handlers]: /nextflow_docs/nextflow_repo/docs/notifications.mdx#workflow-handlers
diff --git a/docs/migrations/dsl1.md b/docs/migrations/dsl1.mdx
similarity index 74%
rename from docs/migrations/dsl1.md
rename to docs/migrations/dsl1.mdx
index a3b532d8f6..a84fd31280 100644
--- a/docs/migrations/dsl1.md
+++ b/docs/migrations/dsl1.mdx
@@ -1,5 +1,3 @@
-(dsl1-page)=
-
 # Migrating from DSL1
 
 In Nextflow version `22.03.0-edge`, DSL2 became the default DSL version. In version `22.12.0-edge`, DSL1 support was removed and the Nextflow documentation was updated to use DSL2 by default. Users who are still using DSL1 should migrate their pipelines to DSL2 to use the latest versions of Nextflow. This page describes the differences between DSL1 and DSL2 and how to migrate to DSL2.
@@ -41,7 +39,7 @@ result.view { it.trim() }
 
 To migrate this code to DSL2, you need to move all of your channel logic throughout the script into a `workflow` definition. Additionally, you must call each process explicitly, passing any input channels as arguments (instead of `from ...`) and receiving any output channels as return values (instead of `into ...`).
 
-See {ref}`workflow-page` page to learn how to define a workflow.
+See [Workflows][workflow-page] to learn how to define a workflow.
 
 You can see the DSL1 Nextflow script from above written in DSL2 here:
 
@@ -100,22 +98,19 @@ Similarly, in DSL2, process outputs can be consumed by multiple consumers automa
 
 In DSL1, the entire Nextflow pipeline must be defined in a single file. For example, `main.nf`. This restriction becomes cumbersome as a pipeline grows and hinders the sharing and reuse of pipeline components.
 
-DSL2 introduces the concept of "module scripts" (or "modules" for short), which are Nextflow scripts that can be "included" by other scripts. While modules are not essential to migrating to DSL2, nor are they mandatory in DSL2, modules can help you organize a large pipeline into multiple smaller files and take advantage of modules created by others. See {ref}`module-page` to learn more about modules.
+DSL2 introduces the concept of "module scripts" (or "modules" for short), which are Nextflow scripts that can be "included" by other scripts. While modules are not essential to migrating to DSL2, nor are they mandatory in DSL2, modules can help you organize a large pipeline into multiple smaller files and take advantage of modules created by others. See [Modules][module-page] to learn more about modules.
 
-:::{note}
+:::note
 DSL2 scripts cannot exceed 64 KB in size. Split large DSL1 scripts into modules to avoid this limit.
 :::
 
 ## Deprecations
 
-<h3>Processes</h3>
-
-- The `set` process input type is no longer supported, use {ref}`tuple <process-input-tuple>` instead.
-
-- The `set` process output type is no longer supported, use {ref}`tuple <process-out-tuple>` instead.
-
-- The `mode flatten` option for process outputs is no longer available. Use the {ref}`operator-flatten` operator on the corresponding output channel instead.
+### Processes
 
+- The `set` process input type is no longer supported, use [tuple][process-input-tuple] instead.
+- The `set` process output type is no longer supported, use [tuple][process-out-tuple] instead.
+- The `mode flatten` option for process outputs is no longer available. Use the [flatten][operator-flatten] operator on the corresponding output channel instead.
 - Unqualified value and file elements in a tuple declaration are no longer allowed. Use an explicit `val` or `path` qualifier. For example:
 
   ```nextflow
@@ -150,27 +145,27 @@ DSL2 scripts cannot exceed 64 KB in size. Split large DSL1 scripts into modules
   }
   ```
 
-<h3>Channels</h3>
+### Channels
 
 - Channel factories should be accessed through the `channel` namespace instead of the `Channel` type, although they can still be accessed through either method.
 - Channel method `bind` has been deprecated in DSL2.
 - Channel method `<<` has been deprecated in DSL2.
 - Channel factory `create` has been deprecated in DSL2.
 
-<h3>Operators</h3>
+### Operators
 
-- Operator `choice` has been deprecated in DSL2. Use {ref}`operator-branch` instead.
+- Operator `choice` has been deprecated in DSL2. Use [branch][operator-branch] instead.
 - Operator `close` has been deprecated in DSL2.
 - Operator `countBy` has been deprecated in DSL2.
 - Operator `into` has been deprecated in DSL2, as it is no longer needed.
-- Operator `fork` has been renamed to {ref}`operator-multimap`.
-- Operator `groupBy` has been deprecated in DSL2. Use {ref}`operator-grouptuple` instead.
-- Operators `print` and `println` have been deprecated in DSL2. Use {ref}`operator-view` instead.
+- Operator `fork` has been renamed to [multiMap][operator-multimap].
+- Operator `groupBy` has been deprecated in DSL2. Use [groupTuple][operator-grouptuple] instead.
+- Operators `print` and `println` have been deprecated in DSL2. Use [view][operator-view] instead.
 - Operator `route` has been deprecated in DSL2.
 - Operator `separate` has been deprecated in DSL2.
-- Operator `spread` has been deprecated in DSL2. Use {ref}`operator-combine` instead.
+- Operator `spread` has been deprecated in DSL2. Use [combine][operator-combine] instead.
 
-<h3>DSL2 Preview</h3>
+### DSL2 Preview
 
 An early preview of DSL2 was available in 2020. Note that some of that early DSL2 syntax has since changed.
 
@@ -201,3 +196,14 @@ An early preview of DSL2 was available in 2020. Note that some of that early DSL
       bye()
   }
   ```
+
+[module-page]: /nextflow_docs/nextflow_repo/docs/module.mdx
+[operator-branch]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#branch
+[operator-combine]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#combine
+[operator-flatten]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#flatten
+[operator-grouptuple]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#grouptuple
+[operator-multimap]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#multimap
+[operator-view]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#view
+[process-input-tuple]: /nextflow_docs/nextflow_repo/docs/process.mdx#input-tuples-tuple
+[process-out-tuple]: /nextflow_docs/nextflow_repo/docs/process.mdx#output-tuples-tuple
+[workflow-page]: /nextflow_docs/nextflow_repo/docs/workflow.mdx
\ No newline at end of file
diff --git a/docs/migrations/index.md b/docs/migrations/index.mdx
similarity index 76%
rename from docs/migrations/index.md
rename to docs/migrations/index.mdx
index 8ac108b5ac..26a297068c 100644
--- a/docs/migrations/index.md
+++ b/docs/migrations/index.mdx
@@ -1,15 +1,7 @@
-(migrations-page)=
+import DocCardList from "@theme/DocCardList";
 
 # Migration notes
 
 This section covers important information for migrating between Nextflow versions. It describes new features, enhancements, breaking changes, deprecations, and other miscellaneous updates that may require action during a migration.
 
-```{toctree}
-:maxdepth: 1
-
-25-10
-25-04
-24-10
-24-04
-dsl1
-```
+<DocCardList />
diff --git a/docs/module.mdx b/docs/module.mdx
new file mode 100644
index 0000000000..48ade168be
--- /dev/null
+++ b/docs/module.mdx
@@ -0,0 +1,278 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Modules
+
+Nextflow scripts can include **definitions** (workflows, processes, and functions) from other scripts. When a script is included in this way, it is referred to as a **module**. Modules can be included by other modules or pipeline scripts and can even be shared across workflows.
+
+:::note
+Modules were introduced in DSL2. If you are still using DSL1, see [Migrating from DSL1][dsl1-page] to learn how to migrate your Nextflow pipelines to DSL2.
+:::
+
+## Module inclusion
+
+You can include any definition from a module into a Nextflow script using the `include` keyword.
+
+For example:
+
+```nextflow
+include { cat } from './some/module'
+
+workflow {
+    data = channel.fromPath('/some/data/*.txt')
+    cat(data)
+}
+```
+
+The above snippet imports a process named `cat`, defined in the module, into the main execution context. This way, `cat` can be invoked in the `workflow` scope.
+
+Nextflow implicitly looks for the script file `./some/module.nf`, resolving the path against the *including* script location.
+
+Module includes are subject to the following rules:
+
+- Relative paths must begin with the `./` prefix.
+- Include statements are not allowed from within a workflow. They must occur at the script level.
+
+## Module directory
+
+<AddedInVersion version="22.10.0" />
+
+A module can be defined as a directory with the same name as the module and with a script named `main.nf`. For example:
+
+```
+some
+└── module
+    └── main.nf
+```
+
+When defined as a directory, the module must be included by specifying the module directory path:
+
+```nextflow
+include { hello } from './some/module'
+```
+
+Module directories allow the use of module scoped binaries scripts. See [Module binaries] for details.
+
+## Multiple inclusions
+
+A Nextflow script can include any number of modules, and an `include` statement can import any number of definitions from a module. Multiple definitions can be included from the same module by using the syntax shown below:
+
+```nextflow
+include { cat; wc } from './some/module'
+
+workflow {
+    data = channel.fromPath('/some/data/*.txt')
+    cat(data)
+    wc(data)
+}
+```
+
+## Module aliases
+
+When including definition from a module, it's possible to specify an *alias* with the `as` keyword. Aliasing allows you to avoid module name clashes, by assigning them different names in the including context. For example:
+
+```nextflow
+include { cat as cat_alpha } from './some/module'
+include { cat as cat_beta } from './other/module'
+
+workflow {
+    cat_alpha(some_data)
+    cat_beta(other_data)
+}
+```
+
+You can also include the same definition multiple times under different names:
+
+```nextflow
+include { cat as cat_alpha; cat as cat_beta } from './some/module'
+
+workflow {
+    cat_alpha(some_data)
+    cat_beta(other_data)
+}
+```
+
+## Module parameters
+
+<DeprecatedInVersion version="24.07.0-edge">
+As a best practice, parameters should be used in the entry workflow and passed to workflows, processes, and functions as explicit inputs.
+</DeprecatedInVersion>
+
+A module can define parameters using the same syntax as a Nextflow workflow script:
+
+```nextflow
+params.message = 'Hello'
+params.target = 'world!'
+
+def sayHello() {
+    println "$params.message $params.target"
+}
+```
+
+When including a module, the module will first use parameters from the including context. For example:
+
+```nextflow
+params.message = 'Hola'
+params.target = 'Mundo'
+
+include { sayHello } from './some/module'
+
+workflow {
+    sayHello()
+}
+```
+
+The above snippet prints:
+
+```
+Hola Mundo
+```
+
+:::note
+The module inherits the parameters defined *before* the `include` statement, therefore any parameters set afterwards will not be used by the module.
+:::
+
+:::tip
+It is best to define all pipeline parameters *before* any `include` statements.
+:::
+
+The `addParams` option can be used to pass parameters to the module without adding them to the including scope.
+
+```nextflow
+params.message = 'Hola'
+params.target = 'Mundo'
+
+include { sayHello } from './some/module' addParams(message: 'Ciao')
+
+workflow {
+    sayHello()
+}
+```
+
+The above snippet prints:
+
+```
+Ciao Mundo
+```
+
+Alternatively, the `params` option can be used to pass parameters to module without adding them to the including scope, *and* without inheriting any parameters from the including scope.
+
+```nextflow
+params.message = 'Hola'
+params.target = 'Mundo'
+
+include { sayHello } from './some/module' params(message: 'Ciao')
+
+workflow {
+    sayHello()
+}
+```
+
+The above snippet prints:
+
+```
+Ciao world!
+```
+
+## Module templates
+
+Process script [templates][process-template] can be included alongside a module in the `templates` directory.
+
+For example, suppose we have a project L with a module that defines two processes, P1 and P2, both of which use templates. The template files can be made available in the local `templates` directory:
+
+```
+Project L
+|── myModules.nf
+└── templates
+    |── P1-template.sh
+    └── P2-template.sh
+```
+
+Then, we have a second project A with a workflow that includes P1 and P2:
+
+```
+Pipeline A
+└── main.nf
+```
+
+Finally, we have a third project B with a workflow that also includes P1 and P2:
+
+```
+Pipeline B
+└── main.nf
+```
+
+With the possibility to keep the template files inside the project L, A and B can use the modules defined in L without any changes. A future project C would do the same, just cloning L (if not available on the system) and including its module.
+
+Beside promoting the sharing of modules across pipelines, there are several advantages to keeping the module template under the script path:
+
+1. Modules are self-contained
+2. Modules can be tested independently from the pipeline(s) that import them
+3. Modules can be made into libraries
+
+Having multiple template locations enables a structured project organization. If a project has several modules, and they all use templates, the project could group module scripts and their templates as needed. For example:
+
+```
+baseDir
+|── main.nf
+|── Phase0-Modules
+    |── mymodules1.nf
+    |── mymodules2.nf
+    └── templates
+        |── P1-template.sh
+        |── P2-template.sh
+|── Phase1-Modules
+    |── mymodules3.nf
+    |── mymodules4.nf
+    └── templates
+        |── P3-template.sh
+        └── P4-template.sh
+└── Phase2-Modules
+    |── mymodules5.nf
+    |── mymodules6.nf
+    └── templates
+        |── P5-template.sh
+        |── P6-template.sh
+        └── P7-template.sh
+```
+
+## Module binaries
+
+<AddedInVersion version="22.10.0" />
+
+Modules can define binary scripts that are locally scoped to the processes defined by the tasks.
+
+To enable this feature, set the following flag in your pipeline script or configuration file:
+
+```nextflow
+nextflow.enable.moduleBinaries = true
+```
+
+The binary scripts must be placed in the module directory names `<module-dir>/resources/usr/bin`:
+
+```
+<module-dir>
+|── main.nf
+└── resources
+    └── usr
+        └── bin
+            |── your-module-script1.sh
+            └── another-module-script2.py
+```
+
+Those scripts will be made accessible like any other command in the task environment, provided they have been granted the Linux execute permissions.
+
+:::note
+This feature requires the use of a local or shared file system for the pipeline work directory, or [Wave containers][wave-page] when using cloud-based executors.
+:::
+
+## Sharing modules
+
+Modules are designed to be easy to share and re-use across different pipelines, which helps eliminate duplicate work and spread improvements throughout the community. While Nextflow does not provide an explicit mechanism for sharing modules, there are several ways to do it:
+
+- Simply copy the module files into your pipeline repository
+- Use [Git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules) to fetch modules from other Git repositories without maintaining a separate copy
+- Use the [nf-core](https://nf-co.re/tools#modules) CLI to install and update modules with a standard approach used by the nf-core community
+
+[dsl1-page]: /nextflow_docs/nextflow_repo/docs/migrations/dsl1.mdx
+[process-template]: /nextflow_docs/nextflow_repo/docs/process.mdx#template
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
diff --git a/docs/notifications.mdx b/docs/notifications.mdx
new file mode 100644
index 0000000000..199028df18
--- /dev/null
+++ b/docs/notifications.mdx
@@ -0,0 +1,316 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Notifications
+
+This page documents how to handle workflow events and send notifications.
+
+## Workflow handlers
+
+### Completion handler
+
+Due to the asynchronous nature of Nextflow, the termination of a script does not correspond to the termination of the running workflow. Thus some information, only available on execution completion, needs to be accessed by using an asynchronous handler.
+
+Nextflow invokes the `onComplete` event handler when the workflow execution is completed. It allows one to access the workflow termination status and other useful information. For example:
+
+```nextflow
+workflow.onComplete {
+    println "Pipeline completed at: $workflow.complete"
+    println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
+}
+```
+
+< AddedInVersion version="25.10.0" />
+
+Entry workflows can define an `onComplete` section instead of using `workflow.onComplete`:
+
+```nextflow
+workflow {
+    main:
+    // ...
+
+    onComplete:
+    println "Pipeline completed at: $workflow.complete"
+    println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
+}
+```
+
+### Error handler
+
+Nextflow invokes the `onError` event handler when a runtime or process error caused the pipeline execution to stop. For example:
+
+```nextflow
+workflow.onError {
+    println "Error: Pipeline execution stopped with the following message: ${workflow.errorMessage}"
+}
+```
+
+:::note
+Both the `onError` and `onComplete` handlers are invoked when an error condition is encountered. The first is called as soon as the error is raised, while the second is called just before the pipeline execution is about to terminate. When using the `finish` [errorStrategy][process-error-strategy], there may be a significant gap between the two, depending on the time required to complete any pending job.
+:::
+
+< AddedInVersion version="25.10.0" />
+
+Entry workflows can define an `onError` section instead of using `workflow.onError`:
+
+```nextflow
+workflow {
+    main:
+    // ...
+
+    onError:
+    println "Error: Pipeline execution stopped with the following message: ${workflow.errorMessage}"
+}
+```
+
+## Mail
+
+The built-in function `sendMail` allows you to send a mail message from a workflow script.
+
+### Basic mail
+
+The mail attributes are specified as named parameters or an equivalent map. For example:
+
+```nextflow
+sendMail(
+    to: 'you@gmail.com',
+    subject: 'Catch up',
+    body: 'Hi, how are you!',
+    attach: '/some/path/attachment/file.txt'
+)
+```
+
+which is equivalent to:
+
+```nextflow
+mail = [
+    to: 'you@gmail.com',
+    subject: 'Catch up',
+    body: 'Hi, how are you!',
+    attach: '/some/path/attachment/file.txt'
+]
+
+sendMail(mail)
+```
+
+The following parameters can be specified:
+
+
+##### `to`
+
+*Multiple email addresses can be specified by separating them with a comma.*
+
+The mail target recipients.
+
+##### `cc`
+
+*Multiple email addresses can be specified by separating them with a comma.*
+
+The mail CC recipients.
+
+##### `bcc`
+
+*Multiple email addresses can be specified by separating them with a comma.*
+
+The mail BCC recipients.
+
+##### `from`
+
+*Multiple email addresses can be specified by separating them with a comma.*
+
+The mail sender address.
+
+##### `subject`
+
+The mail subject.
+
+##### `charset`
+
+The mail content charset (default: `UTF-8`).
+
+##### `text`
+
+The mail plain text content.
+
+##### `body`
+
+The mail body content. It can be either plain text or HTML content.
+
+##### `type`
+
+The mail body mime type. If not specified it's automatically detected.
+
+##### `attach`
+
+Single file or a list of files to be included as mail attachments.
+
+### Advanced mail
+
+Another version of `sendMail` allows a more idiomatic syntax:
+
+```nextflow
+sendMail {
+    to 'you@gmail.com'
+    from 'me@gmail.com'
+    attach '/some/path/attachment/file.txt'
+    attach '/other/path/image.png'
+    subject 'Catch up'
+
+    '''
+    Hi there,
+    Look! Multi-lines
+    mail content!
+    '''
+}
+```
+
+The same attributes listed in the table in the previous section are allowed.
+
+:::tip
+A string expression at the end is implicitly interpreted as the mail body content, therefore the `body` parameter can be omitted as shown above.
+:::
+
+:::tip
+To send an email that includes text and HTML content, use both the `text` and `body` attributes. The first is used for the plain text content, while the second is used for the rich HTML content.
+:::
+
+### Mail attachments
+
+When using the curly brackets syntax, the `attach` parameter can be repeated two or more times to include multiple attachments in the mail message.
+
+Moreover for each attachment it's possible to specify any of the following options:
+
+##### `contentId`
+
+Defines the `Content-ID` header field for the attachment.
+
+##### `disposition`
+
+Defines the `Content-Disposition` header field for the attachment.
+
+##### `fileName`
+
+Defines the `filename` parameter of the `Content-Disposition` header field.
+
+##### `description`
+
+Defines the `Content-Description` header field for the attachment.
+
+For example:
+
+```nextflow
+sendMail {
+    to 'you@dot.com'
+    attach '/some/file.txt', fileName: 'manuscript.txt'
+    attach '/other/image.png', disposition: 'inline'
+    subject 'Sending documents'
+    '''
+    the mail body
+    '''
+}
+```
+
+### Mail configuration
+
+If no mail server configuration is provided, Nextflow tries to send the email using the external mail command eventually provided by the underlying system (e.g. `sendmail` or `mail`).
+
+If your system does not provide access to any of the above you can configure a SMTP server in the `nextflow.config` file. For example:
+
+```groovy
+mail {
+    smtp.host = 'your.smtp-server.com'
+    smtp.port = 475
+    smtp.user = 'my-user'
+}
+```
+
+:::note
+Some versions of Java (e.g. Java 11 Corretto) do not default to TLS v1.2, and as a result may have issues with 3rd party integrations that enforce TLS v1.2 (e.g. Azure Active Directory OIDC). This problem can be addressed by setting the following config option:
+
+```groovy
+mail {
+    smtp.ssl.protocols = 'TLSv1.2'
+}
+```
+:::
+
+See the [mail scope][config-mail] section to learn more the mail server configuration options.
+
+### AWS SES configuration
+
+<AddedInVersion version="23.06.0-edge" />
+
+Nextflow supports the [AWS Simple Email Service](https://aws.amazon.com/ses/) API as an alternative provider to send emails in place of an SMTP server.
+
+To enable this feature, set the following environment variable in the launch environment:
+
+```bash
+export NXF_ENABLE_AWS_SES=true
+```
+
+Make also sure to add the following AWS IAM permission to the AWS user (or role) used to launch the pipeline execution:
+
+```
+ses:SendRawEmail
+```
+
+The following snippet shows how to configure Nextflow to send emails through SES:
+
+```groovy
+mail {
+    smtp.host = 'email-smtp.us-east-1.amazonaws.com'
+    smtp.port = 587
+    smtp.user = '<Your AWS SES access key>'
+    smtp.password = '<Your AWS SES secret key>'
+    smtp.auth = true
+    smtp.starttls.enable = true
+    smtp.starttls.required = true
+}
+```
+
+## Mail notification
+
+You can use the `sendMail` function with a [workflow completion handler][metadata-completion-handler] to notify a workflow completion. For example:
+
+```nextflow
+workflow.onComplete {
+
+    def msg = """\
+        Pipeline execution summary
+        ---------------------------
+        Completed at: ${workflow.complete}
+        Duration    : ${workflow.duration}
+        Success     : ${workflow.success}
+        workDir     : ${workflow.workDir}
+        exit status : ${workflow.exitStatus}
+        """
+        .stripIndent()
+
+    sendMail(to: 'you@gmail.com', subject: 'My pipeline execution', body: msg)
+}
+```
+
+This is useful to send a custom notification message. Note however that Nextflow includes a built-in notification mechanism which is the most convenient way to notify the completion of a workflow execution in most cases. Read the following section to learn about it.
+
+## Workflow notification
+
+Nextflow includes built-in workflow notification features that automatically sends a notification message when a workflow execution terminates.
+
+To enable simply specify the `-N` option when launching the pipeline execution. For example:
+
+```bash
+nextflow run <pipeline name> -N <recipient address>
+```
+
+It will send a notification mail when the execution completes.
+
+:::warning
+By default the notification message is sent with the `sendmail` system tool, which is assumed to be available in the environment where Nextflow is running. Make sure it's properly installed and configured. Alternatively, you can provide the SMTP server configuration settings to use the Nextflow built-in mail support, which doesn't require any external system tool.
+:::
+
+See the [Mail configuration](#mail-configuration) section to learn about the available mail delivery options and configuration settings.
+
+See [Completion handler](#completion-handler) to learn more about the workflow notification configuration details.
+
+[config-mail]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#mail
+[config-notification]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#notification
+[process-error-strategy]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#errorstrategy
diff --git a/docs/overview.md b/docs/overview.mdx
similarity index 88%
rename from docs/overview.md
rename to docs/overview.mdx
index 21cdcde62b..b56d238636 100644
--- a/docs/overview.md
+++ b/docs/overview.mdx
@@ -1,5 +1,3 @@
-(overview-page)=
-
 # Overview
 
 ## Why Nextflow?
@@ -8,7 +6,7 @@ The rise of big data has made it increasingly necessary to be able to analyze an
 
 The Nextflow language is inspired by [the Unix philosophy](https://en.wikipedia.org/wiki/Unix_philosophy), in which many simple command line tools can be chained together into increasingly complex tasks. Similarly, a Nextflow script consists of composing many simple processes into increasingly complex pipelines. Each process executes a given tool or scripting language, and by specifying the process inputs and outputs, Nextflow coordinates the execution of tasks for you.
 
-The Nextflow runtime integrates with many popular execution platforms (HPC schedulers, cloud providers) and software tools (Git, Docker, Conda), allowing you to fully describe a computational pipeline with all of its dependencies and run it in nearly any environment -- write once, run anywhere.
+The Nextflow runtime integrates with many popular execution platforms (HPC schedulers, cloud providers) and software tools (Git, Docker, Conda), allowing you to fully describe a computational pipeline with all of its dependencies and run it in nearly any environment - write once, run anywhere.
 
 ## Processes and dataflow
 
@@ -63,7 +61,7 @@ The above example defines two processes. Their execution order is not determined
 
 When the workflow is executed, it creates two processes (`blast_search` and `extract_top_hits`) connected by the channel `query_ch`. Each process executes a task and emits a value for each input that it receives. Whenever `blast_search` emits a value, `extract_top_hits` receives it through the `query_ch` channel.
 
-See {ref}`process-page`, {ref}`dataflow-page`, and {ref}`workflow-page` to learn more about these features.
+Read the [Channels][channels-page] and [Dataflow][dataflow-page] pages to learn more about these features.
 
 ## Execution abstraction
 
@@ -91,13 +89,13 @@ The following cloud platforms are supported:
 - [Google Cloud Platform (GCP)](https://cloud.google.com/)
 - [Kubernetes](https://kubernetes.io/)
 
-Read the {ref}`executor-page` to learn more about the Nextflow executors.
+See [Executors][executors-page] to learn more.
 
 ## Scripting language
 
 Nextflow is a workflow language based on [Java](https://en.wikipedia.org/wiki/Java_(programming_language)) and [Groovy](https://groovy-lang.org/). It is designed to simplify writing scalable and reproducible pipelines. In most cases, users can leverage their existing programming skills to develop Nextflow pipelines without the steep learning curve that usually comes with a new programming language.
 
-See {ref}`script-page` for more information about the Nextflow scripting language.
+See [Scripts][scripts-page] for more information about the Nextflow scripting language.
 
 ## Configuration options
 
@@ -114,4 +112,10 @@ process {
 }
 ```
 
-Read the {ref}`config-page` section to learn more about the Nextflow configuration file and settings.
+See [Configuration][configuration-page] to learn more about the Nextflow configuration file and settings.
+
+[channels-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[configuration-page]: /nextflow_docs/nextflow_repo/docs/config.mdx
+[executors-page]: /nextflow_docs/nextflow_repo/docs/executor.mdx
+[dataflow-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[scripts-page]: /nextflow_docs/nextflow_repo/docs/script.mdx
diff --git a/docs/plugins/developing-plugins.mdx b/docs/plugins/developing-plugins.mdx
new file mode 100644
index 0000000000..764b27ba25
--- /dev/null
+++ b/docs/plugins/developing-plugins.mdx
@@ -0,0 +1,530 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Developing plugins
+
+This page describes how to develop plugins for Nextflow.
+
+## Nextflow plugin template
+
+The [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/) is a scaffold for plugin development. It uses [Gradle](https://gradle.org/), a build automation tool optimized for Java and Groovy projects, as well as the [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle).
+
+You can use the `nextflow plugin create` sub-command to create plugins using the plugin template. See [Creating a plugin][gradle-plugin-create] for more information.
+
+:::note
+The Nextflow Gradle plugin is currently available as a public preview. See [Migrating to the Nextflow plugin registry][plugin-registry-page>] for more information.
+:::
+
+### Structure
+
+The plugin template includes the source directories, build configuration files, and metadata required for development, testing, and publishing. Depending on the developer’s preference, plugins can be written in Java or Groovy.
+
+For example, a plugin created from the plugin template with the name `nf-hello` and organization `nextflow` will have the following structure:
+
+```console
+nf-hello
+├── .github/workflows/build.yml
+├── COPYING
+├── Makefile
+├── README.md
+├── build.gradle
+├── gradle
+│   └── wrapper
+│       ├── gradle-wrapper.jar
+│       └── gradle-wrapper.properties
+├── gradlew
+├── settings.gradle
+├── src
+│   ├── main
+│   │   └── groovy
+│   │       └── nextflow
+│   │           └── hello
+│   │               ├── HelloExtension.groovy
+│   │               ├── HelloFactory.groovy
+│   │               ├── HelloObserver.groovy
+│   │               └── HelloPlugin.groovy
+│   └── test
+│       └── groovy
+│           └── nextflow
+│               └── hello
+│                   └── HelloObserverTest.groovy
+└── validation
+    └── main.nf
+    └── nextflow.config
+```
+
+This structure contains the following key files and folders:
+
+- `.github/workflows/build.yml`: GitHub Action which implements continuous integration for the plugin.
+
+- `build.gradle`: The Gradle build script.
+
+- `COPYING`: The project license, detailing the terms under which the code can be used and distributed.​
+
+- `gradle/wrapper/`: Helper files for the Gradle Wrapper.
+
+- `gradlew`: The Gradle Wrapper script, which allows you to use Gradle without installing it into your environment.
+
+- `Makefile`: Defines common tasks for building, testing, and publishing the plugin with Make.​
+
+- `README.md`: The project README, which provides an overview of the project, including its purpose, features, and instructions for usage and development.​
+
+- `settings.gradle`: The Gradle project configuration, which specifies project-specific settings such as the project name and included modules.
+
+- `src/main/groovy/<ORGANIZATION>/`: The main source directory, which contains the plugin source code and resources.​
+
+- `src/test/groovy/<ORGANIZATION>/`: The test source directory, which contains the plugin unit tests.
+
+- `validation`: A small Nextflow pipeline which serves as an end-to-end test for the plugin.
+
+The plugin template also implements the following example features:
+
+- A custom trace observer that prints a message when the workflow starts and when the workflow completes (see `HelloObserver`).
+
+- A custom function called `sayHello` (see `HelloExtension`).
+
+### Nextflow Gradle plugin
+
+The [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle) simplifies the development of Nextflow plugins. It provides default configuration required for Nextflow integration, as well as custom Gradle tasks for building, testing, and publishing plugins.
+
+It is versioned and published to the [Gradle Plugin Portal](https://plugins.gradle.org/), and can be declared and managed like any other dependency in the `build.gradle` file:
+
+```nextflow
+plugins {
+    id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.6'
+}
+```
+
+:::note
+You can develop Nextflow plugins without the Gradle plugin. However, this approach is only suggested if you are an advanced developer and your project is incompatible with the Gradle plugin.
+:::
+
+### Make commands
+
+The plugin template includes a Makefile which wraps the most important Gradle tasks provided by the Nextflow Gradle plugin.
+
+These tasks can be executed with [Make](https://www.gnu.org/software/make/). For example:
+
+```bash
+make assemble
+```
+
+The following `make` commands are available:
+
+##### `assemble`
+
+Compiles the Nextflow plugin code and assembles it into a zip archive.
+
+##### `install`
+
+Installs the plugin into the local Nextflow plugins directory.
+
+##### `release`
+
+Publishes the plugin. See [Publish a plugin][gradle-plugin-publish] for more information.
+
+##### `test`
+
+Runs plugin unit tests. See [Test a plugin][gradle-plugin-test] for more information.
+
+## Extension points
+
+Nextflow’s plugin system exposes various extension points. This section gives examples of typical extension points and how to use them.
+
+### Commands
+
+Plugins can define custom CLI commands that are executable with the `nextflow plugin` command.
+
+To implement a plugin-specific command, implement the `PluginExecAware` interface in your plugin entry point (the class that extends `BasePlugin`). Alternatively, implement the `PluginAbstractExec` trait, which provides an abstract implementation with some boilerplate code. This trait requires you to implement the `getCommands()` and `exec()` methods. For example:
+
+```groovy
+import nextflow.cli.PluginAbstractExec
+import nextflow.plugin.BasePlugin
+
+class MyPlugin extends BasePlugin implements PluginAbstractExec {
+    @Override
+    List<String> getCommands() {
+        [ 'hello' ]
+    }
+
+    @Override
+    int exec(String cmd, List<String> args) {
+        if( cmd == 'hello' ) {
+            println "Hello! You gave me these arguments: ${args.join(' ')}"
+            return 0
+        }
+        else {
+            System.err.println "Invalid command: ${cmd}"
+            return 1
+        }
+    }
+}
+```
+
+The command can be run using the `nextflow plugin` command:
+
+```bash
+nextflow plugin my-plugin:hello --alpha --beta
+```
+
+See the [plugin][cli-plugin] for usage information.
+
+### Configuration
+
+Plugins can access the resolved Nextflow configuration through the session object using `session.config.navigate()`. Several extension points provide the session object for this reason. This method allows you to query any configuration option safely. If the option isn’t defined, it will return null.
+
+A common practice is to use a custom config scope to define any configuration for your plugin. For example:
+
+```groovy
+import nextflow.Session
+import nextflow.trace.TraceObserver
+
+class MyObserver implements TraceObserver {
+
+    @Override
+    void onFlowCreate(Session session) {
+        final message = session.config.navigate('myplugin.createMessage')
+        println message
+    }
+}
+```
+
+This option can then be set in your configuration file:
+
+```groovy
+// dot syntax
+myplugin.createMessage = "I'm alive!"
+
+// block syntax
+myplugin {
+    createMessage = "I'm alive!"
+}
+```
+
+<AddedInVersion version="25.04.0" />
+
+<ChangedInVersion version="25.04.0">
+The `nextflow.config.schema` package was renamed to `nextflow.config.spec`.
+</ChangedInVersion>
+
+Plugins can declare their configuration options by implementing the `ConfigScope` interface and declaring each config option as a field with the `@ConfigOption` annotation. For example:
+
+```groovy
+import nextflow.config.spec.ConfigOption
+import nextflow.config.spec.ConfigScope
+import nextflow.config.spec.ScopeName
+import nextflow.script.dsl.Description
+
+@ScopeName('myplugin')
+@Description('''
+    The `myplugin` scope allows you to configure the `nf-myplugin` plugin.
+''')
+class MyPluginConfig implements ConfigScope {
+
+    @ConfigOption
+    @Description('''
+        Message to print to standard output when a run is initialized.
+    ''')
+    final String createMessage
+
+    // no-arg constructor is required to enable validation of config options
+    MyPluginConfig() {
+    }
+
+    MyPluginConfig(Map opts) {
+        this.createMessage = opts.createMessage
+    }
+}
+```
+
+This approach is not required to support plugin config options. However, it allows Nextflow to recognize plugin definitions when validating the configuration. See [Configuration scopes][config-scopes-page] for more information.
+
+### Executors
+
+Plugins can define custom executors that can be used with the `executor` process directive.
+
+To implement an executor, create a class in your plugin that extends the [`Executor`](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/executor/Executor.groovy) class and implements the `ExtensionPoint` interface. Add the `@ServiceName` annotation to your class with the name of your executor. For example:
+
+```groovy
+import nextflow.executor.Executor
+import nextflow.util.ServiceName
+import org.pf4j.ExtensionPoint
+
+@ServiceName('my-executor')
+class MyExecutor extends Executor implements ExtensionPoint {
+
+    // ...
+
+}
+```
+
+You can then use this executor in your pipeline:
+
+```groovy
+process hello {
+    executor 'my-executor'
+
+    // ...
+}
+```
+
+:::tip
+See the source code of Nextflow's built-in executors for examples of how to implement various executor components.
+:::
+
+### Filesystems
+
+Plugins can define custom filesystems that Nextflow can use to interact with external storage systems using a single interface. For more information about accessing remote files, see [Remote files][remote-files].
+
+To implement a custom filesystem, create a class in your plugin that extends [`FileSystemProvider`](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/nio/file/spi/FileSystemProvider.html). Implement the `getScheme()` method to define the URI scheme for your filesystem. For example:
+
+```groovy
+import java.nio.file.spi.FileSystemProvider
+
+class MyFileSystemProvider extends FileSystemProvider {
+
+    @Override
+    String getScheme() {
+        return 'myfs'
+    }
+
+    // ...
+}
+```
+
+You can then use this filesystem in your pipeline:
+
+```nextflow
+input = file('myfs://<PATH_TO_INPUT_FILE>')
+```
+
+See [Developing a Custom File System Provider](https://docs.oracle.com/javase/8/docs/technotes/guides/io/fsp/filesystemprovider.html) for more information and the `nf-amazon` plugin (`S3FileSystemProvider`) for an example of a custom filesystem.
+
+:::tip
+Custom filesystems are an advanced plugin extension. Before creating a new filesystem, check that your use case cannot already be supported by an existing filesystem such as HTTP or S3.
+:::
+
+### Functions
+
+<AddedInVersion version="22.10.0" />
+
+Plugins can define custom functions that can be included in Nextflow pipelines.
+
+To implement a custom function, create a plugin class that extends the `PluginExtensionPoint` class and implement your function with the `Function` annotation. For example:
+
+```groovy
+import nextflow.Session
+import nextflow.plugin.extension.Function
+import nextflow.plugin.extension.PluginExtensionPoint
+
+class MyExtension extends PluginExtensionPoint {
+
+    @Override
+    void init(Session session) {}
+
+    @Function
+    String reverseString(String origin) {
+        origin.reverse()
+    }
+}
+```
+
+You can then add this function to your pipeline:
+
+```nextflow
+include { reverseString } from 'plugin/my-plugin'
+
+channel.of( reverseString('hi') )
+```
+
+Alternatively, you can use an alias:
+
+```nextflow
+include { reverseString as anotherReverseMethod } from 'plugin/my-plugin'
+```
+
+### Operators
+
+<AddedInVersion version="22.04.0" />
+
+Plugins can define custom channel factories and operators that can then be included in pipelines.
+
+To implement a custom channel factory or operator, create a class in your plugin that extends the `PluginExtensionPoint` class and implement your function with the `Factory` or `Operator` annotation. For example:
+
+```groovy
+import groovyx.gpars.dataflow.DataflowReadChannel
+import groovyx.gpars.dataflow.DataflowWriteChannel
+import nextflow.Session
+import nextflow.plugin.extension.Factory
+import nextflow.plugin.extension.Operator
+import nextflow.plugin.extension.PluginExtensionPoint
+
+class MyExtension extends PluginExtensionPoint {
+
+    @Override
+    void init(Session session) {}
+
+    @Factory
+    DataflowWriteChannel fromQuery(Map opts, String query) {
+        // ...
+    }
+
+    @Operator
+    DataflowWriteChannel sqlInsert(DataflowReadChannel source, Map opts) {
+        // ...
+    }
+
+}
+```
+
+You can then use the custom channel factories or operators in your pipeline:
+
+```nextflow
+include { sqlInsert; fromQuery as fromTable } from 'plugin/nf-sqldb'
+
+def sql = 'select * from FOO'
+channel
+    .fromTable(sql, db: 'test', emitColumns: true)
+    .sqlInsert(into: 'BAR', columns: 'id', db: 'test')
+```
+
+:::note
+The above snippet is based on the [nf-sqldb](https://github.com/nextflow-io/nf-sqldb) plugin. The `fromQuery` factory is included under the alias `fromTable`.
+:::
+
+:::tip
+Before creating a custom operator, consider whether the operator can be defined as a [function](#functions) that can be composed with existing operators such as `map` or `subscribe`. Functions are easier to implement and can be used anywhere in your pipeline, not just channel logic.
+:::
+
+### Process directives
+
+Plugins that implement a custom executor will likely need to access [process directives][process-directives] that affect the task execution. When an executor receives a task, the process directives can be accessed through that task’s configuration. Custom executors should try to support all process directives that have executor-specific behavior and are relevant to the executor.
+
+Nextflow does not provide the ability to define custom process directives in a plugin. Instead, use the [`ext`][process-ext] directive directive to provide custom process settings to your executor. Use specific names that are not likely to conflict with other plugins or existing pipelines.
+
+For example, a custom executor can use existing process directives and a custom setting through the `ext` directive:
+
+```groovy
+class MyExecutor extends Executor {
+
+    @Override
+    TaskHandler createTaskHandler(TaskRun task) {
+        final cpus = task.config.cpus
+        final memory = task.config.memory
+        final myOption = task.config.ext.myOption
+
+        println "This task is configured with cpus=${cpus}, memory=${memory}, myOption=${myOption}"
+
+        // ...
+    }
+
+    // ...
+
+}
+```
+
+### Trace observers
+
+<ChangedInVersion version="25.04.0">
+The `TraceObserver` interface is now deprecated. Use [TraceObserverV2](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserverV2.groovy) and [TraceObserverFactoryV2](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserverFactoryV2.groovy) instead.
+</ChangedInVersion>
+
+A *trace observer* is an entity that can listen and react to workflow events, such as when a workflow starts, a task is completed, or a file is published. Several components in Nextflow, such as the execution report and DAG visualization, are implemented as trace observers.
+
+Plugins can define custom trace observers that react to workflow events with custom behavior. To implement a trace observer, create a class that implements the `TraceObserver` trait and another class that implements the `TraceObserverFactory` interface. Implement any of the hooks defined in `TraceObserver` and implement the `create()` method in your observer factory. For example:
+
+```groovy
+import java.nio.file.Path
+
+import nextflow.processor.TaskHandler
+import nextflow.trace.TraceObserver
+import nextflow.trace.TraceRecord
+
+class MyObserver implements TraceObserver {
+
+    @Override
+    void onFlowBegin() {
+        println "Okay, let's begin!"
+    }
+
+    @Override
+    void onProcessComplete(TaskHandler handler, TraceRecord trace) {
+        println "I completed a task! It's name is '${handler.task.name}'"
+    }
+
+    @Override
+    void onProcessCached(TaskHandler handler, TraceRecord trace) {
+        println "I found a task in the cache! It's name is '${handler.task.name}'"
+    }
+
+    @Override
+    void onFilePublish(Path destination, Path source) {
+        println "I published a file! It's located at ${path.toUriString()}"
+    }
+
+    @Override
+    void onFlowError(TaskHandler handler, TraceRecord trace) {
+        println "Uh oh, something went wrong..."
+    }
+
+    @Override
+    void onFlowComplete() {
+        println 'All done!'
+    }
+}
+```
+
+You can then use your trace observer by simply enabling the plugin in your pipeline. In the above example, the observer must also be enabled with a config option:
+
+```nextflow
+myplugin.enabled = true
+```
+
+See the [`TraceObserver` source code](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy) for descriptions of the available workflow events.
+
+## Environment variables
+
+The following environment variables are available to develop and test plugins:
+
+##### `NXF_PLUGINS_MODE`
+
+The plugin execution mode. Either `prod` for production or `dev` for development.
+
+##### `NXF_PLUGINS_DIR`
+
+The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins` in production and `./plugins` in development).
+
+##### `NXF_PLUGINS_DEFAULT`
+
+Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: true).
+
+##### `NXF_PLUGINS_DEV`
+
+Comma-separated list of development plugin root directories.
+
+##### `NXF_PLUGINS_TEST_REPOSITORY`
+
+
+<AddedInVersion version="23.04.0" />
+
+Comma-separated list of URIs for additional plugin registries or meta files, which will be used in addition to the default registry.
+
+The URI should refer to a plugin repository JSON file or a specific plugin JSON meta file. In the latter case, it should match the pattern `https://host.name/some/path/<PLUGIN_NAME>-X.Y.Z-meta.json`. For example:
+
+```bash
+# custom plugin repository at https://github.com/my-org/plugins
+export NXF_PLUGINS_TEST_REPOSITORY="https://raw.githubusercontent.com/my-org/plugins/main/plugins.json"
+
+# custom plugin release
+export NXF_PLUGINS_TEST_REPOSITORY="https://github.com/nextflow-io/nf-hello/releases/download/0.3.0/nf-hello-0.3.0-meta.json"
+
+nextflow run main.nf -plugins nf-hello
+```
+
+This variable is useful for testing a plugin release before publishing it to the main registry.
+
+[cli-plugin]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#plugin
+[config-scopes-page]: /nextflow_docs/nextflow_repo/docs/developer/config-scopes.mdx#config-scopes
+[gradle-plugin-create]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#creating-a-plugin
+[process-directives]: /nextflow_docs/nextflow_repo/docs/process.mdx#directives
+[process-ext]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#ext
+[remote-files]: /nextflow_docs/nextflow_repo/docs/working-with-files.mdx#remote-files
diff --git a/docs/plugins/plugin-registry.mdx b/docs/plugins/plugin-registry.mdx
new file mode 100644
index 0000000000..df6983ea8d
--- /dev/null
+++ b/docs/plugins/plugin-registry.mdx
@@ -0,0 +1,66 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Nextflow plugin registry
+
+The [Nextflow plugin registry](https://registry.nextflow.io/) is a central repository for Nextflow plugins. It hosts an index of plugin metadata that supports plugin discovery, accessibility, and version tracking.
+
+Nextflow 25.10 and later can use the plugin registry as a drop-in replacement for the [legacy plugin index](https://github.com/nextflow-io/plugins) hosted on GitHub. See [Migrating to the Nextflow plugin registry][migrate-plugin-page] for more information about migrating to the Nextflow plugin registry.
+
+:::note
+The Nextflow plugin registry is currently available as a public preview. Plugin developers can access the registry by contacting [info@nextflow.io](mailto:info@nextflow.io) to obtain access to the registry.
+:::
+
+## Claiming a plugin
+
+Ownership of a plugin is required to publish plugins to the Nextflow plugin registry.
+
+To claim ownership of a plugin:
+
+1. Open the [Nextflow plugin registry](https://registry.nextflow.io/) in a browser.
+
+2. Log in to [Seqera](https://cloud.seqera.io/login) with your GitHub or Google account, or by providing an email address.
+
+    :::note
+    If you are logging in for the first time, Seqera will send an authentication link to your email address to complete the login process.
+    :::
+
+3. Go to the **My plugins** page and select **Claim a plugin**.
+
+4. Enter your unique plugin name or select the plugin you wish to claim in the **Plugin name** field.
+
+5. Enter your organization name in the **Provider** field.
+
+    :::note
+    This organization must match with the organization specified when publishing your plugin.
+    :::
+
+6. Select **Submit Request**.
+
+The plugin will show as **PENDING REVIEW** under **Pending Ownership Requests** until an admin approves the claim. Admin approval is required only once.
+
+## Creating an access token
+
+An API access token is required to publish plugins to the Nextflow plugin registry.
+
+To create an API access token:
+
+1. Open the [Nextflow plugin registry](https://registry.nextflow.io/) in a browser.
+
+2. Log in to [Seqera](https://cloud.seqera.io/login) with your GitHub or Google account, or by providing an email address.
+
+    :::note
+    If you are logging in for the first time, Seqera will send an authentication link to your email address to complete the login process.
+    :::
+
+3. Go to the **Access tokens** page.
+
+4. Under **Create New Access Token**, enter a descriptive name for the **Token name** and select the token duration from the **Expiry** drop down.
+
+5. Select **Generate token**.
+
+6. Copy and past token somewhere safe, you won't be able to see it again.
+
+Once you have your token, see [Publishing a plugin][gradle-plugin-publish] for instructions on how to use it.
+
+[gradle-plugin-publish]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#publishing-a-plugin
+[migrate-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/migrate-plugin.mdx
diff --git a/docs/plugins/plugins.mdx b/docs/plugins/plugins.mdx
new file mode 100644
index 0000000000..cd3613975d
--- /dev/null
+++ b/docs/plugins/plugins.mdx
@@ -0,0 +1,60 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Overview
+
+## What are plugins
+
+Nextflow plugins are extensions that enhance the functionality of Nextflow. They allow users to add new capabilities and integrate with external services without bloating their pipeline code or modifying Nextflow itself.
+
+There are two types of Nextflow plugins: core plugins and third-party plugins. The main features of each plugin type are described below.
+
+<h3>Core plugins</h3>
+
+Core plugins do not require configuration. The latest versions of core plugins are automatically installed when a Nextflow pipeline requests them. Core plugins include:
+
+* `nf-amazon`: Support for Amazon Web Services.
+* `nf-azure`: Support for Microsoft Azure.
+* `nf-cloudcache`: Support for the cloud cache.
+* `nf-console`: Implementation of the Nextflow [REPL console](https://seqera.io/blog/introducing-nextflow-console/).
+* `nf-google`: Support for Google Cloud.
+* `nf-tower`: Support for [Seqera Platform](https://seqera.io/platform/).
+* `nf-wave`: Support for [Wave containers service](https://seqera.io/wave/).
+
+Specific versions of core plugins can be declared in Nextflow configuration files or by using the `-plugins` option. See [Using plugins][using-plugins-page] for more information.
+
+:::note
+The automatic retrieval of core plugins can be disabled by setting `NXF_PLUGINS_DEFAULT=false`. See [Environment variables][dev-plugins-env-vars] for more information.
+:::
+
+<h3>Third-party plugins</h3>
+
+Third-party plugins must be configured via Nextflow configuration files or at runtime. To configure a plugin via configuration files, use the `plugins` block. For example:
+
+```groovy
+plugins {
+    id 'nf-hello@0.5.0'
+}
+```
+
+To configure plugins at runtime, use the `-plugins` option. For example:
+
+```bash
+nextflow run main.nf -plugins nf-hello@0.5.0
+```
+
+See [Using plugins][using-plugins-page] for more information.
+
+## Versioning
+
+Nextflow plugins are free to use any versioning convention. Many plugins, including all core plugins, use [Semantic Versioning](https://semver.org/), which helps developers communicate the kind of changes in a release.
+
+Semantic versions have the form MAJOR.MINOR.PATCH (e.g., 0.5.0):
+
+* MAJOR: Increment for backward-incompatible changes.
+* MINOR: Increment for backward-compatible feature additions.
+* PATCH: Increment for backward-compatible bug fixes.
+
+Optional pre-release and build metadata can be added (e.g., 1.2.1-alpha+001) as extensions to the base version format.
+
+[dev-plugins-env-vars]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#environment-variables
+[using-plugins-page]: /nextflow_docs/nextflow_repo/docs/plugins/using-plugins.mdx
diff --git a/docs/plugins/using-plugins.mdx b/docs/plugins/using-plugins.mdx
new file mode 100644
index 0000000000..3c0264756e
--- /dev/null
+++ b/docs/plugins/using-plugins.mdx
@@ -0,0 +1,77 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Using plugins
+
+Nextflow core plugins require no additional configuration. When a pipeline uses a core plugin, Nextflow automatically downloads and uses the latest compatible plugin version. In contrast, third-party plugins must be explicitly declared. When a pipeline uses one or more third-party plugins, Nextflow must be configured to download and use the plugin.
+
+## Identifiers
+
+A plugin identifier consists of the plugin name and version, separated by an `@` symbol:
+
+```
+nf-hello@0.5.0
+```
+
+The plugin version is optional. If it is not specified, Nextflow will download the latest version of the plugin that meets the minimum Nextflow version requirements specified by the plugin.
+
+:::note
+Plugin versions are required for [offline usage](#offline-usage).
+:::
+
+<AddedInVersion version="25.04.0" />
+
+The plugin version can be prefixed with `~` to pin the major and minor versions and allow the latest patch release to be used. For example, `nf-amazon@~2.9.0` will resolve to the latest version matching `2.9.x`. When working offline, Nextflow will resolve version ranges against the local plugin cache defined by `NXF_PLUGINS_DIR`.
+
+:::tip
+It is recommended to pin the major and minor version of each plugin to minimize the risk of breaking changes while allowing patch updates to be used automatically.
+:::
+
+## Configuration
+
+Plugins can be configured via Nextflow configuration files or at runtime.
+
+To configure a plugin via configuration files, use the `plugins` block. For example:
+
+```nextflow
+plugins {
+    id 'nf-hello@0.5.0'
+    id 'nf-amazon@2.9.0'
+}
+```
+
+To configure plugins at runtime, use the `-plugins` option. For example:
+
+```bash
+nextflow run main.nf -plugins nf-hello@0.5.0,nf-amazon@2.9.0
+```
+
+:::note
+Plugin declarations in Nextflow configuration files are ignored when specifying plugins via the `-plugins` option.
+:::
+
+## Caching
+
+When Nextflow downloads plugins, it caches them in the directory specified by `NXF_PLUGINS_DIR` (`$HOME/.nextflow/plugins` by default).
+
+## Offline usage
+
+When running Nextflow in an offline environment, any required plugins must be downloaded and moved into the offline environment prior to any runs.
+
+To use Nextflow plugins in an offline environment:
+
+1. Install a self-contained version of Nextflow in an environment with an internet connection. See [Standalone distribution][install-standalone] for more information.
+
+2. Run `nextflow plugin install <PLUGIN_NAME>@<VERSION>` for each required plugin to download it. Alternatively, run the pipeline once, which will automatically download all plugins required by the pipeline.
+
+3. Copy the `nextflow` binary and `$HOME/.nextflow` directory to the offline environment.
+
+4. Specify each plugin and its version in Nextflow configuration files or at runtime. See [Configuration][using-plugins-config] for more information.
+
+    :::warning
+    Nextflow will attempt to download newer versions of plugins if their versions are not set. See [Identifiers][using-plugins-identifiers] for more information.
+    :::
+
+[install-standalone]: /nextflow_docs/nextflow_repo/docs/install.mdx#standalone-distribution
+[using-plugins-config]: /nextflow_docs/nextflow_repo/docs/plugins/using-plugins.mdx#configuration
+[using-plugins-identifiers]: /nextflow_docs/nextflow_repo/docs/plugins/using-plugins.mdx#identifiers
+
diff --git a/docs/process.mdx b/docs/process.mdx
new file mode 100644
index 0000000000..afc6684fef
--- /dev/null
+++ b/docs/process.mdx
@@ -0,0 +1,1350 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Processes
+
+In Nextflow, a **process** is a specialized function for executing scripts in a scalable and portable manner.
+
+Here is an example process definition:
+
+```nextflow
+process hello {
+    output:
+    path 'hello.txt'
+
+    script:
+    """
+    echo 'Hello world!' > hello.txt
+    """
+}
+```
+
+See [Process][syntax-process] for a full description of the process syntax.
+
+## Script
+
+The `script` section defines, as a string expression, the script that is executed by the process.
+
+A process may contain only one script, and if the `script` guard is not explicitly declared, the script must be the final statement in the process definition.
+
+The script string is executed as a [Bash](<http://en.wikipedia.org/wiki/Bash_(Unix_shell)>) script in the host environment. It can be any command or script that you would normally execute on the command line or in a Bash script. Naturally, the script may only use commands that are available in the host environment.
+
+The script section can be a simple string or a multi-line string. The latter approach makes it easier to write scripts with multiple commands spanning multiple lines. For example:
+
+```nextflow
+process blast {
+  """
+  blastp -db $db -query query.fa -outfmt 6 > blast_result
+  cat blast_result | head -n 10 | cut -f 2 > top_hits
+  blastdbcmd -db $db -entry_batch top_hits > sequences
+  """
+}
+```
+
+As explained in the script tutorial section, strings can be defined using single-quotes or double-quotes, and multi-line strings are defined by three single-quote or three double-quote characters.
+
+There is a subtle but important difference between them. Like in Bash, strings delimited by a `"` character support variable substitutions, while strings delimited by `'` do not.
+
+In the above code fragment, the `$db` variable is replaced by the actual value defined elsewhere in the pipeline script.
+
+:::warning
+Since Nextflow uses the same Bash syntax for variable substitutions in strings, you must manage them carefully depending on whether you want to evaluate a *Nextflow* variable or a *Bash* variable.
+:::
+
+When you need to access a system environment variable in your script, you have two options.
+
+If you don't need to access any Nextflow variables, you can define your script section with single-quotes:
+
+```nextflow
+process echo_path {
+  '''
+  echo "The path is: $PATH"
+  '''
+}
+```
+
+Otherwise, you can define your script with double-quotes and escape the system environment variables by prefixing them with a back-slash `\` character, as shown in the following example:
+
+```nextflow
+process blast {
+  """
+  blastp -db \$DB -query query.fa -outfmt 6 > blast_result
+  cat blast_result | head -n $MAX | cut -f 2 > top_hits
+  blastdbcmd -db \$DB -entry_batch top_hits > sequences
+  """
+}
+```
+
+In this example, `$MAX` is a Nextflow variable that must be defined elsewhere in the pipeline script. Nextflow replaces it with the actual value before executing the script. Meanwhile, `$DB` is a Bash variable that must exist in the execution environment, and Bash will replace it with the actual value during execution.
+
+### Scripts *à la carte*
+
+The process script is interpreted by Nextflow as a Bash script by default, but you are not limited to Bash.
+
+You can use your favourite scripting language (Perl, Python, R, etc), or even mix them in the same pipeline.
+
+A pipeline may be composed of processes that execute very different tasks. With Nextflow, you can choose the scripting language that best fits the task performed by a given process. For example, for some processes R might be more useful than Perl, whereas for others you may need to use Python because it provides better access to a library or an API, etc.
+
+To use a language other than Bash, simply start your process script with the corresponding [shebang](<http://en.wikipedia.org/wiki/Shebang_(Unix)>). For example:
+
+```nextflow
+process perl_task {
+    """
+    #!/usr/bin/perl
+
+    print 'Hi there!' . '\n';
+    """
+}
+
+process python_task {
+    """
+    #!/usr/bin/python
+
+    x = 'Hello'
+    y = 'world!'
+    print "%s - %s" % (x,y)
+    """
+}
+
+workflow {
+    perl_task()
+    python_task()
+}
+```
+
+:::tip
+Since the actual location of the interpreter binary file can differ across platforms, it is wise to use the `env` command followed by the interpreter name, e.g. `#!/usr/bin/env perl`, instead of the absolute path, in order to make your script more portable.
+:::
+
+### Conditional scripts
+
+The `script` section is like a function that returns a string. This means that you can write arbitrary code to determine the script, as long as the final statement is a string.
+
+If-else statements based on task inputs can be used to produce a different script. For example:
+
+```nextflow
+mode = 'tcoffee'
+
+process align {
+    input:
+    path sequences
+
+    script:
+    if( mode == 'tcoffee' )
+        """
+        t_coffee -in $sequences > out_file
+        """
+
+    else if( mode == 'mafft' )
+        """
+        mafft --anysymbol --parttree --quiet $sequences > out_file
+        """
+
+    else if( mode == 'clustalo' )
+        """
+        clustalo -i $sequences -o out_file
+        """
+
+    else
+        error "Invalid alignment mode: ${mode}"
+}
+```
+
+In the above example, the process will execute one of several scripts depending on the value of the `mode` parameter. By default it will execute the `tcoffee` command.
+
+### Template
+
+Process scripts can be externalized to **template** files, which allows them to be reused across different processes and tested independently from the pipeline execution.
+
+A template can be used in place of an embedded script using the `template` function in the script section:
+
+```nextflow
+process hello {
+    input:
+    val STR
+
+    script:
+    template 'hello.sh'
+}
+
+workflow {
+    channel.of('this', 'that') | hello
+}
+```
+
+By default, Nextflow looks for the template script in the `templates` directory located alongside the Nextflow script in which the process is defined. An absolute path can be used to specify a different location. However, this practice is discouraged because it hinders pipeline portability.
+
+An example template script is provided below:
+
+```bash
+#!/bin/bash
+echo "process started at `date`"
+echo $STR
+echo "process completed"
+```
+
+Variables prefixed with the dollar character (`$`) are interpreted as Nextflow variables when the template script is executed by Nextflow and Bash variables when executed directly. For example, the above script can be executed from the command line by providing each input as an environment variable:
+
+```bash
+STR='Hello!' bash templates/my_script.sh
+```
+
+The following caveats should be considered:
+
+- Template scripts are recommended only for Bash scripts. Languages that do not prefix variables with `$` (e.g. Python and R) can't be executed directly as a template script.
+
+- Variables escaped with `\$` will be interpreted as Bash variables when executed by Nextflow, but will not be interpreted as variables when executed from the command line. This practice should be avoided to ensure that the template script behaves consistently.
+
+- Template variables are evaluated even if they are commented out in the template script. If a template variable is missing, it will cause the pipeline to fail regardless of where it occurs in the template.
+
+:::tip
+Template scripts are generally discouraged due to the caveats described above. The best practice for using a custom script is to embed it in the process definition at first and move it to a separate file with its own command line interface once the code matures.
+:::
+
+### Shell
+
+<DeprecatedInVersion version="24.11.0-edge">
+Use the `script` section instead. Consider using the [strict syntax][strict-syntax-page], which provides error checking to help distinguish between Nextflow variables and Bash variables in the process script.
+</DeprecatedInVersion>
+
+The `shell` section is a string expression that defines the script that is executed by the process. It is an alternative to the [Script][process-script] definition with one important difference: it uses the exclamation mark `!` character, instead of the usual dollar `$` character, to denote Nextflow variables.
+
+This way, it is possible to use both Nextflow and Bash variables in the same script without having to escape the latter, which makes process scripts easier to read and maintain. For example:
+
+```nextflow
+process hello {
+    input:
+    val str
+
+    shell:
+    '''
+    echo "User $USER says !{str}"
+    '''
+}
+
+workflow {
+    channel.of('Hello', 'Hola', 'Bonjour') | hello
+}
+```
+
+In the above example, `$USER` is treated as a Bash variable, while `!{str}` is treated as a Nextflow variable.
+
+:::note
+- Shell script definitions require the use of single-quote `'` delimited strings. When using double-quote `"` delimited strings, dollar variables are interpreted as Nextflow variables as usual. See [String interpolation][string-interpolation] for more information.
+- Variables prefixed with `!` must always be enclosed in curly brackets, i.e. `!{str}` is a valid variable whereas `!str` is ignored.
+- Shell scripts support the use of the [Template][process-template] mechanism. The same rules are applied to the variables defined in the template script.
+:::
+
+### Native execution
+
+The `exec` section executes the given code without launching a job.
+
+For example:
+
+```nextflow
+process hello {
+    input:
+    val name
+
+    exec:
+    println "Hello Mr. $name"
+}
+
+workflow {
+    channel.of('a', 'b', 'c') | hello
+}
+```
+
+will display:
+
+```
+Hello Mr. b
+Hello Mr. a
+Hello Mr. c
+```
+
+A native process is very similar to a [function][syntax-function]. However, it provides additional capabilities such as parallelism, caching, and progress logging.
+
+## Stub
+
+<AddedInVersion version="20.11.0-edge" />
+
+You can define a command *stub*, which replaces the actual process command when the `-stub-run` or `-stub` command-line option is enabled:
+
+```nextflow
+process salmon_index {
+    input:
+    path transcriptome
+
+    output:
+    path 'index'
+
+    script:
+    """
+    salmon index --threads $task.cpus -t $transcriptome -i index
+    """
+
+    stub:
+    """
+    mkdir index
+    touch index/seq.bin
+    touch index/info.json
+    touch index/refseq.bin
+    """
+}
+```
+
+The `stub` section can be defined before or after the `script` section. When the pipeline is executed with the `-stub-run` option and a process's `stub` is not defined, the `script` section is executed.
+
+This feature makes it easier to quickly prototype the workflow logic without using the real commands. The developer can use it to provide a dummy script that mimics the execution of the real one in a quicker manner. In other words, it is a way to perform a dry-run.
+
+## Inputs
+
+The `input` section defines the input of a process, similar to function arguments. A process may have at most one input section, which must contain at least one input declaration.
+
+The input section follows the syntax shown below:
+
+```
+input:
+  <input qualifier> <input name>
+```
+
+An input declaration consists of a *qualifier* and a *name*. The input qualifier defines the type of data to be received. This information is used by Nextflow to apply the semantic rules associated with each qualifier, and handle it properly depending on the target execution platform (grid, cloud, etc).
+
+When a process is invoked in a workflow, it must be provided a channel or dataflow value for each input in the process input section, similar to calling a function with specific arguments. The examples provided in the following sections demonstrate how a process is invoked.
+
+The following input qualifiers are available:
+
+- `val`: Access the input value by name in the process script.
+- `path`: Handle the input value as a path, staging the file properly in the execution context.
+- `env`: Use the input value to set an environment variable in the process script.
+- `stdin`: Forward the input value to the process `stdin` special file.
+- `tuple`: Handle a group of input values having any of the above qualifiers.
+- `each`: Execute the process for each element in the input collection.
+
+See [process reference][process-reference-inputs] for the full list of input methods and options.
+
+### Input variables (`val`)
+
+The `val` qualifier accepts any data type. It can be accessed in the process script by using the specified input name, as shown in the following example:
+
+```nextflow
+process echo {
+  input:
+  val x
+
+  script:
+  """
+  echo "process job $x"
+  """
+}
+
+workflow {
+  def num = channel.of(1,2,3)
+  echo(num)
+}
+```
+
+In the above example, the process is executed three times: once for each value emitted by the `num` channel. The resulting output is similar to the one shown below:
+
+```
+process job 3
+process job 1
+process job 2
+```
+
+:::note
+Processes do not necessarily process items in the order that they are received. In the above example, the value `3` was processed before the others.
+:::
+
+:::note
+When the process declares exactly one input, the pipe `|` operator can be used to provide inputs to the process, instead of passing it as a parameter. Both methods have identical semantics:
+
+```nextflow
+process echo {
+  input:
+  val x
+
+  script:
+  """
+  echo "process job $x"
+  """
+}
+
+workflow {
+  channel.of(1,2,3) | echo
+}
+```
+:::
+
+### Input files (`path`)
+
+The `path` qualifier allows you to provide input files to the process execution context. Nextflow will stage the files into the process execution directory, and they can be accessed in the script by using the specified input name. For example:
+
+```nextflow
+process blast {
+  input:
+  path query_file
+
+  script:
+  """
+  blastp -query ${query_file} -db nr
+  """
+}
+
+workflow {
+  def proteins = channel.fromPath( '/some/path/*.fa' )
+  blast(proteins)
+}
+```
+
+In the above example, all the files ending with the suffix `.fa` are sent over the channel `proteins`. These files are received by the process, which executes a BLAST query on each of them.
+
+It's worth noting that in the above example, the name of the file in the file-system is not used. You can access the file without even knowing its name, because you can reference it in the process script by the input name.
+
+There may be cases where your task needs to use a file whose name is fixed, i.e. it does not have to change along with the actual provided file. In this case, you can specify a fixed name with the `name` attribute in the input file parameter definition, as shown in the following example:
+
+```nextflow
+input:
+path query_file, name: 'query.fa'
+```
+
+or, using a shorter syntax:
+
+```nextflow
+input:
+path 'query.fa'
+```
+
+The previous example can be re-written as shown below:
+
+```nextflow
+process blast {
+  input:
+  path 'query.fa'
+
+  script:
+  """
+  blastp -query query.fa -db nr
+  """
+}
+
+workflow {
+  def proteins = channel.fromPath( '/some/path/*.fa' )
+  blast(proteins)
+}
+```
+
+In this example, each file received by the process is staged with the name `query.fa` in a different execution context (i.e. the folder where a task is executed).
+
+:::tip
+This feature allows you to execute the process command multiple times without worrying about the file names changing. In other words, Nextflow helps you write pipeline tasks that are self-contained and decoupled from the execution environment. As a best practice, you should avoid referencing files in your process script other than those defined in your input section.
+:::
+
+Channel factories like `channel.fromPath` produce file objects, but a `path` input can also accept a string literal path. The string value should be an absolute path, i.e. it must be prefixed with a `/` character or a supported URI protocol (`file://`, `http://`, `s3://`, etc), and it cannot contain special characters (`\n`, etc).
+
+```nextflow
+process cat {
+  input:
+  path x
+
+  script:
+  """
+  cat $x
+  """
+}
+
+workflow {
+  cat('/some/data/file.txt')
+}
+```
+
+:::note
+Process `path` inputs have nearly the same interface as described in [Path][stdlib-types-path], with one difference which is relevant when files are staged into a subdirectory. Given the following input:
+
+```nextflow
+path x, name: 'my-dir/file.txt'
+```
+
+In this case, `x.name` returns the file name with the parent directory (e.g. `my-dir/file.txt`), whereas normally it would return the file name (e.g. `file.txt`). You can use `x.fileName.name` to get the file name.
+:::
+
+### Multiple input files
+
+A `path` input can also accept a collection of files instead of a single value. In this case, the input variable will be a list.
+
+When the input has a fixed file name and a collection of files is received by the process, the file name will be appended with a numerical suffix representing its ordinal position in the list. For example:
+
+```nextflow
+process blast {
+    input:
+    path 'seq'
+
+    script:
+    """
+    echo seq*
+    """
+}
+
+workflow {
+    def fasta = channel.fromPath( "/some/path/*.fa" ).buffer(size: 3)
+    blast(fasta)
+}
+```
+
+will output:
+
+```
+seq1 seq2 seq3
+seq1 seq2 seq3
+...
+```
+
+The target input file name may contain the `*` and `?` wildcards, which can be used to control the name of staged files. The following table shows how the wildcards are replaced depending on the cardinality of the received input collection.
+
+| Arity       | Name pattern | Staged file names                                                                                       |
+| ----------- | ------------ | ------------------------------------------------------------------------------------------------------- |
+| any         | `*`          | named as the source file                                                                                |
+| one         | `file*.ext`  | `file.ext`                                                                                              |
+| one         | `file?.ext`  | `file1.ext`                                                                                             |
+| one         | `file??.ext` | `file01.ext`                                                                                            |
+| many        | `file*.ext`  | `file1.ext`, `file2.ext`, `file3.ext`, ..                                                               |
+| many        | `file?.ext`  | `file1.ext`, `file2.ext`, `file3.ext`, ..                                                               |
+| many        | `file??.ext` | `file01.ext`, `file02.ext`, `file03.ext`, ..                                                            |
+| many        | `dir/*`      | named as the source file, created in `dir` subdirectory                                                 |
+| many        | `dir??/*`    | named as the source file, created in a progressively indexed subdirectory e.g. `dir01/`, `dir02/`, etc. |
+| many        | `dir*/*`     | (as above)                                                                                              |
+
+The following example shows how a wildcard can be used in the input file definition:
+
+```nextflow
+process blast {
+    input:
+    path 'seq?.fa'
+
+    script:
+    """
+    cat seq1.fa seq2.fa seq3.fa
+    """
+}
+
+workflow {
+    def fasta = channel.fromPath( "/some/path/*.fa" ).buffer(size: 3)
+    blast(fasta)
+}
+```
+
+:::note
+Rewriting input file names according to a named pattern is an extra feature and not at all required. The normal file input syntax introduced in the [Input files (`path`)][process-input-path] section is valid for collections of multiple files as well. To handle multiple input files while preserving the original file names, use a variable identifier or the `*` wildcard.
+:::
+
+<AddedInVersion version="23.09.0-edge" />
+
+The `arity` option can be used to enforce the expected number of files, either as a number or a range.
+
+For example:
+
+```nextflow
+input:
+path('one.txt', arity: '1')         // exactly one file is expected
+path('pair_*.txt', arity: '2')      // exactly two files are expected
+path('many_*.txt', arity: '1..*')   // one or more files are expected
+```
+
+When a task is executed, Nextflow will check whether the received files for each path input match the declared arity, and fail if they do not. When the arity is `'1'`, the corresponding input variable will be a single file; otherwise, it will be a list of files.
+
+### Dynamic input file names
+
+When the input file name is specified by using the `name` option or a string literal, you can also use other input values as variables in the file name string. For example:
+
+```nextflow
+process grep {
+  input:
+  val x
+  path "${x}.fa"
+
+  script:
+  """
+  cat ${x}.fa | grep '>'
+  """
+}
+```
+
+In the above example, the input file name is determined by the current value of the `x` input value.
+
+This approach allows input files to be staged in the task directory with a name that is coherent with the current execution context.
+
+:::tip
+In most cases, you won't need to use dynamic file names, because each task is executed in its own directory, and input files are automatically staged into this directory by Nextflow. This behavior guarantees that input files with the same name won't overwrite each other. The above example is useful specifically when there are potential file name conflicts within a single task.
+:::
+
+### Input environment variables (`env`)
+
+The `env` qualifier allows you to define an environment variable in the process execution context based on the input value. For example:
+
+```nextflow
+process echo_env {
+    input:
+    env 'HELLO'
+
+    script:
+    '''
+    echo "$HELLO world!"
+    '''
+}
+
+workflow {
+    channel.of('hello', 'hola', 'bonjour', 'ciao') | echo_env
+}
+```
+
+```
+hello world!
+ciao world!
+bonjour world!
+hola world!
+```
+
+### Standard input (`stdin`)
+
+The `stdin` qualifier allows you to forward the input value to the [standard input](http://en.wikipedia.org/wiki/Standard_streams#Standard_input_.28stdin.29) of the process script. For example:
+
+```nextflow
+process cat {
+  input:
+  stdin
+
+  script:
+  """
+  cat -
+  """
+}
+
+workflow {
+  channel.of('hello', 'hola', 'bonjour', 'ciao')
+    | map { v -> v + '\n' }
+    | cat
+}
+```
+
+will output:
+
+```
+hola
+bonjour
+ciao
+hello
+```
+
+### Input tuples (`tuple`)
+
+The `tuple` qualifier groups multiple values into a single input definition. Each element in the tuple is associated with a corresponding element in the `tuple` definition. For example:
+
+```nextflow
+process cat {
+    input:
+    tuple val(id), path('input.txt')
+
+    script:
+    """
+    echo "Processing $id"
+    cat input.txt > copy
+    """
+}
+
+workflow {
+  channel.of( [1, 'alpha.txt'], [2, 'beta.txt'], [3, 'delta.txt'] ) | cat
+}
+```
+
+In the above example, the `tuple` input consists of the value `x` and the file `input.txt`.
+
+A `tuple` definition may contain any of the following qualifiers, as previously described: `val`, `env`, `path` and `stdin`. Files specified with the `path` qualifier are treated exactly the same as standalone `path` inputs.
+
+### Input repeaters (`each`)
+
+The `each` qualifier allows you to repeat the execution of a process for each item in a collection, each time a new value is received. For example:
+
+```nextflow
+process align {
+  input:
+  path seq
+  each mode
+
+  script:
+  """
+  t_coffee -in $seq -mode $mode > result
+  """
+}
+
+workflow {
+  sequences = channel.fromPath('*.fa')
+  methods = ['regular', 'espresso', 'psicoffee']
+
+  align(sequences, methods)
+}
+```
+
+In the above example, each time a file of sequences is emitted from the `sequences` channel, the process executes *three* tasks, each running a T-coffee alignment with a different value for the `mode` parameter. This behavior is useful when you need to repeat the same task over a given set of parameters.
+
+Input repeaters can be applied to files as well. For example:
+
+```nextflow
+process align {
+  input:
+  path seq
+  each mode
+  each path(lib)
+
+  script:
+  """
+  t_coffee -in $seq -mode $mode -lib $lib > result
+  """
+}
+
+workflow {
+  sequences = channel.fromPath('*.fa')
+  methods = ['regular', 'espresso']
+  libraries = [ file('PQ001.lib'), file('PQ002.lib'), file('PQ003.lib') ]
+
+  align(sequences, methods, libraries)
+}
+```
+
+In the above example, each sequence input file emitted by the `sequences` channel triggers six alignment tasks, three with the `regular` method against each library file, and three with the `espresso` method.
+
+:::note
+When multiple repeaters are defined, the process is executed for each *combination* of them.
+:::
+
+:::note
+Input repeaters do not support tuples. Use the [`combine`][operator-combine] or [`cross`][operator-cross] operator to combine the repeated input with the other inputs to produce all of the desired input combinations.
+:::
+
+### Multiple inputs
+
+A process can declare multiple inputs, which allows it to accept inputs from multiple dataflow sources.
+
+:::warning
+Do not supply more than one channel when calling a process with multiple inputs. Invoking a process with multiple channels can lead to [non-deterministic behavior][cache-nondeterministic-inputs]. All additional inputs should be dataflow values.
+:::
+
+When a process is defined with multiple inputs, it waits for a value from each input and launches a new task with the combined values. When one of the inputs is a channel, the process repeats until all values in the channel are consumed. If the channel is empty, the process will not launch any tasks.
+
+For example:
+
+```nextflow
+process echo {
+  input:
+  val x
+  val y
+
+  script:
+  """
+  echo $x and $y
+  """
+}
+
+workflow {
+  x = channel.value(1)
+  y = channel.of('a', 'b', 'c')
+  echo(x, y)
+}
+```
+
+The above example executes the `echo` process three times. The dataflow value `x` is reused for each value in `y`. It outputs:
+
+```
+1 and a
+1 and b
+1 and c
+```
+
+:::note
+In general, multiple input channels should be used to process *combinations* of different inputs, using the `each` qualifier or value channels. Having multiple queue channels as inputs is equivalent to using the [`merge`][operator-merge] operator, which is not recommended as it may lead to [non-deterministic process inputs][cache-nondeterministic-inputs].
+:::
+
+See also: [Singleton outputs](#singleton-outputs).
+
+## Outputs
+
+The `output` section defines the outputs of a process, similar to a function return. A process may have at most one output section, which must contain at least one output declaration.
+
+The output section follows the syntax shown below:
+
+```
+output:
+  <output qualifier> <output name> [, <option>: <option value>]
+```
+
+An output declaration consists of a *qualifier* and a *name*. Some optional attributes can also be specified.
+
+When a process is invoked, each process output is returned as a channel (except under [certain conditions][process-out-singleton]). The examples provided in the following sections demonstrate how to access the outputs of a process.
+
+The following output qualifiers are available:
+
+- `val`: Emit the variable with the specified name.
+- `path`: Emit a file produced by the process with the specified name.
+- `env`: Emit the variable defined in the process environment with the specified name.
+- `stdout`: Emit the `stdout` of the executed process.
+- `tuple`: Emit multiple values.
+- `eval`: Emit the result of a script or command evaluated in the task execution context.
+
+Refer to the [process reference][process-reference-outputs] for the full list of available output methods and options.
+
+### Output variables (`val`)
+
+The `val` qualifier allows you to output any Nextflow variable defined in the process. A common use case is to output a variable that was defined in the `input` section, as shown in the following example:
+
+```nextflow
+process echo {
+  input:
+  each x
+
+  output:
+  val x
+
+  script:
+  """
+  echo $x > file
+  """
+}
+
+workflow {
+  methods = ['prot', 'dna', 'rna']
+
+  received = echo(methods)
+  received.view { method -> "Received: $method" }
+}
+```
+
+The output value can be a value literal, an input variable, any other Nextflow variable in the process scope, or a value expression. For example:
+
+```nextflow
+process cat {
+  input:
+  path infile
+
+  output:
+  val x
+  val 'BB11'
+  val "${infile.baseName}.out"
+
+  script:
+  x = infile.name
+  """
+  cat $x > file
+  """
+}
+
+workflow {
+  ch_dummy = channel.fromPath('*').first()
+  (ch_var, ch_str, ch_exp) = cat(ch_dummy)
+
+  ch_var.view { var -> "ch_var: $var" }
+  ch_str.view { str -> "ch_str: $str" }
+  ch_exp.view { exp -> "ch_exp: $exp" }
+}
+```
+
+### Output files (`path`)
+
+The `path` qualifier allows you to output one or more files produced by the process. For example:
+
+```nextflow
+process random_number {
+  output:
+  path 'result.txt'
+
+  script:
+  '''
+  echo $RANDOM > result.txt
+  '''
+}
+
+workflow {
+  numbers = random_number()
+  numbers.view { file -> "Received: ${file.text}" }
+}
+```
+
+In the above example, the `random_number` process creates a file named `result.txt` which contains a random number. Since a `path` output with the same name is declared, that file is emitted by the corresponding process output. A downstream process or operator with a compatible input will be able to receive it.
+
+Refer to the [process reference][process-reference-outputs] for the list of available options for `path` outputs.
+
+### Multiple output files
+
+When an output file name contains a `*` or `?` wildcard character, it is interpreted as a [glob][glob] path matcher. This allows you to capture multiple files into a list and emit the list as a single value. For example:
+
+```nextflow
+process split_letters {
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf 'Hola' | split -b 1 - chunk_
+    """
+}
+
+workflow {
+    split_letters
+        | flatten
+        | view { chunk -> "File: ${chunk.name} => ${chunk.text}" }
+}
+```
+
+It prints:
+
+```
+File: chunk_aa => H
+File: chunk_ab => o
+File: chunk_ac => l
+File: chunk_ad => a
+```
+
+By default, all the files matching the specified glob pattern are emitted as a single list. However, as the above example demonstrates, the [`flatten`][operator-flatten] operator can be used to transform the list of files into a channel that emits each file individually.
+
+Some caveats on glob pattern behavior:
+
+- Input files are not included (unless `includeInputs` is `true`)
+- Directories are included, unless the `**` pattern is used to recurse through directories
+
+:::warning
+Although the input files matching an output glob pattern are not included in the resulting output, these files may still be transferred from the task scratch directory to the original task work directory. Therefore, to avoid unnecessary file copies, avoid using loose wildcards when defining output files, e.g. `path '*'`. Instead, use a prefix or a suffix to restrict the set of matching files to only the expected ones, e.g. `path 'prefix_*.sorted.bam'`.
+:::
+
+Read more about glob syntax at the following link [What is a glob?][glob]
+
+<AddedInVersion version="23.09.0-edge" />
+
+The `arity` option can be used to enforce the expected number of files, either as a number or a range.
+
+For example:
+
+```nextflow
+output:
+path('one.txt', arity: '1')         // exactly one file is expected
+path('pair_*.txt', arity: '2')      // exactly two files are expected
+path('many_*.txt', arity: '1..*')   // one or more files are expected
+```
+
+When a task completes, Nextflow will check whether the produced files for each path output match the declared arity, and fail if they do not. When the arity is `'1'`, the corresponding output will be a single file; otherwise, it will be a list of files.
+
+### Dynamic output file names
+
+When an output file name needs to be expressed dynamically, it is possible to define it using a dynamic string which references variables in the `input` section or in the script global context. For example:
+
+```nextflow
+process align {
+  input:
+  val species
+  path seq
+
+  output:
+  path "${species}.aln"
+
+  script:
+  """
+  t_coffee -in $seq > ${species}.aln
+  """
+}
+```
+
+In the above example, each process execution produces an alignment file whose name depends on the actual value of the `species` input.
+
+:::tip
+The management of output files in Nextflow is often misunderstood.
+
+With other tools it is generally necessary to organize the output files into some kind of directory structure or to guarantee a unique file name scheme, so that result files don't overwrite each other and so they can be referenced unequivocally by downstream tasks.
+
+With Nextflow, in most cases, you don't need to manage the naming of output files, because each task is executed in its own unique directory, so files produced by different tasks can't overwrite each other. Also, metadata can be associated with outputs by using the [tuple output][process-out-tuple] qualifier, instead of including them in the output file name.
+
+One example in which you'd need to manage the naming of output files is when you use the `publishDir` directive to have output files also in a specific path of your choice. If two tasks have the same filename for their output and you want them to be in the same path specified by `publishDir`, the last task to finish will overwrite the output of the task that finished before. You can dynamically change that by adding the `saveAs` option to your `publishDir` directive.
+
+To sum up, the use of output files with static names over dynamic ones is preferable whenever possible, because it will result in simpler and more portable code.
+:::
+
+### Output environment variables (`env`)
+
+The `env` qualifier allows you to output a variable defined in the process execution environment:
+
+```nextflow file=./snippets/process-out-env.nf
+```
+
+### Standard output (`stdout`)
+
+The `stdout` qualifier allows you to output the `stdout` of the executed process:
+
+```nextflow file=./snippets/process-stdout.nf
+```
+
+### Eval output (`eval`)
+
+<AddedInVersion version="24.02.0-edge" />
+
+The `eval` qualifier allows you to capture the standard output of an arbitrary command evaluated the task shell interpreter context:
+
+```nextflow file=./snippets/process-out-eval.nf
+```
+
+Only one-line Bash commands are supported. You can use a semi-colon `;` to specify multiple Bash commands on a single line, and many interpreters can execute arbitrary code on the command line, e.g. `python -c 'print("Hello world!")'`.
+
+If the command fails, the task will also fail. In Bash, you can append `|| true` to a command to suppress any command failure.
+
+### Output tuples (`tuple`)
+
+The `tuple` qualifier outputs multiple values in a single output as a [tuple][script-tuples]. For example:
+
+```nextflow
+process blast {
+  input:
+    val species
+    path query
+
+  output:
+    tuple val(species), path('result')
+
+  script:
+    """
+    blast -db nr -query $query > result
+    """
+}
+
+workflow {
+  ch_species = channel.of('human', 'cow', 'horse')
+  ch_query = channel.fromPath('*.fa')
+
+  blast(ch_species, ch_query)
+}
+```
+
+In the above example, a `blast` task is executed for each pair of `species` and `query` that are received. Each task produces a new tuple containing the value for `species` and the file `result`.
+
+A `tuple` definition may contain any of the following qualifiers, as previously described: `val`, `path`, `env` and `stdout`. Files specified with the `path` qualifier are treated exactly the same as standalone `path` inputs.
+
+:::note
+While parentheses for input and output qualifiers are generally optional, they are required when specifying elements in an input/output tuple.
+
+Here's an example with a single path output (parentheses optional):
+
+```nextflow
+process hello {
+    output:
+    path 'result.txt', hidden: true
+
+    script:
+    """
+    echo 'another new line' >> result.txt
+    """
+}
+```
+
+And here's an example with a tuple output (parentheses required):
+
+```nextflow
+process hello {
+    output:
+    tuple path('last_result.txt'), path('result.txt', hidden: true)
+
+    script:
+    """
+    echo 'another new line' >> result.txt
+    echo 'another new line' > last_result.txt
+    """
+}
+```
+:::
+
+### Naming outputs
+
+The `emit` option is used to define the name of a process output, which can be used to access the output by name in the calling workflow. For example:
+
+```nextflow
+process hello_bye {
+    output:
+    path 'hello.txt', emit: hello
+    stdout emit: bye
+
+    script:
+    """
+    echo "hello" > hello.txt
+    echo "bye"
+    """
+}
+
+workflow {
+    hello_bye()
+    hello_bye.out.hello.view()
+}
+```
+
+See [Calling processes and workflows][workflow-process-invocation] for more details.
+
+### Optional outputs
+
+Normally, if a specified output is not produced by the task, the task will fail. Setting `optional: true` will cause the task to not fail, and instead emit nothing to the corresponding output channel.
+
+```nextflow
+output:
+path("output.txt"), optional: true
+```
+
+In this example, the process is normally expected to produce an `output.txt` file, but in this case, if the file is missing, the task will not fail. The output channel will only contain values for those tasks that produced `output.txt`.
+
+:::note
+While this option can be used with any process output, it cannot be applied to individual elements of a [tuple](#output-tuples-tuple) output. The entire tuple must be optional or not optional.
+:::
+
+### Singleton outputs
+
+When a process is only supplied with dataflow values, regular values, or no inputs, it returns outputs as dataflow values. For example:
+
+```nextflow
+file=./snippets/process-out-singleton.nf
+```
+
+In the above example, the `echo` process is invoked with a regular value that is wrapped in a dataflow value. As a result, `echo` returns a dataflow value and `greet` is executed three times.
+
+If the call to `echo` was changed to `echo( channel.of('hello') )`, the process would instead return a channel, and `greet` would be executed only once.
+
+See also: [Multiple inputs][process-multiple-inputs].
+
+## When
+
+:::note
+As a best practice, conditional logic should be implemented in the calling workflow (e.g. using an `if` statement or [`filter`][operator-filter] operator) instead of the process definition.
+:::
+
+The `when` section allows you to define a condition that must be satisfied in order to execute the process. The condition can be any expression that returns a boolean value.
+
+It can be useful to enable/disable the process execution depending on the state of various inputs and parameters. For example:
+
+```nextflow
+process blast_search {
+  input:
+  path proteins
+  val dbtype
+
+  when:
+  proteins.name =~ /^BB11.*/ && dbtype == 'nr'
+
+  script:
+  """
+  blastp -query $proteins -db nr
+  """
+}
+```
+
+## Directives
+
+Directives are optional settings that affect the execution of the current process.
+
+By default, directives are evaluated when the process is defined. However, if the value is a dynamic string or closure, it will be evaluated separately for each task, which allows task-specific variables like `task` and `val` inputs to be used.
+
+Some directives are only supported by specific executors. See [Executors][executor-page] for more information about each executor.
+
+Refer to the [process reference][process-reference-directives] for the full list of process directives. If you are new to Nextflow, here are some commonly-used operators to learn first:
+
+General:
+- [errorStrategy][process-error-strategy]]: strategy for handling task failures
+- [tag][process-executor]: the [executor][executor-page] to execute tasks
+- [executor][process-tag]: a semantic name used to differentiate between task executions of the same process
+
+Resource requirements:
+- [cpus][process-cpus]: the number of CPUs to request for each task
+- [memory][process-memory]: the amount of memory to request for each task
+- [time][process-time]: the amount of walltime to request for each task
+
+Software dependencies:
+- [conda][process-conda]: list of conda packages to provision for tasks
+- [container][process-container]: container image to use for tasks
+
+### Using task directive values
+
+The `task` object also contains the values of all process directives for the given task, which allows you to access these settings at runtime. For examples:
+
+```nextflow
+process hello {
+  script:
+  """
+  some_tool --cpus $task.cpus --mem $task.memory
+  """
+}
+```
+
+In the above snippet, `task.cpus` and `task.memory` hold the values for the [cpus directive][process-cpus] and [memory directive][process-memory] directives, respectively, which were resolved for this task based on the process configuration.
+
+### Dynamic directives
+
+A directive can be assigned *dynamically*, during the process execution, so that its actual value can be evaluated based on the process inputs.
+
+To be defined dynamically, the directive's value needs to be expressed using a [closure][script-closure]. For example:
+
+```nextflow
+process hello {
+  executor 'sge'
+  queue { entries > 100 ? 'long' : 'short' }
+
+  input:
+  tuple val(entries), path('data.txt')
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+In the above example, the [queue][process-queue] directive is evaluated dynamically, depending on the input value `entries`. When it is larger than 100, jobs will be submitted to the `long` queue, otherwise the `short` queue will be used.
+
+All directives can be assigned a dynamic value except the following:
+
+- [executor][process-executor]
+- [label][process-label]
+- [maxForks][process-maxforks]
+
+<AddedInVersion version="25.10.0" />
+
+Dynamic directives can be specified without a closure when using the [strict syntax][strict-syntax-page]:
+
+```nextflow
+queue (entries > 100 ? 'long' : 'short')
+```
+
+Directives will be evaluated dynamically if they reference task inputs. Process configuration options must still be specified with a closure to be dynamic.
+
+### Dynamic task resources
+
+It's a very common scenario that different instances of the same process may have very different needs in terms of computing resources. In such situations requesting, for example, an amount of memory too low will cause some tasks to fail. Instead, using a higher limit that fits all the tasks in your execution could significantly decrease the execution priority of your jobs.
+
+[Dynamic directives](#dynamic-directives) can be used to adjust the requested task resources when a task fails and is re-executed. For example:
+
+```nextflow
+process hello {
+    memory { 2.GB * task.attempt }
+    time { 1.hour * task.attempt }
+
+    errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+    maxRetries 3
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+In the above example the [memory][process-memory] and execution [time][process-time] limits are defined dynamically. The first time the process is executed the `task.attempt` is set to `1`, thus it will request 2 GB of memory and 1 hour of wall time.
+
+If the task execution fails with an exit status between 137 and 140, the task is re-executed; otherwise, the run is terminated immediately. The re-executed task will have `task.attempt` set to `2`, and will request 4 GB of memory and 2 hours of wall time.
+
+The [ maxRetries][process-maxretries] directive sets the maximum number of times the same task can be re-executed.
+
+:::tip
+Directives with named arguments, such as `accelerator` and `disk`, must use a more verbose syntax when they are dynamic. For example:
+
+```nextflow
+// static request
+disk 375.GB, type: 'local-ssd'
+
+// dynamic request
+disk { [request: 375.GB * task.attempt, type: 'local-ssd'] }
+```
+:::
+
+Task resources can also be defined in terms of task inputs. For example:
+
+```nextflow
+process hello {
+    memory { 8.GB + 1.GB * Math.ceil(input_file.size() / 1024 ** 3) }
+
+    input:
+    path input_file
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+In this example, each task requests 8 GB of memory, plus the size of the input file rounded up to the next GB. This way, each task requests only as much memory as it needs based on the size of the inputs. The specific function that you use should be tuned for each process.
+
+### Dynamic task resources with previous execution trace
+
+<AddedInVersion version="24.10.0" />
+
+Task resource requests can be updated relative to the [trace file][trace-report] metrics of the previous task attempt. The metrics can be accessed through the `task.previousTrace` variable. For example:
+
+```nextflow
+process hello {
+    memory { task.attempt > 1 ? task.previousTrace.memory * 2 : (1.GB) }
+    errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+    maxRetries 3
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+In the above example, the [memory][process-memory] is set according to previous trace record metrics. In the first attempt, when no trace metrics are available, it is set to 1 GB. In each subsequent attempt, the requested memory is doubled. See [Trace file][trace-report] for more information about trace records.
+
+### Dynamic retry with backoff
+
+There are cases in which the required execution resources may be temporary unavailable e.g. network congestion. In these cases immediately re-executing the task will likely result in the identical error. A retry with an exponential backoff delay can better recover these error conditions:
+
+```nextflow
+process hello {
+  errorStrategy { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+  maxRetries 5
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+[cache-nondeterministic-inputs]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#non-deterministic-process-inputs
+[channel-types]: /nextflow_docs/nextflow_repo/docs/channel.mdx#channel-types
+[channel-type-value]: /nextflow_docs/nextflow_repo/docs/channel.mdx#value-channel
+[channel-value]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#value
+[executor-page]: /nextflow_docs/nextflow_repo/docs/executor.mdx
+[glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html.mdx#glob
+[operator-combine]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#combine
+[operator-filter]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#filter
+[operator-flatten]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#flatten
+[operator-cross]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#cross
+[operator-merge]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#merge
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-cpus]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cpus
+[process-error-strategy]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#errorstrategy
+[process-executor]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#executor
+[process-input-path]: /nextflow_docs/nextflow_repo/docs/process.mdx#input-files-path
+[process-label]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#label
+[process-maxforks]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#maxforks
+[process-maxretries]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#maxretries
+[process-memory]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#memory
+[process-out-singleton]: /nextflow_docs/nextflow_repo/docs/process.mdx#singleton-outputs
+[process-out-tuple]: /nextflow_docs/nextflow_repo/docs/process.mdx#output-tuples-tuple
+[process-queue]: nextflow_docs/nextflow_repo/docs/reference/process.mdx#queue
+[process-tag]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#tag
+[process-time]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#time
+[process-script]: /nextflow_docs/nextflow_repo/docs/process.mdx#script
+[process-multiple-inputs]: /nextflow_docs/nextflow_repo/docs/process.mdx#multiple-inputs
+[process-reference-directives]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#directives
+[process-reference-inputs]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#inputs
+[process-reference-outputs]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#outputs
+[process-template]: /nextflow_docs/nextflow_repo/docs/process.mdx#template
+[script-closure]: /nextflow_docs/nextflow_repo/docs/script.mdx#closures
+[script-tuples]: /nextflow_docs/nextflow_repo/docs/script.mdx#tuples
+[stdlib-types-path]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#path
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[string-interpolation]: /nextflow_docs/nextflow_repo/docs/script.mdx#string-interpolation
+[syntax-function]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx#function
+[syntax-process]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx#process
+[trace-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
+[workflow-process-invocation]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#calling-processes-and-workflows
diff --git a/docs/reference/channel.mdx b/docs/reference/channel.mdx
new file mode 100644
index 0000000000..b578d7c96e
--- /dev/null
+++ b/docs/reference/channel.mdx
@@ -0,0 +1,542 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Channel factories
+
+## empty
+
+The `channel.empty` factory method, by definition, creates a channel that doesn't emit any value.
+
+See also: [ifEmpty]operator-ifempty].
+
+## from
+
+<DeprecatedInVersion version="19.09.0-edge">
+Use [channel.of](#of) or [channel.fromList](#fromlist) instead.
+</DeprecatedInVersion>
+
+The `channel.from` method allows you to create a channel emitting any sequence of values that are specified as the method argument, for example:
+
+```nextflow
+ch = channel.from( 1, 3, 5, 7 )
+ch.subscribe { v -> println "value: $v" }
+```
+
+The first line in this example creates a variable `ch` which holds a channel object. This channel emits the values specified as a parameter in the `from` method. Thus the second line will print the following:
+
+```
+value: 1
+value: 3
+value: 5
+value: 7
+```
+
+The following example shows how to create a channel from a *range* of numbers or strings:
+
+```nextflow
+zeroToNine = channel.from( 0..9 )
+strings = channel.from( 'A'..'Z' )
+```
+
+:::note
+When the `channel.from` argument is an object implementing the (Java) [Collection](http://docs.oracle.com/javase/7/docs/api/java/util/Collection.html) interface, the resulting channel emits the collection entries as individual items.
+:::
+
+Thus the following two declarations produce an identical result even though in the first case the items are specified as multiple arguments while in the second case as a single list object argument:
+
+```nextflow
+channel.from( 1, 3, 5, 7, 9 )
+channel.from( [1, 3, 5, 7, 9] )
+```
+
+But when more than one argument is provided, they are always managed as *single* emissions. Thus, the following example creates a channel emitting three entries each of which is a list containing two elements:
+
+```nextflow
+channel.from( [1, 2], [5,6], [7,9] )
+```
+
+## fromLineage
+
+<AddedInVersion version="25.04.0" />
+
+:::warning *Experimental: may change in a future release.*
+:::
+
+The `channel.fromLineage` factory creates a channel that emits files from the [lineage][cli-lineage] store that match the given key-value params:
+
+```nextflow
+channel
+    .fromLineage(workflowRun: 'lid://0d1d1622ced3e4edc690bec768919b45', label: ['alpha', 'beta'])
+    .view()
+```
+
+The above snippet emits files published by the given workflow run that are labeled as `alpha` and `beta`.
+
+Available options:
+
+##### `label`
+
+List of labels associated with the desired files.
+
+##### `taskRun`
+
+LID of the task run that produced the desired files.
+
+##### `workflowRun`
+
+LID of the workflow run that produced the desired files.
+
+## fromList
+
+<AddedInVersion version="19.10.0" />
+
+The `channel.fromList` method allows you to create a channel emitting the values provided as a list of elements, for example:
+
+```nextflow
+channel
+    .fromList( ['a', 'b', 'c', 'd'] )
+    .view { v -> "value: $v" }
+```
+
+Prints:
+
+```
+value: a
+value: b
+value: c
+value: d
+```
+
+See also: [channel.of](#of) factory method.
+
+## fromPath
+
+You can create a channel emitting one or more file paths by using the `channel.fromPath` method and specifying a path
+string as an argument. For example:
+
+```nextflow
+myFileChannel = channel.fromPath( '/data/some/bigfile.txt' )
+```
+
+The above line creates a channel and binds it to a [Path](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Path.html)
+object for the specified file.
+
+:::note
+`channel.fromPath` does not check whether the file exists.
+:::
+
+Whenever the `channel.fromPath` argument contains a `*` or `?` wildcard character it is interpreted as a [glob][glob] path matcher.
+For example:
+
+```nextflow
+myFileChannel = channel.fromPath( '/data/big/*.txt' )
+```
+
+This example creates a channel and emits as many `Path` items as there are files with `txt` extension in the `/data/big` folder.
+
+:::tip
+Two asterisks, i.e. `**`, works like `*` but crosses directory boundaries. This syntax is generally used for matching complete paths. Curly brackets specify a collection of sub-patterns.
+:::
+
+For example:
+
+```nextflow
+files = channel.fromPath( 'data/**.fa' )
+moreFiles = channel.fromPath( 'data/**/*.fa' )
+pairFiles = channel.fromPath( 'data/file_{1,2}.fq' )
+```
+
+The first line returns a channel emitting the files ending with the suffix `.fa` in the `data` folder *and* recursively in all its sub-folders. While the second one only emits the files which have the same suffix in *any* sub-folder in the `data` path. Finally the last example emits two files: `data/file_1.fq` and `data/file_2.fq`.
+
+:::note
+As in Linux Bash, the `*` wildcard does not catch hidden files (i.e. files whose name starts with a `.` character).
+:::
+
+Multiple paths or glob patterns can be specified using a list:
+
+```nextflow
+channel.fromPath( ['/some/path/*.fq', '/other/path/*.fastq'] )
+```
+
+In order to include hidden files, you need to start your pattern with a period character or specify the `hidden: true` option. For example:
+
+```nextflow
+expl1 = channel.fromPath( '/path/.*' )
+expl2 = channel.fromPath( '/path/.*.fa' )
+expl3 = channel.fromPath( '/path/*', hidden: true )
+```
+
+The first example returns all hidden files in the specified path. The second one returns all hidden files ending with the `.fa` suffix. Finally the last example returns all files (hidden and non-hidden) in that path.
+
+By default a [glob][glob] pattern only looks for regular file paths that match the specified criteria, i.e. it won't return directory paths.
+
+You can use the `type` option specifying the value `file`, `dir` or `any` in order to define what kind of paths you want. For example:
+
+```nextflow
+myFileChannel = channel.fromPath( '/path/*b', type: 'dir' )
+myFileChannel = channel.fromPath( '/path/a*', type: 'any' )
+```
+
+The first example will return all *directory* paths ending with the `b` suffix, while the second will return any file or directory starting with a `a` prefix.
+
+Available options:
+
+##### `checkIfExists`
+
+When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
+
+##### `followLinks`
+
+When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
+
+##### `glob`
+
+When `true` interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
+
+##### `hidden`
+
+When `true` includes hidden files in the resulting paths (default: `false`)
+
+##### `maxDepth`
+
+Maximum number of directory levels to visit (default: no limit)
+
+##### `relative`
+
+When `true` returned paths are relative to the top-most common directory (default: `false`)
+
+##### `type`
+
+Type of paths returned, either `file`, `dir` or `any` (default: `file`)
+
+## fromFilePairs
+
+The `channel.fromFilePairs` method creates a channel emitting the file pairs matching a [glob][glob] pattern provided
+by the user. The matching files are emitted as tuples in which the first element is the grouping key of the matching pair and the second element is the list of files (sorted in lexicographical order). For example:
+
+```nextflow
+channel
+    .fromFilePairs('/my/data/SRR*_{1,2}.fastq')
+    .view()
+```
+
+It will produce an output similar to the following:
+
+```
+[SRR493366, [/my/data/SRR493366_1.fastq, /my/data/SRR493366_2.fastq]]
+[SRR493367, [/my/data/SRR493367_1.fastq, /my/data/SRR493367_2.fastq]]
+[SRR493368, [/my/data/SRR493368_1.fastq, /my/data/SRR493368_2.fastq]]
+[SRR493369, [/my/data/SRR493369_1.fastq, /my/data/SRR493369_2.fastq]]
+[SRR493370, [/my/data/SRR493370_1.fastq, /my/data/SRR493370_2.fastq]]
+[SRR493371, [/my/data/SRR493371_1.fastq, /my/data/SRR493371_2.fastq]]
+```
+
+:::note
+The glob pattern must contain at least one `*` wildcard character.
+:::
+
+Multiple glob patterns can be specified using a list:
+
+```nextflow
+channel.fromFilePairs( ['/some/data/SRR*_{1,2}.fastq', '/other/data/QFF*_{1,2}.fastq'] )
+```
+
+Alternatively, it is possible to implement a custom file pair grouping strategy providing a closure which, given the current file as parameter, returns the grouping key. For example:
+
+```nextflow
+channel
+    .fromFilePairs('/some/data/*', size: -1) { file -> file.extension }
+    .view { ext, files -> "Files with the extension $ext are $files" }
+```
+
+Available options:
+
+##### `checkIfExists`
+
+When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
+
+##### `followLinks`
+
+When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
+
+##### `flat`
+
+When `true` the matching files are produced as sole elements in the emitted tuples (default: `false`).
+
+##### `hidden`
+
+When `true` includes hidden files in the resulting paths (default: `false`)
+
+##### `maxDepth`
+
+Maximum number of directory levels to visit (default: no limit)
+
+##### `size`
+
+Defines the number of files each emitted item is expected to hold (default: 2). Set to `-1` for any.
+
+##### `type`
+
+Type of paths returned, either `file`, `dir` or `any` (default: `file`)
+
+## fromSRA
+
+<AddedInVersion version="19.04.0" />
+
+The `channel.fromSRA` method queries the [NCBI SRA](https://www.ncbi.nlm.nih.gov/sra) database and returns a channel emitting the FASTQ files matching the specified criteria i.e project or accession number(s). For example:
+
+```nextflow
+channel
+    .fromSRA('SRP043510')
+    .view()
+```
+
+It returns:
+
+```
+[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz]
+[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz]
+[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz]
+[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz]
+[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz]
+[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz]
+(remaining omitted)
+```
+
+Multiple accession IDs can be specified using a list object:
+
+```nextflow
+ids = ['ERR908507', 'ERR908506', 'ERR908505']
+channel
+    .fromSRA(ids)
+    .view()
+```
+
+```
+[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]]
+[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]]
+[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]
+```
+
+:::note
+Each read pair is implicitly managed and returned as a list of files.
+:::
+
+This method uses the NCBI [ESearch](https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch) API behind the scenes, therefore it allows the use of any query term supported by this API.
+
+To access the ESearch API, you must provide your [NCBI API keys](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities) through one of the following ways:
+
+- The `apiKey` option:
+  ```nextflow
+  channel.fromSRA(ids, apiKey:'0123456789abcdef')
+  ```
+
+- The `NCBI_API_KEY` variable in your environment:
+  ```bash
+  export NCBI_API_KEY=0123456789abcdef
+  ```
+
+Available options:
+
+##### `apiKey`
+
+NCBI user API key.
+
+##### `cache`
+
+Enable/disable the caching API requests (default: `true`).
+
+##### `max`
+
+Maximum number of entries that can be retried (default: unlimited) .
+
+##### `protocol`
+
+Allow choosing the protocol for the resulting remote URLs. Available choices: `ftp`, `http`, `https` (default: `ftp`).
+
+##### `retryPolicy`
+
+Set a retry policy in case the SRA request fails with a retriable error.
+The retry policy is set as a Map specifying the different policy properties.
+
+Available retry policy properties:
+
+| Property      | Description                                     | Default |
+| ------------- |-------------------------------------------------| ------- |
+| `delay`       | Delay when retrying failed SRA requests.        | `500ms` |
+| `jitter`      | Jitter value when retrying failed SRA requests. | `0.25`  |
+| `maxAttempts` | Max attempts when retrying failed SRA requests. | `3`     |
+| `maxDelay`    | Max delay when retrying failed SRA requests.    | `30s`   |
+
+The following code snippet shows an example for using the `channel.fromSRA` factory method with a custom `retryPolicy`.
+
+```nextflow
+channel.fromSRA(ids, retryPolicy: [delay: '250ms', maxAttempts: 5])
+```
+
+## interval
+
+The `interval` method emits an incrementing index (starting from zero) at a periodic interval. For example:
+
+```nextflow
+channel.interval('1s').view()
+```
+
+The above snippet will emit 0, 1, 2, and so on, every second, forever. You can use an operator such as [take][operator-take] or [until][operator-until] to close the channel based on a stopping condition.
+
+An optional closure can be used to transform the index. Additionally, returning `channel.STOP` will close the channel. For example:
+
+```nextflow
+ch = channel.interval('1s') { i ->
+    i == 10 ? channel.STOP : i
+}
+ch.view()
+```
+
+## of
+
+<AddedInVersion version="19.10.0" />
+
+The `channel.of` method allows you to create a channel that emits the arguments provided to it, for example:
+
+```nextflow
+ch = channel.of( 1, 3, 5, 7 )
+ch.view { v -> "value: $v" }
+```
+
+The first line in this example creates a variable `ch` which holds a channel object. This channel emits the arguments
+supplied to the `of` method. Thus the second line prints the following:
+
+```
+value: 1
+value: 3
+value: 5
+value: 7
+```
+
+Ranges of values are expanded accordingly:
+
+```nextflow
+channel
+    .of(1..23, 'X', 'Y')
+    .view()
+```
+
+Prints:
+
+```
+1
+2
+3
+4
+:
+23
+X
+Y
+```
+
+See also: [channel.fromList](#fromlist) factory method.
+
+## topic
+
+<AddedInVersion version="23.11.0-edge" />
+
+:::note
+In versions of Nextflow prior to 25.04, this feature requires the `nextflow.preview.topic` feature flag to be enabled.
+:::
+
+A *topic channel* is a channel that can receive values from many sources *implicitly* based on a matching *topic name*.
+
+:::tip
+You can think of it as a channel that is shared across many different processes using the same topic name.
+:::
+
+A process output can be assigned to a topic using the `topic` option on an output, for example:
+
+```nextflow
+process hello {
+    output:
+    val('hello'), topic: my_topic
+
+    // ...
+}
+
+process bye {
+    output:
+    val('bye'), topic: my_topic
+
+    // ...
+}
+```
+
+The `channel.topic` function returns the topic channel for the given name, which can be used as input to a process or operator, like any other channel:
+
+```nextflow
+channel.topic('my-topic').view()
+```
+
+This approach is a convenient way to collect related items from many different sources without explicitly connecting them (e.g. using the `mix` operator).
+
+:::warning
+Any process that consumes a topic channel (directly or indirectly) should not send any outputs to that topic, or else the pipeline will hang forever.
+:::
+
+See also: [Options][process-additional-options] for process outputs.
+
+## value
+
+The `channel.value` function creates a dataflow value bound to the given argument. For example:
+
+```nextflow
+v1 = channel.value( 'Hello there' )
+v2 = channel.value( [1,2,3,4,5] )
+```
+
+The first line creates a dataflow value bound to the string `'Hello there'`. The second line creates a dataflow value bound to the list `[1,2,3,4,5]`, which is treated as a single value in dataflow logic.
+
+## watchPath
+
+The `channel.watchPath` method watches a folder for one or more files matching a specified pattern. As soon as there
+is a file that meets the specified condition, it is emitted over the channel that is returned by the `watchPath` method.
+The condition on files to watch can be specified by using `*` or `?` wildcard characters i.e. by specifying a [glob][glob] path matching criteria.
+
+For example:
+
+```nextflow
+channel
+    .watchPath( '/path/*.fa' )
+    .subscribe { fa -> println "Fasta file: $fa" }
+```
+
+By default it watches only for new files created in the specified folder. Optionally, it is possible to provide a second
+argument that specifies what event(s) to watch. The supported events are:
+
+- `create`: A new file is created (default)
+- `modify`: A file is modified
+- `delete`: A file is deleted
+
+You can specify more than one of these events by using a comma separated string as shown below:
+
+```nextflow
+channel
+    .watchPath( '/path/*.fa', 'create,modify' )
+    .subscribe { fa -> println "File created or modified: $fa" }
+```
+
+:::warning
+The `channel.watchPath` factory waits endlessly for files that match the specified pattern and event(s), which means
+that it will cause your pipeline to run forever. Consider using the `take` or `until` operator to close the channel when
+a certain condition is met (e.g. after receiving 10 files, receiving a file named `DONE`).
+:::
+
+:::note
+The `channel.watchPath` factory only works with local and shared filesystems. It does not support object storage such as S3.
+:::
+
+See also: [channel.fromPath](#frompath) factory method.
+
+[cli-lineage]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lineage
+[glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+[operator-ifempty]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#ifempty
+[process-additional-options]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#options
+[operator-take]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#take
+[operator-until]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#until
diff --git a/docs/reference/cli.mdx b/docs/reference/cli.mdx
new file mode 100644
index 0000000000..f171e1df6c
--- /dev/null
+++ b/docs/reference/cli.mdx
@@ -0,0 +1,1799 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# CLI reference
+
+This page lists all of the available options and subcommands for the [Nextflow CLI][cli-page].
+
+## Options
+
+The top-level options are meant to be invoked in relation to the core Nextflow application and are applied to all commands. For options specific to any command, refer the CLI Commands section.
+
+Available options:
+
+##### `-C`
+
+Comma-separated list of configuration files which are used as the configuration set. Any other default configuration files are ignored.
+
+##### `-D`
+
+Set JVM properties.
+
+##### `-bg`
+
+Execute nextflow in background.
+
+##### `-c, -config`
+
+Comma-separated list of configuration files which are added to the configuration set.
+
+##### `-d, -dockerize`
+
+<DeprecatedInVersion version="23.09.0-edge">
+</DeprecatedInVersion>
+
+Launch nextflow via Docker (experimental).
+
+##### `-h`
+
+Print this help.
+
+##### `-log`
+
+Set nextflow log file path.
+
+##### `-q, -quiet`
+
+Do not print information messages.
+
+##### `-remote-debug`
+
+Enable JVM interactive remote debugging (experimental).
+
+##### `-syslog`
+
+Send logs to syslog server (e.g. localhost:514).
+
+##### `-trace`
+
+Enable trace level logging for the specified packages. Multiple packages can be provided separating them with a comma, e.g. `-trace nextflow,io.seqera`.
+
+##### `-v, -version`
+
+Print the program version.
+
+##### `-E`
+
+Exports all current system environment.
+
+## Commands
+
+### `auth`
+
+<AddedInVersion version="25.09.0-edge" />
+
+Manage Seqera Platform authentication.
+
+**Usage**
+
+```console
+$ nextflow auth <subcommand> [options]
+```
+
+**Description**
+
+The `auth` command provides authentication and configuration management for Seqera. For Seqera Cloud, it uses an OAuth2 authentication flow to generate and save a Personal Access Token (PAT) locally. For Seqera Enterprise installations, it uses direct PAT authentication. Credentials are saved to `~/.nextflow/seqera-auth.config`. An `includeConfig` statement is automatically added to `~/.nextflow/config` or the configuration file set using `$NXF_HOME`.
+
+**Options**
+
+##### `-h, -help`
+
+Prints the command usage information.
+
+#
+
+**Subcommands**
+
+##### `login`
+
+Authenticates with Seqera and saves credentials. Sets Seqera primary compute environment, monitoring, and workspace.
+
+The following options are available:
+
+######  `-u, -url`
+
+Specifies your Seqera API endpoint (default: `https://api.cloud.seqera.io`)
+
+##### `logout`
+
+Removes Seqera authentication and revokes the Seqera Cloud access token (if applicable).
+
+##### `config`
+
+Sets Seqera primary compute environment, monitoring, and workspace.
+
+##### `status`
+
+Shows Seqera authentication status and configuration.
+
+#
+
+**Examples**
+
+Authenticate with Seqera Cloud:
+
+```console
+$ nextflow auth login
+```
+
+Authenticate with an Enterprise installation:
+
+```console
+$ nextflow auth login -u https://tower.example.com/api
+```
+
+View current authentication status:
+
+```console
+$ nextflow auth status
+```
+
+Configure Seqera settings:
+
+```console
+$ nextflow auth config
+```
+
+Remove authentication:
+
+```console
+$ nextflow auth logout
+```
+
+### `clean`
+
+Clean up *cache* and *work* directories.
+
+**Usage**
+
+```console
+$ nextflow clean [run_name|session_id] [options]
+```
+
+**Description**
+
+Upon invocation within a directory, `nextflow` creates a project specific `.nextflow.log` file, `.nextflow` cache directory as well as a `work` directory. The `clean` command is designed to facilitate removal of these files from previous executions. A list of run names and session ids can be generated by invoking `nextflow log -q`.
+
+If no run name or session id is provided, it will clean the latest run.
+
+**Options**
+
+##### `-after`
+
+Clean up runs executed *after* the specified one.
+
+##### `-before`
+
+Clean up runs executed *before* the specified one.
+
+##### `-but`
+
+Clean up all runs *except* the specified one.
+
+##### `-n, -dry-run`
+
+Print names of files to be removed without deleting them.
+
+##### `-f, -force`
+
+Force clean command.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-k, -keep-logs`
+
+Removes only temporary files but retains execution log entries and metadata.
+
+##### `-q, -quiet`
+
+Do not print names of files removed.
+
+
+#
+
+**Examples**
+
+Dry run to remove work directories for the run name `boring_euler`:
+
+```console
+$ nextflow clean boring_euler -n
+
+Would remove work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
+Would remove work/3f/70944c7a549b6221e1ccc7b4b21b62
+Would remove work/0e/2ebdba85f76f6068b21a1bcbf10cab
+```
+
+Remove work directories for the run name `boring_euler`.
+
+```console
+$ nextflow clean boring_euler -f
+
+Removed work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
+Removed work/3f/70944c7a549b6221e1ccc7b4b21b62
+Removed work/0e/2ebdba85f76f6068b21a1bcbf10cab
+```
+
+Remove the execution entries *except* for a specific execution.
+
+```console
+$ nextflow clean -but tiny_leavitt -f
+
+Removed work/1f/f1ea9158fb23b53d5083953121d6b6
+Removed work/bf/334115deec60929dc18edf0010032a
+Removed work/a3/06521d75da296d4dd7f4f8caaddad8
+```
+
+Dry run to remove the execution data *before* a specific execution.
+
+```console
+$ nextflow clean -before tiny_leavitt -n
+
+Would remove work/5d/ad76f7b7ab3500cf616814ef644b61
+Would remove work/c4/69a82b080a477612ba8d8e4c27b579
+Would remove work/be/a4fa2aa38f76fd324958c81c2e4603
+Would remove work/54/39116773891c47a91e3c1733aad4de
+```
+
+Dry run to remove the execution data *after* a specific execution.
+
+```console
+$ nextflow clean -after focused_payne -n
+
+Would remove work/1f/f1ea9158fb23b53d5083953121d6b6
+Would remove work/bf/334115deec60929dc18edf0010032a
+Would remove work/a3/06521d75da296d4dd7f4f8caaddad8
+```
+
+Dry run to remove the temporary execution data for a specific execution, while keeping the log files.
+
+```console
+$ nextflow clean -keep-logs tiny_leavitt -n
+
+Would remove temp files from work/1f/f1ea9158fb23b53d5083953121d6b6
+Would remove temp files from work/bf/334115deec60929dc18edf0010032a
+Would remove temp files from work/a3/06521d75da296d4dd7f4f8caaddad8
+```
+
+### `clone`
+
+Clone a remote project into a folder.
+
+**Usage**
+
+```console
+$ nextflow clone [options] [project]
+```
+
+**Description**
+
+The `clone` command downloads a pipeline from a Git-hosting platform into the *current directory* and modifies it accordingly. For downloading a pipeline into the global cache `~/.nextflow/assets`, please refer to the `nextflow pull` command.
+
+**Options**
+
+##### `-d, -deep`
+
+Create a shallow clone of the specified depth.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-hub` (`github`)
+
+Service hub where the project is hosted. Options: `gitlab` or `bitbucket`.
+
+##### `-r` (`master`)
+
+Revision to clone - It can be a git branch, tag, or revision number.
+
+##### `-user`
+
+Private repository user name.
+
+#
+
+**Examples**
+
+Clone the latest revision of a pipeline.
+
+```console
+$ nextflow clone nextflow-io/hello
+nextflow-io/hello cloned to: hello
+```
+
+Clone a specific revision of a pipeline.
+
+```console
+$ nextflow clone nextflow-io/hello -r v1.1
+nextflow-io/hello cloned to: hello
+```
+
+### `config`
+
+Print the resolved pipeline configuration.
+
+**Usage**
+
+```console
+$ nextflow config [options] [project name or path]
+```
+
+**Description**
+
+The `config` command is used for printing the project's configuration i.e. the `nextflow.config` and is especially useful for understanding the resolved profiles and parameters that Nextflow will use run a pipeline. For in-depth information, please refer the [Config profiles][config-profiles] section.
+
+**Options**
+
+##### `-flat`
+
+Print config using flat notation.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-profile`
+
+Choose a configuration profile.
+
+##### `-properties`
+Print config using Java properties notation.
+
+##### `-a, -show-profiles`
+
+Show all configuration profiles.
+
+##### `-sort`
+
+Sort config attributes.
+
+##### `-value`
+
+<AddedInVersion version="23.08.0-edge" />
+
+Print the value of a config option, or fail if the option is not defined.
+
+#
+
+**Examples**
+
+Print out the inferred config using a the default group key-value notation.
+
+```console
+$ nextflow config
+
+docker {
+    enabled = true
+}
+
+process {
+    executor = 'local'
+}
+```
+
+Print out the config using a flat notation.
+
+```console
+$ nextflow config -flat
+
+docker.enabled = true
+process.executor = 'local'
+```
+
+Print out the config using the Java properties notation.
+
+```console
+$ nextflow config -properties
+
+docker.enabled = true
+process.executor = local
+```
+
+Print out the value of a specific configuration property.
+
+```console
+$ nextflow config -value process.executor
+local
+```
+
+Print out all profiles from the project's configuration.
+
+```console
+$ nextflow config -show-profiles
+
+docker {
+    enabled = true
+}
+
+profiles {
+    standard {
+        process {
+            executor = 'local'
+        }
+    }
+    cloud {
+        process {
+            executor = 'cirrus'
+            container = 'cbcrg/imagex'
+        }
+    }
+}
+```
+
+### `console`
+
+Launch the Nextflow interactive console.
+
+**Usage**
+
+```console
+$ nextflow console
+```
+
+**Description**
+
+The `console` command provides a Graphical User Interface (GUI) and an interactive REPL (Read-Eval-Print-Loop) for quick experimentation.
+
+**Options**
+
+None available
+
+**Examples**
+
+Launch the `console` GUI.
+
+```console
+$ nextflow console
+```
+
+### `drop`
+
+Delete the local copy of a project.
+
+**Usage**
+
+```console
+$ nextflow drop [options] [project]
+```
+
+**Description**
+
+The `drop` command is used to remove the projects which have been downloaded into the global cache. Please refer the `list` command for generating a list of downloaded pipelines.
+
+**Options**
+
+##### `-f`
+
+Delete the repository without taking care of local changes.
+
+##### `-h, -help`
+
+Print the command usage.
+
+#
+
+**Examples**
+
+Drop the `nextflow-io/hello` project.
+
+```console
+$ nextflow drop nextflow-io/hello
+```
+
+Forcefully drop the `nextflow-io/hello` pipeline, ignoring any local changes.
+
+```console
+$ nextflow drop nextflow-io/hello -f
+```
+
+### `fs`
+
+Perform basic filesystem operations.
+
+**Usage**
+
+```console
+$ nextflow fs [subcommands]
+```
+
+**Description**
+
+The `fs` command is used to perform filesystem operations like copy, move, delete, list directory, etc. Like the `file()` method, it can work with local files, remote URLs, and remote object storage. Storage credentials can be provided through the same manner as launching a pipeline (Nextflow config, environment vars, etc).
+
+**Options**
+
+##### `-h, -help`
+
+Print the command usage.
+
+#
+
+**Examples**
+
+List a directory.
+
+```console
+$ nextflow fs list <directory>
+```
+
+Print the contents of a file to standard output.
+
+```console
+$ nextflow fs cat <file>
+```
+
+Copy a file or directory.
+
+```console
+$ nextflow fs cp <source> <target>
+```
+
+Move a file or directory.
+
+```console
+$ nextflow fs mv <source> <target>
+```
+
+Delete a file or directory.
+
+```console
+$ nextflow fs rm <path>
+```
+
+<AddedInVersion version="23.10.0" />
+
+Print file or directory attributes.
+
+```console
+$ nextflow fs stat <path>
+```
+
+### `help`
+
+Print the top-level help or specific help for a command.
+
+**Usage**
+
+```console
+$ nextflow help [options] [command]
+```
+
+**Description**
+
+The `help` command prints out the overview of the CLI interface and enumerates the top-level *options* and *commands*. Note that this command is equivalent to simply invoking `nextflow` at the command line.
+
+**Options**
+
+##### `-h, -help`
+
+Print the command usage.
+
+#
+
+**Examples**
+
+Invoke the `help` option for the `drop` command.
+
+```console
+$ nextflow help drop
+
+Delete the local copy of a project
+Usage: drop [options] name of the project to drop
+   Options:
+     -f
+          Delete the repository without taking care of local changes
+          Default: false
+     -h, -help
+          Print the command usage
+          Default: false
+```
+
+### `info`
+
+Print project or system runtime information.
+
+**Usage**
+
+```console
+$ nextflow info [options] [project]
+```
+
+**Description**
+
+The `info` command prints out the nextflow runtime information about the hardware as well as the software versions of the Nextflow version and build, operating system, and Groovy and Java runtime. It can also be used to display information about a specific project.
+
+If no run name or session id is provided, it will clean the latest run.
+
+**Options**
+
+##### `-u, -check-updates`
+
+Check for remote updates.
+
+##### `-d`
+
+Show detailed information.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-o` (`text`)
+
+Output format, either `text`, `json` or `yaml`.
+
+#
+
+**Examples**
+
+Display Nextflow runtime and system info:
+
+```console
+$ nextflow info
+
+  Version: 20.07.1 build 5412
+  Created: 24-07-2020 15:18 UTC (20:48 IDT)
+  System: Mac OS X 10.15.6
+  Runtime: Groovy 2.5.11 on OpenJDK 64-Bit Server VM 1.8.0_192-b01
+  Encoding: UTF-8 (UTF-8)
+```
+
+Display information about a specific project:
+
+```console
+$ nextflow info nextflow-io/hello
+
+  project name: nextflow-io/hello
+  repository  : https://github.com/nextflow-io/hello
+  local path  : /Users/evanfloden/.nextflow/assets/nextflow-io/hello
+  main script : main.nf
+  revisions   :
+  * master (default)
+    mybranch
+    testing
+    v1.1 [t]
+    v1.2 [t]
+```
+
+### `inspect`
+
+<AddedInVersion version="23.09.0-edge" />
+
+Inspect process settings in a pipeline project. Currently only supports the `container` directive.
+
+**Usage**
+
+```console
+$ nextflow inspect [options] [project]
+```
+
+**Description**
+
+The `inspect` command allows you to determine the container for each process in a pipeline without running the pipeline. It prints to stdout a listing of containers for each process, formatted either as JSON or Nextflow configuration.
+
+**Options**
+
+##### `-concretize`
+
+Build the container images resolved by the inspect command.
+
+##### `-format` (`json`)
+
+Inspect output format. Can be `json` or `config`.
+
+##### `-i, -ignore-errors`
+
+Ignore errors while inspecting the pipeline.
+
+##### `-params-file`
+
+Load script parameters from a JSON/YAML file.
+
+##### `-profile`
+
+Use the given configuration profile(s).
+
+##### `-r, revision`
+
+Revision of the project to inspect (either a git branch, tag or commit SHA number).
+
+#
+
+**Examples**
+
+Get the list of containers used by a pipeline.
+
+```console
+$ nextflow inspect nextflow-io/hello
+```
+
+Specify parameters as with the `run` command:
+
+```console
+$ nextflow inspect main.nf --alpha 1 --beta hello
+```
+
+### `kuberun`
+
+Launch a Nextflow pipeline on a Kubernetes cluster.
+
+**Usage**
+
+```console
+$ nextflow kuberun [options] [project]
+```
+
+**Description**
+
+The `kuberun` command builds upon the `run` command and offers a deep integration with the Kubernetes execution environment. This command deploys the Nextflow runtime as a Kubernetes pod and assumes that you've already installed the `kubectl` CLI. The `kuberun` command does not allow the execution of local Nextflow scripts. See [kubernetes][k8s-page] for more information.
+
+**Options**
+
+The `kuberun` command supports the following options from [`run`](#run):
+
+- `-cache`
+- `-disable-jobs-cancellation`
+- `-dsl1`
+- `-dsl2`
+- `-dump-channels`
+- `-dump-hashes`
+- `-e.<key>=<value>`
+- `-entry`
+- `-h, -help`
+- `-hub`
+- `-latest`
+- `-main-script`
+- `-name`
+- `-offline`
+- `-params-file`
+- `-plugins`
+- `-preview`
+- `-process.<key>=<value>`
+- `-profile`
+- `-qs, -queue-size`
+- `-resume`
+- `-r, -revision`
+- `-stub, -stub-run`
+- `-user`
+- `-with-conda`
+- `-with-dag`
+- `-N, -with-notification`
+- `-with-report`
+- `-with-spack`
+- `-with-timeline`
+- `-with-tower`
+- `-with-trace`
+- `-with-wave`
+- `-with-weblog`
+- `-without-spack`
+- `-without-wave`
+- `-w, -work-dir`
+
+The following new options are also available:
+
+##### `-head-cpus`
+
+Specify number of CPUs requested for the Nextflow pod.
+
+##### `-head-image`
+
+Specify the container image for the Nextflow driver pod.
+
+##### `-head-memory`
+
+Specify amount of memory requested for the Nextflow pod.
+
+##### `-head-prescript`
+
+Specify script to be run before the Nextflow pod starts.
+
+##### `-n, -namespace`
+
+Specify the K8s namespace to use.
+
+##### `-remoteConfig`
+
+Add the specified file from the K8s cluster to configuration set.
+
+##### `-remoteProfile`
+
+Choose a configuration profile in the remoteConfig.
+
+##### `-v, -volume-mount`
+
+Volume claim mounts, e.g. `my-pvc:/mnt/path`.
+
+#
+
+**Examples**
+
+Execute a pipeline into a Kubernetes cluster.
+
+```console
+$ nextflow kuberun nextflow-io/hello
+```
+
+### `launch`
+
+<AddedInVersion version="25.10.0" />
+
+Launch a workflow in [Seqera Platform](https://seqera.io/platform/).
+
+**Usage**
+
+```console
+$ nextflow launch [options] [project]
+```
+
+**Description**
+
+The `launch` command launches a pipeline run in Seqera Platform. To log in and configure the execution environment, use the [`auth`](#auth) command.
+
+**Options**
+
+##### `-compute-env`
+
+The compute environment for workflow execution.
+
+##### `-c, -config`
+
+A configuration file to add to the configuration set.
+
+##### `-entry`
+
+The entry workflow to be executed.
+
+##### `-h, -help`
+
+Prints command usage information.
+
+##### `-latest`
+
+Whether to pull the latest changes before execution.
+
+##### `-name`
+
+A mnemonic name to assign to the run.
+
+##### `-main-script`
+
+The script file to be executed when launching a project directory or repository.
+
+##### `-params-file`
+
+A JSON or YAML file to load parameters from.
+
+##### `-profile`
+
+A configuration profile.
+
+##### `-resume`
+
+Whether to resume an execution using cached results from a previous run.
+
+##### `-r, -revision`
+
+The project revision to run. Can be a git branch, tag, or commit hash.
+
+##### `-stub-run, -stub`
+
+Whether to replace scripts with command stubs when executing the run.
+
+##### `-w, -work-dir`
+
+The directory where intermediate result files are stored.
+
+##### `-workspace`
+
+The Seqera Platform workspace name.
+
+**Examples**
+
+Execute a pipeline in Seqera Platform.
+
+```console
+$ nextflow launch nextflow-io/hello
+```
+
+### `lineage`
+
+<AddedInVersion version="25.04.0" />
+
+:::warning{title="Experimental: may change in a future release."}
+:::
+
+Inspect lineage metadata for Nextflow runs.
+
+**Usage**
+
+```console
+$ nextflow lineage SUBCOMMAND [arg ..]
+```
+
+**Description**
+
+The `lineage` command is used to inspect lineage metadata.
+
+See the [Data lineage][data-lineage-page] guide to learn how to get started with data lineage.
+
+**Options**
+
+##### `-h, -help`
+
+Print the command usage.
+
+**Subcommands**
+
+##### `check <lid>`
+
+Validate the checksum of output lineage record.
+
+##### `diff <lid-1> <lid-2>`
+
+Display a git-style diff between two lineage records.
+
+##### `find <field-1>=<value-1> [<field-2>=<value-2> ...]`
+
+Find all lineage records that match the given field values.
+
+##### `list`
+
+List the Nextflow runs with lineage enabled, printing the corresponding lineage ID (LID) for each run.
+
+##### `render <lid> [path]`
+
+Render the lineage graph for a lineage record as an HTML file (default output path: `./lineage.html`).
+
+The lineage record should be of type `FileOutput`, `TaskRun`, or `WorkflowRun`.
+
+##### `view <lid>`
+
+View a lineage record.
+
+### `lint`
+
+Lint Nextflow scripts and config files.
+
+**Usage**
+
+```console
+$ nextflow lint [options] [paths]
+```
+
+**Description**
+
+The `lint` command parses and analyzes the given Nextflow scripts and config files, formats them if specified, and prints any errors. Directories are recursively scanned for scripts and config files to lint.
+
+**Options**
+
+##### `-exclude`
+
+File pattern to exclude from linting. Can be specified multiple times (default: `.git, .nf-test, work`).
+
+##### `-format`
+
+Format scripts and config files that have no errors.
+
+##### `-o, -output`
+
+Output mode for reporting errors: `full`, `extended`, `concise`, `json` (default: `full`).
+
+##### `-sort-declarations`
+
+Sort script declarations in Nextflow scripts (default: `false`).
+
+##### `-spaces`
+
+Number of spaces to indent (default: `4`).
+
+##### `-tabs`
+
+Indent with tabs (default: `false`).
+
+#
+
+**Examples**
+
+Lint a specific file.
+
+```console
+$ nextflow lint main.nf
+```
+
+Lint all files in the current directory (and subdirectories) with concise output.
+
+```console
+$ nextflow lint -o concise .
+```
+
+Lint and format all files in the current directory (and subdirectories) and use two spaces per indent.
+
+```console
+$ nextflow lint -format -spaces 2 .
+```
+
+### `list`
+
+List all downloaded projects.
+
+**Usage**
+
+```console
+$ nextflow list [options]
+```
+
+**Description**
+
+The `list` commands prints a list of the projects which are already downloaded into the global cache `~/.nextflow/assets`.
+
+**Options**
+
+##### `-h, -help`
+
+Print the command usage.
+
+#
+
+**Examples**
+
+List the downloaded pipelines.
+
+```console
+$ nextflow list
+
+nextflow-io/hello
+nextflow-hub/fastqc
+```
+
+### `log`
+
+Print the execution history and log information.
+
+**Usage**
+
+```console
+$ nextflow log [options] [run_name | session_id]
+```
+
+**Description**
+
+The `log` command is used to query the execution metadata associated with pipelines executed by Nextflow. The list of executed pipelines can be generated by running `nextflow log`. Instead of run name, it's also possible to use a session id. Moreover, this command contains multiple options to facilitate the queries and is especially useful while debugging a pipeline and while inspecting pipeline execution metadata.
+
+**Options**
+
+##### `-after`
+
+Show log entries for runs executed *after* the specified one.
+
+##### `-before`
+
+Show log entries for runs executed *before* the specified one.
+
+##### `-but`
+
+Show log entries for runs executed *but* the specified one.
+
+##### `-f, -fields`
+
+Comma-separated list of fields to include in the printed log. Use the `-l` option to see the list of available fields.
+
+##### `-F, -filter`
+
+Filter log entries by a custom expression, e.g. `process =~ /hello.*/ && status == 'COMPLETED'`.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-l, -list-fields`
+
+Show all available fields.
+
+##### `-quiet`
+
+Show only run names.
+
+##### `-s`
+
+Character used to separate column values.
+
+##### `-t, -template`
+
+Text template used to each record in the log.
+
+#
+
+**Examples**
+
+Listing the execution logs of previous invocations of all pipelines in a project.
+
+```console
+$ nextflow log
+
+TIMESTAMP           DURATION        RUN NAME        STATUS  REVISION ID     SESSION ID                              COMMAND
+2020-10-07 11:52:24 2.1s            focused_payne   OK      96eb04d6a4      af6adaaa-ad4f-48a2-9f6a-b121e789adf5    nextflow run nextflow-io/hello -r master
+2020-10-07 11:53:00 3.1s            tiny_leavitt    OK      e3b475a61b      4d3b95c5-4385-42b6-b430-c865a70d56a4    nextflow run ./tutorial.nf
+2020-10-07 11:53:29 2.5s            boring_euler    OK      e3b475a61b      a6276975-7173-4208-ae09-ab9d6dce8737    nextflow run tutorial.nf
+```
+
+Listing only the *run names* of the execution logs of all pipelines invocations in a project.
+
+```console
+$ nextflow log -quiet
+
+focused_payne
+tiny_leavitt
+boring_euler
+```
+
+List the execution entries *only* a specific execution.
+
+```console
+$ nextflow log tiny_leavitt
+
+work/1f/f1ea9158fb23b53d5083953121d6b6
+work/bf/334115deec60929dc18edf0010032a
+work/a3/06521d75da296d4dd7f4f8caaddad8
+```
+
+List the execution entries *after* a specific execution.
+
+```console
+$ nextflow log -after tiny_leavitt
+
+work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
+work/3f/70944c7a549b6221e1ccc7b4b21b62
+work/0e/2ebdba85f76f6068b21a1bcbf10cab
+```
+
+List the execution entries *before* a specific execution.
+
+```console
+$ nextflow log -before tiny_leavitt
+
+work/5d/ad76f7b7ab3500cf616814ef644b61
+work/c4/69a82b080a477612ba8d8e4c27b579
+work/be/a4fa2aa38f76fd324958c81c2e4603
+work/54/39116773891c47a91e3c1733aad4de
+```
+
+List the execution entries *except* for a specific execution.
+
+```console
+$ nextflow log -but tiny_leavitt
+
+work/5d/ad76f7b7ab3500cf616814ef644b61
+work/c4/69a82b080a477612ba8d8e4c27b579
+work/be/a4fa2aa38f76fd324958c81c2e4603
+work/54/39116773891c47a91e3c1733aad4de
+```
+
+Filter specific fields from the execution log of a process.
+
+```console
+$ nextflow log tiny_leavitt -f 'process,exit,hash,duration'
+
+split_letters       0       1f/f1ea91       112ms
+convert_to_upper    0       bf/334115       144ms
+convert_to_upper    0       a3/06521d       139ms
+```
+
+Filter fields from the execution log of a process based on a criteria.
+
+```console
+$ nextflow log tiny_leavitt -F 'process =~ /split_letters/'
+
+work/1f/f1ea9158fb23b53d5083953121d6b6
+```
+
+### `plugin`
+
+Manage plugins and run plugin-specific commands.
+
+```console
+$ nextflow plugin <subcommand> [options]
+```
+
+##### `create`
+
+<AddedInVersion version="25.04.0" />
+
+Create a plugin scaffold using the [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/). See [Creating a plugin][gradle-plugin-create] for more information.
+
+##### `install <plugin[@version],..>`
+
+Install a plugin. Multiple plugins can be specified as a comma-separated list. Each plugin id consists of a name and optional version separated by a `@`.
+
+##### `<plugin>:<subcommand> [options]`
+
+Execute a plugin-specific command.
+
+### `pull`
+
+Download or update a project.
+
+**Usage**
+
+```console
+$ nextflow pull [options] [project]
+```
+
+**Description**
+
+The `pull` command downloads a pipeline from a Git-hosting platform into the global cache `~/.nextflow/assets` and modifies it accordingly. For downloading a pipeline into a local directory, please refer to the `nextflow clone` command.
+
+**Options**
+
+##### `-all`
+
+Update all downloaded projects.
+
+##### `-d, -deep`
+
+Create a shallow clone of the specified depth.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-hub` (`github`)
+
+Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
+
+##### `-r, -revision`
+
+Revision of the project to run (either a git branch, tag or commit hash).
+
+When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
+
+##### `-user`
+
+Private repository user name.
+
+#
+
+**Examples**
+
+Download a new pipeline or pull the latest revision for a specific project.
+
+```console
+$ nextflow pull nextflow-io/hello
+
+Checking nextflow-io/hello ...
+done - revision: 96eb04d6a4 [master]
+```
+
+Pull the latest revision for all downloaded projects.
+
+```console
+$ nextflow pull -all
+
+Checking nextflow-io/hello ...
+done - revision: 96eb04d6a4 [master]
+Checking nextflow-hub/fastqc ...
+done - revision: 087659b18e [master]
+```
+
+Download a specific revision of a new project or pull the latest revision for a specific project.
+
+```console
+$ nextflow pull nextflow-io/hello -r v1.1
+
+Checking nextflow-io/hello ...
+checkout-out at AnyObjectId[1c3e9e7404127514d69369cd87f8036830f5cf64] - revision: 1c3e9e7404 [v1.1]
+```
+
+### `run`
+
+Execute a pipeline.
+
+**Usage**
+
+```console
+$ nextflow run [options] [project]
+```
+
+**Description**
+
+The `run` command is used to execute a local pipeline script or remote pipeline project.
+
+**Options**
+
+##### `-E`
+
+Exports all current system environment.
+
+##### `-ansi-log`
+
+Enable/disable ANSI console logging.
+
+##### `-bucket-dir`
+
+Remote bucket where intermediate result files are stored. When running a hybrid workflow, `-bucket-dir` and `-work-dir` should define separate work directories for remote tasks and local tasks, respectively.
+
+##### `-cache`
+
+Enable/disable processes caching.
+
+##### `-d, -deep`
+
+Create a shallow clone of the specified depth.
+
+##### `-disable-jobs-cancellation`
+
+Prevent the cancellation of child jobs on execution termination
+
+##### `-dsl1`
+
+<DeprecatedInVersion version="23.09.0-edge">
+</DeprecatedInVersion>
+
+Execute the workflow using DSL1 syntax.
+
+##### `-dsl2`
+
+<DeprecatedInVersion version="23.09.0-edge">
+</DeprecatedInVersion>
+
+Execute the workflow using DSL2 syntax.
+
+##### `-dump-channels`
+
+Dump channels for debugging purpose.
+
+##### `-dump-hashes`
+Dump task hash keys for debugging purposes.
+
+<AddedInVersion version="23.10.0">
+You can use `-dump-hashes json` to dump the task hash keys as JSON for easier post-processing. See the [caching and resuming tip][cache-compare-hashes] for more details.
+</AddedInVersion>
+
+##### `-e.<key>=<value>`
+
+Add the specified variable to execution environment.
+
+##### `-entry`
+
+<DeprecatedInVersion version="24.10.0">
+Use params in the entry workflow to call different workflows from the command line.
+</DeprecatedInVersion>
+
+Entry workflow to be executed.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-hub` (`github`)
+
+Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
+
+##### `-latest`
+
+Pull latest changes before run.
+
+##### `-lib`
+
+Library extension path.
+
+##### `-main-script` (`main.nf`)
+
+<AddedInVersion version="20.09.1-edge" />
+
+The script file to be executed when launching a project directory or repository.
+
+
+##### `-name`
+
+Assign a mnemonic name to the a pipeline run.
+
+##### `-offline`
+
+Do not check for remote project updates.
+
+##### `-o, -output-dir` (`results`)
+
+<AddedInVersion version="24.10.0" />
+
+Directory where workflow outputs are stored.
+
+##### `-params-file`
+
+Load script parameters from a JSON/YAML file.
+
+##### `-plugins`
+
+Comma separated list of plugin ids to be applied in the pipeline execution.
+
+##### `-preview`
+
+<AddedInVersion version="22.06.0-edge" />
+
+Run the workflow script skipping the execution of all processes.
+
+##### `-process.<key>=<value>`
+
+Set process config options.
+
+##### `-profile`
+
+Choose a configuration profile.
+
+##### `-qs, -queue-size`
+
+Max number of processes that can be executed in parallel by each executor.
+
+##### `-resume`
+
+Execute the script using the cached results, useful to continue executions that was stopped by an error.
+
+##### `-r, -revision`
+
+Revision of the project to run (either a git branch, tag or commit hash).
+
+When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
+
+##### `-stub-run, -stub`
+
+Execute the workflow replacing process scripts with command stubs
+
+##### `-test`
+
+Test a script function with the name specified.
+
+##### `-user`
+
+Private repository user name.
+
+##### `-with-apptainer`
+
+Enable process execution in an Apptainer container.
+
+##### `-with-charliecloud`
+
+Enable process execution in a Charliecloud container.
+
+##### `-with-cloudcache`
+
+Enable the use of the Cloud cache plugin for storing cache metadata to an object storage bucket.
+
+##### `-with-conda`
+
+Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
+
+##### `-with-dag` (`dag-<timestamp>.html`)
+
+Create pipeline DAG file.
+
+Create pipeline DAG file.
+
+<ChangedInVersion version="23.10.0">
+The default format was changed from `dot` to `html`.
+</ChangedInVersion>
+
+##### `-with-docker`
+
+Enable process execution in a Docker container.
+
+##### `-N, -with-notification`
+
+Send a notification email on workflow completion to the specified recipients.
+
+##### `-with-podman`
+
+Enable process execution in a Podman container.
+
+##### `-with-report` (`report-<timestamp>.html`)
+
+Create workflow execution HTML report.
+
+##### `-with-singularity`
+
+Enable process execution in a Singularity container.
+
+##### `-with-spack`
+
+Use the specified Spack environment package or file (must end with `.yaml`)
+
+##### `-with-timeline` (`timeline-<timestamp>.html`)
+
+Create workflow execution timeline.
+
+##### `-with-tower` (`https://api.cloud.seqera.io`)
+
+Monitor workflow execution with [Seqera Platform](https://seqera.io/) (formerly Tower Cloud).
+
+##### `-with-trace` (`trace-<timestamp>.txt`)
+
+Create workflow execution trace file.
+
+##### `-with-wave` (`https://wave.seqera.io`)
+
+Enable the use of Wave containers.
+
+##### `-with-weblog` (`http://localhost`)
+
+Send workflow status messages via HTTP to target URL.
+
+##### `-without-conda`
+
+Disable process execution with Conda.
+
+##### `-without-docker`
+
+Disable process execution with Docker.
+
+##### `-without-podman`
+
+Disable process execution in a Podman container.
+
+##### `-without-spack`
+
+Disable process execution with Spack.
+
+##### `-without-wave`
+
+Disable the use of Wave containers.
+
+##### `-w, -work-dir` (`work`)
+
+Directory where intermediate result files are stored.
+
+#
+
+**Examples**
+
+- Run a specific revision of a remote pipeline.
+
+  ```console
+  $ nextflow run nextflow-io/hello -r v1.1
+
+  N E X T F L O W  ~  version 20.07.1
+  Launching `nextflow-io/hello` [grave_cajal] - revision: 1c3e9e7404 [v1.1]
+  ```
+
+- Choose a `profile` for running the project. Assumes that a profile named `docker` has already been defined in the config file.
+
+  ```console
+  $ nextflow run main.nf -profile docker
+  ```
+
+- Execute a pipeline and generate the summary HTML report. See [Reports][tracing-page] for more information:
+
+  ```console
+  $ nextflow run main.nf -with-report
+  ```
+
+- Execute a pipeline with a custom queue size. By default, the queue size is the number of available CPUs.
+
+  ```console
+  $ nextflow run nextflow-io/hello -qs 4
+  ```
+
+- Invoke the pipeline with a specific workflow as the entry-point.
+
+  ```console
+  $ nextflow run main.nf -entry workflow_A
+  ```
+
+- Execute a pipeline with integrated monitoring in [Seqera Platform](https://seqera.io).
+
+  ```console
+  $ nextflow run nextflow-io/hello -with-tower
+  ```
+
+- Execute a pipeline with a custom parameters file (YAML or JSON).
+
+  ```console
+  $ nextflow run main.nf -params-file pipeline_params.yml
+  ```
+
+See [Pipeline parameters][cli-params] for more information about writing custom parameters files.
+
+### `secrets`
+
+Manage [pipeline secrets][secrets-page].
+
+**Usage**
+
+```console
+$ nextflow secrets <SUBCOMMAND> [OPTIONS]
+```
+
+**Options**
+
+##### `-h, -help`
+
+Print the command usage.
+
+**Subcommands**
+
+##### `list`
+
+List secrets available in the current store.
+
+##### `get <secret>`
+
+Retrieve a secret value.
+
+##### `set <secret> <value> `
+
+Create or update a secret.
+
+##### `delete <secret>`
+
+Delete a secret.
+
+#
+
+**Examples**
+
+- Set a secret:
+
+    ```console
+    $ nextflow secrets set FOO "Hello world"
+    ```
+
+- List secrets:
+
+    ```console
+    $ nextflow secrets list
+    ```
+
+- Get a secret:
+
+    ```console
+    $ nextflow secrets get FOO
+    ```
+
+- Delete a secret:
+
+    ```console
+    $ nextflow secrets delete FOO
+    ```
+
+### `self-update`
+
+Update the nextflow runtime to the latest available version.
+
+**Usage**
+
+```console
+$ nextflow self-update
+```
+
+**Description**
+
+The `self-update` command directs the `nextflow` CLI to update itself to the latest stable release.
+
+**Examples**
+
+Update Nextflow.
+
+```console
+$ nextflow self-update
+
+      N E X T F L O W
+      version 20.07.1 build 5412
+      created 24-07-2020 15:18 UTC (20:48 IDT)
+      cite doi:10.1038/nbt.3820
+      http://nextflow.io
+
+
+Nextflow installation completed. Please note:
+- the executable file `nextflow` has been created in the folder: /usr/local/bin
+```
+
+### `view`
+
+View a project's script file(s).
+
+**Usage**
+
+```console
+$ nextflow view [options] [project]
+```
+
+**Description**
+
+The `view` command is used to inspect the pipelines that are already stored in the global nextflow cache. For downloading a pipeline into the global cache `~/.nextflow/assets`, refer to the `pull` command.
+
+**Options**
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-l`
+
+List repository content.
+
+##### `-q`
+
+Hide header line.
+
+#
+
+**Examples**
+
+Viewing the contents of a downloaded pipeline.
+
+```console
+$ nextflow view nextflow-io/hello
+
+== content of file: .nextflow/assets/nextflow-io/hello/main.nf
+#!/usr/bin/env nextflow
+
+process sayHello {
+  input:
+    val x
+  output:
+    stdout
+  script:
+    """
+    echo '$x world!'
+    """
+}
+
+workflow {
+  channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
+}
+```
+
+List the folder structure of the downloaded pipeline:
+
+```console
+$ nextflow view -l nextflow-io/hello
+
+== content of path: .nextflow/assets/nextflow-io/hello
+.git
+.gitignore
+LICENSE
+README.md
+main.nf
+nextflow.config
+```
+
+View the contents of a downloaded pipeline without omitting the header:
+
+```console
+$ nextflow view -q nextflow-io/hello
+
+#!/usr/bin/env nextflow
+
+process sayHello {
+  input:
+    val x
+  output:
+    stdout
+  script:
+    """
+    echo '$x world!'
+    """
+}
+
+workflow {
+  channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
+}
+```
+
+[cache-compare-hashes]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#comparing-the-hashes-of-two-runs
+[config-profiles]: /nextflow_docs/nextflow_repo/docs/config.mdx#config-profiles
+[gradle-plugin-create]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#creating-a-plugin
+[cli-page]: /nextflow_docs/nextflow_repo/docs/cli.mdx
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[data-lineage-page]: /nextflow_docs/nextflow_repo/docs/tutorials/data-lineage.mdx
+[k8s-page]: /nextflow_docs/nextflow_repo/docs/kubernetes.mdx
+[secrets-page]: /nextflow_docs/nextflow_repo/docs/secrets.mdx
+[tracing-page]: /nextflow_docs/nextflow_repo/docs/reports.mdx
diff --git a/docs/reference/config.md b/docs/reference/config.md
deleted file mode 100644
index d63be59f50..0000000000
--- a/docs/reference/config.md
+++ /dev/null
@@ -1,1744 +0,0 @@
-(config-options)=
-
-# Configuration options
-
-This page lists all of the available settings in the {ref}`Nextflow configuration <config-page>`.
-
-(config-unscoped)=
-
-## Unscoped options
-
-The following settings are available:
-
-`bucketDir`
-: The remote work directory used by hybrid workflows. Equivalent to the `-bucket-dir` option of the `run` command.
-
-`cleanup`
-: Delete all files associated with a run in the work directory when the run completes successfully (default: `false`).
-
-: :::{warning}
-  This option will prevent the use of the *resume* feature on subsequent executions of that pipeline run.
-  :::
-  :::{warning}
-  This option is not supported for remote work directories, such as Amazon S3, Google Cloud Storage, and Azure Blob Storage.
-  :::
-
-`outputDir`
-: :::{versionadded} 24.10.0
-  :::
-: The pipeline output directory. Equivalent to the `-output-dir` option of the `run` command.
-
-`resume`
-: Enable the use of previously cached task executions. Equivalent to the `-resume` option of the `run` command.
-
-`workDir`
-: The pipeline work directory. Equivalent to the `-work-dir` option of the `run` command.
-
-(config-apptainer)=
-
-## `apptainer`
-
-The `apptainer` scope controls how [Apptainer](https://apptainer.org) containers are executed by Nextflow.
-
-The following settings are available:
-
-`apptainer.autoMounts`
-: Automatically mount host paths in the executed container (default: `true`). It requires the `user bind control` feature to be enabled in your Apptainer installation.
-
-`apptainer.cacheDir`
-: The directory where remote Apptainer images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
-
-`apptainer.enabled`
-: Execute tasks with Apptainer containers (default: `false`).
-
-`apptainer.engineOptions`
-: Specify additional options supported by the Apptainer engine i.e. `apptainer [OPTIONS]`.
-
-`apptainer.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`apptainer.libraryDir`
-: Directory where remote Apptainer images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
-
-`apptainer.noHttps`
-: Pull the Apptainer image with http protocol (default: `false`).
-
-`apptainer.ociAutoPull`
-: :::{versionadded} 23.12.0-edge
-  :::
-: When enabled, OCI (and Docker) container images are pulled and converted to the SIF format by the Apptainer run command, instead of Nextflow (default: `false`).
-
-  :::{note}
-  Leave `ociAutoPull` disabled if you are willing to build a Singularity/Apptainer native image with Wave (see the {ref}`wave-singularity` section).
-  :::
-
-`apptainer.pullTimeout`
-: The amount of time the Apptainer pull can last, exceeding which the process is terminated (default: `20 min`).
-
-`apptainer.registry`
-: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`apptainer.runOptions`
-: Specify extra command line options supported by `apptainer exec`.
-
-(config-aws)=
-
-## `aws`
-
-The `aws` scope controls the interactions with AWS, including AWS Batch and S3.
-
-The following settings are available:
-
-`aws.accessKey`
-: AWS account access key.
-
-`aws.profile`
-: :::{versionadded} 22.12.0-edge
-  :::
-: AWS profile from `~/.aws/credentials`.
-
-`aws.region`
-: AWS region (e.g. `us-east-1`).
-
-`aws.secretKey`
-: AWS account secret key.
-
-`aws.batch.cliPath`
-: The path where the AWS command line tool is installed in the host AMI.
-
-`aws.batch.delayBetweenAttempts`
-: Delay between download attempts from S3 (default: `10 sec`).
-
-`aws.batch.executionRole`
-: The AWS Batch [Execution Role](https://docs.aws.amazon.com/batch/latest/userguide/execution-IAM-role.html) ARN that needs to be used to execute the Batch Job. It is mandatory when using AWS Fargate.
-
-`aws.batch.jobRole`
-: The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
-
-`aws.batch.logsGroup`
-: :::{versionadded} 22.09.0-edge
-  :::
-: The name of the logs group used by Batch Jobs (default: `/aws/batch/job`).
-
-`aws.batch.maxParallelTransfers`
-: Max parallel upload/download transfer operations *per job* (default: `4`).
-
-`aws.batch.maxSpotAttempts`
-: :::{versionadded} 22.04.0
-  :::
-: :::{versionchanged} 24.08.0-edge
-  The default value was changed from `5` to `0`.
-  :::
-: Max number of execution attempts of a job interrupted by a EC2 Spot reclaim event (default: `0`)
-
-`aws.batch.maxTransferAttempts`
-: Max number of downloads attempts from S3 (default: `1`).
-
-`aws.batch.platformType`
-: The compute platform type used by AWS Batch. Can be either `ec2` or `fargate`. Set to `fargate` to use [AWS Fargate](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html).
-
-`aws.batch.retryMode`
-: The [retry mode](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-retries.html) used to handle rate-limiting by AWS APIs. Can be one of `standard`, `legacy`, `adaptive`, or `built-in` (default: `standard`).
-
-`aws.batch.schedulingPriority`
-: :::{versionadded} 23.01.0-edge
-  :::
-: The scheduling priority for all tasks when using [fair-share scheduling](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/) (default: `0`).
-
-`aws.batch.shareIdentifier`
-: :::{versionadded} 22.09.0-edge
-  :::
-: The share identifier for all tasks when using [fair-share scheduling](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/).
-
-`aws.batch.terminateUnschedulableJobs`
-: :::{versionadded} 25.03.0-edge
-  :::
-: When `true`, jobs that cannot be scheduled due to lack of resources or misconfiguration are terminated and handled as task failures (default: `false`).
-
-`aws.batch.volumes`
-: List of container mounts. Mounts can be specified as simple e.g. `/some/path` or canonical format e.g. `/host/path:/mount/path[:ro|rw]`.
-
-`aws.client.anonymous`
-: Allow the access of public S3 buckets without providing AWS credentials (default: `false`). Any service that does not accept unsigned requests will return a service access error.
-
-`aws.client.connectionTimeout`
-: The amount of time to wait (in milliseconds) when initially establishing a connection before timing out (default: `10000`).
-
-`aws.client.endpoint`
-: The AWS S3 API entry point e.g. `https://s3-us-west-1.amazonaws.com`. The endpoint must include the protocol prefix e.g. `https://`.
-
-`aws.client.maxConnections`
-: The maximum number of open HTTP connections used by the S3 client (default: `50`).
-
-`aws.client.maxDownloadHeapMemory`
-: The maximum size for the heap memory buffer used by concurrent downloads. It must be at least 10 times the `minimumPartSize` (default:`400 MB`).
-
-`aws.client.maxErrorRetry`
-: The maximum number of retry attempts for failed retryable requests (default: `-1`).
-
-`aws.client.minimumPartSize`
-: :::{versionadded} 25.06.0-edge
-  :::
-: The minimum part size used for multipart S3 transfers (default: `8 MB`).
-
-`aws.client.multipartThreshold`
-: :::{versionadded} 25.06.0-edge
-  :::
-: The object size threshold used for multipart S3 transfers (default: same as `aws.cllient.minimumPartSize`).
-
-`aws.client.protocol`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The protocol to use when connecting to AWS. Can be `http` or `https` (default: `'https'`).
-
-`aws.client.proxyHost`
-: The proxy host to connect through.
-
-`aws.client.proxyPassword`
-: The password to use when connecting through a proxy.
-
-`aws.client.proxyPort`
-: The port to use when connecting through a proxy.
-
-`aws.client.proxyScheme`
-: :::{versionadded} 25.06.0-edge
-  :::
-: The protocol scheme to use when connecting through a proxy. Can be `http` or `https` (default: `'http'`).
-
-`aws.client.proxyUsername`
-: The user name to use when connecting through a proxy.
-
-`aws.client.requesterPays`
-: :::{versionadded} 24.05.0-edge
-  :::
-: Use [Requester Pays](https://docs.aws.amazon.com/AmazonS3/latest/userguide/RequesterPaysBuckets.html) for S3 buckets (default: `false`).
-
-`aws.client.s3Acl`
-: Specify predefined bucket permissions, also known as [canned ACL](https://docs.aws.amazon.com/AmazonS3/latest/userguide/acl-overview.html#canned-acl). Can be one of `Private`, `PublicRead`, `PublicReadWrite`, `AuthenticatedRead`, `LogDeliveryWrite`, `BucketOwnerRead`, `BucketOwnerFullControl`, or `AwsExecRead`.
-
-`aws.client.s3PathStyleAccess`
-: Use the path-based access model to access objects in S3-compatible storage systems (default: `false`).
-
-`aws.client.signerOverride`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The name of the signature algorithm to use for signing requests made by the client.
-
-`aws.client.socketSendBufferSizeHint`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The Size hint (in bytes) for the low level TCP send buffer (default: `0`).
-
-`aws.client.socketRecvBufferSizeHint`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The Size hint (in bytes) for the low level TCP receive buffer (default: `0`).
-
-`aws.client.socketTimeout`
-: The amount of time to wait (in milliseconds) for data to be transferred over an established, open connection before the connection is timed out (default: `50000`).
-
-`aws.client.storageClass`
-: The S3 storage class applied to stored objects, one of \[`STANDARD`, `STANDARD_IA`, `ONEZONE_IA`, `INTELLIGENT_TIERING`\] (default: `STANDARD`).
-
-`aws.client.storageEncryption`
-: The S3 server side encryption to be used when saving objects on S3. Can be `AES256` or `aws:kms` (default: none).
-
-`aws.client.storageKmsKeyId`
-: :::{versionadded} 22.05.0-edge
-  :::
-: The AWS KMS key Id to be used to encrypt files stored in the target S3 bucket.
-
-`aws.client.targetThroughputInGbps`
-: :::{versionadded} 25.06.0-edge
-  :::
-: The target network throughput (in Gbps) used for S3 uploads and downloads (default: `10`).
-
-`aws.client.userAgent`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The HTTP user agent header passed with all HTTP requests.
-
-`aws.client.uploadChunkSize`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The size of a single part in a multipart upload (default: `100 MB`).
-
-`aws.client.uploadMaxAttempts`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The maximum number of upload attempts after which a multipart upload returns an error (default: `5`).
-
-`aws.client.uploadMaxThreads`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The maximum number of threads used for multipart upload (default: `10`).
-
-`aws.client.uploadRetrySleep`
-: :::{deprecated} 25.06.0-edge
-  This option is no longer supported.
-  :::
-: The time to wait after a failed upload attempt to retry the part upload (default: `500ms`).
-
-`aws.client.uploadStorageClass`
-: The S3 storage class applied to stored objects. Can be `STANDARD`, `STANDARD_IA`, `ONEZONE_IA`, or `INTELLIGENT_TIERING` (default: `STANDARD`).
-
-(config-azure)=
-
-## `azure`
-
-The `azure` scope allows you to configure the interactions with Azure, including Azure Batch and Azure Blob Storage.
-
-The following settings are available:
-
-`azure.activeDirectory.servicePrincipalId`
-: The service principal client ID. Defaults to environment variable `AZURE_CLIENT_ID`.
-
-`azure.activeDirectory.servicePrincipalSecret`
-: The service principal client secret. Defaults to environment variable `AZURE_CLIENT_SECRET`.
-
-`azure.activeDirectory.tenantId`
-: The Azure tenant ID. Defaults to environment variable `AZURE_TENANT_ID`.
-
-`azure.azcopy.blobTier`
-: The blob [access tier](https://learn.microsoft.com/en-us/azure/storage/blobs/access-tiers-overview) used by `azcopy` to upload files to Azure Blob Storage. Valid options are `None`, `Hot`, or `Cool` (default: `None`).
-
-`azure.azcopy.blockSize`
-: The block size (in MB) used by `azcopy` to transfer files between Azure Blob Storage and compute nodes (default: `4`).
-
-`azure.batch.accountKey`
-: The batch service account key. Defaults to environment variable `AZURE_BATCH_ACCOUNT_KEY`.
-
-`azure.batch.accountName`
-: The batch service account name. Defaults to environment variable `AZURE_BATCH_ACCOUNT_NAME`.
-
-`azure.batch.allowPoolCreation`
-: Enable the automatic creation of batch pools specified in the Nextflow configuration file (default: `false`).
-
-`azure.batch.autoPoolMode`
-: Enable the automatic creation of batch pools depending on the pipeline resources demand (default: `true`).
-
-`azure.batch.copyToolInstallMode`
-: The mode in which the `azcopy` tool is installed by Nextflow (default: `'node'`).
-
-: The following options are available:
-
-  `'node'`
-  : The `azcopy` tool is installed once during the pool creation.
-
-  `'task'`
-  : The `azcopy` tool is installed for each task execution.
-
-  `'off'`
-  : The `azcopy` tool is not installed.
-
-`azure.batch.deleteJobsOnCompletion`
-: :::{versionchanged} 23.08.0-edge
-  Default value was changed from `true` to `false`.
-  :::
-: Delete all jobs when the workflow completes (default: `false`).
-
-`azure.batch.deletePoolsOnCompletion`
-: Delete all compute node pools when the workflow completes (default: `false`).
-
-`azure.batch.deleteTasksOnCompletion`
-: :::{versionadded} 23.08.0-edge
-  :::
-: Delete each task when it completes (default: `true`).
-: Although this setting is enabled by default, failed tasks will not be deleted unless it is explicitly enabled. This way, the default behavior is that successful tasks are deleted while failed tasks are preserved for debugging purposes.
-
-`azure.batch.endpoint`
-: The batch service endpoint e.g. `https://nfbatch1.westeurope.batch.azure.com`.
-
-`azure.batch.jobMaxWallClockTime`
-: :::{versionadded} 25.04.0
-  :::
-: The maximum elapsed time that jobs may run, measured from the time they are created (default: `30d`).
-: If jobs do not complete within this time limit, the Batch service terminates them and any tasks still running.
-
-`azure.batch.location`
-: The name of the batch service region, e.g. `westeurope` or `eastus2`. Not needed when the endpoint is specified.
-
-`azure.batch.poolIdentityClientId`
-: :::{versionadded} 25.05.0-edge
-  :::
-: The client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) that is available on all Azure Batch node pools. This identity is used by Fusion to authenticate to Azure storage. If set to `'auto'`, Fusion will use the first available managed identity.
-
-`azure.batch.pools.<name>.autoScale`
-: Enable autoscaling feature for the pool identified with `<name>`.
-
-`azure.batch.pools.<name>.fileShareRootPath`
-: The internal root mount point when mounting File Shares. Must be `/mnt/resource/batch/tasks/fsmounts` for CentOS nodes or `/mnt/batch/tasks/fsmounts` for Ubuntu nodes (default: CentOS).
-
-`azure.batch.pools.<name>.lowPriority`
-: Enable the use of low-priority VMs (default: `false`).
-
-: :::{warning}
-  As of September 30, 2025, Low Priority VMs will no longer be supported in Azure Batch accounts that use Batch Managed mode for pool allocation. You may continue to use this setting to configure Spot VMs in Batch accounts configured with User Subscription mode.
-  :::
-
-`azure.batch.pools.<name>.maxVmCount`
-: The max number of virtual machines when using auto scaling.
-
-`azure.batch.pools.<name>.mountOptions`
-: The mount options for mounting the file shares (default: `-o vers=3.0,dir_mode=0777,file_mode=0777,sec=ntlmssp`).
-
-`azure.batch.pools.<name>.offer`
-: The offer type of the virtual machine type used by the pool identified with `<name>` (default: `centos-container`).
-
-`azure.batch.pools.<name>.privileged`
-: Enable the task to run with elevated access. Ignored if `runAs` is set (default: `false`).
-
-`azure.batch.pools.<name>.publisher`
-: The publisher of virtual machine type used by the pool identified with `<name>` (default: `microsoft-azure-batch`).
-
-`azure.batch.pools.<name>.runAs`
-: The username under which the task is run. The user must already exist on each node of the pool.
-
-`azure.batch.pools.<name>.scaleFormula`
-: The [scale formula](https://docs.microsoft.com/en-us/azure/batch/batch-automatic-scaling) for the pool identified with `<name>`.
-
-`azure.batch.pools.<name>.scaleInterval`
-: The interval at which to automatically adjust the Pool size according to the autoscale formula. Must be at least 5 minutes and at most 168 hours (default: `10 mins`).
-
-`azure.batch.pools.<name>.schedulePolicy`
-: The scheduling policy for the pool identified with `<name>`. Can be either `spread` or `pack` (default: `spread`).
-
-`azure.batch.pools.<name>.sku`
-: The ID of the Compute Node agent SKU which the pool identified with `<name>` supports (default: `batch.node.centos 8`).
-
-`azure.batch.pools.<name>.startTask.privileged`
-: :::{versionadded} 24.03.0-edge
-  :::
-: Enable the `startTask` to run with elevated access (default: `false`).
-
-`azure.batch.pools.<name>.startTask.script`
-: :::{versionadded} 24.03.0-edge
-  :::
-: The `startTask` that is executed as the node joins the Azure Batch node pool.
-
-`azure.batch.pools.<name>.virtualNetwork`
-: :::{versionadded} 23.03.0-edge
-  :::
-: The subnet ID of a virtual network in which to create the pool.
-
-`azure.batch.pools.<name>.vmCount`
-: The number of virtual machines provisioned by the pool identified with `<name>`.
-
-`azure.batch.pools.<name>.vmType`
-: The virtual machine type used by the pool identified with `<name>`.
-
-`azure.batch.terminateJobsOnCompletion`
-: :::{versionadded} 23.05.0-edge
-  :::
-: When the workflow completes, set all jobs to terminate on task completion (default: `true`).
-
-`azure.managedIdentity.clientId`
-: The client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview). Defaults to environment variable `AZURE_MANAGED_IDENTITY_USER`.
-
-`azure.managedIdentity.system`
-: When `true`, use the system-assigned [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) to authenticate Azure resources. Defaults to environment variable `AZURE_MANAGED_IDENTITY_SYSTEM`.
-
-`azure.registry.password`
-: The password to connect to a private container registry.
-
-`azure.registry.server`
-: The container registry from which to pull the Docker images (default: `docker.io`).
-
-`azure.registry.userName`
-: The username to connect to a private container registry.
-
-`azure.retryPolicy.delay`
-: Delay when retrying failed API requests (default: `250ms`).
-
-`azure.retryPolicy.jitter`
-: Jitter value when retrying failed API requests (default: `0.25`).
-
-`azure.retryPolicy.maxAttempts`
-: Max attempts when retrying failed API requests (default: `10`).
-
-`azure.retryPolicy.maxDelay`
-: Max delay when retrying failed API requests (default: `90s`).
-
-`azure.storage.accountKey`
-: The blob storage account key. Defaults to environment variable `AZURE_STORAGE_ACCOUNT_KEY`.
-
-`azure.storage.accountName`
-: The blob storage account name. Defaults to environment variable `AZURE_STORAGE_ACCOUNT_NAME`.
-
-`azure.storage.fileShares.<name>.mountOptions`
-: The file share mount options.
-
-`azure.storage.fileShares.<name>.mountPath`
-: The file share mount path.
-
-`azure.storage.sasToken`
-: The blob storage shared access signature (SAS) token, which can be provided instead of an account key. Defaults to environment variable `AZURE_STORAGE_SAS_TOKEN`.
-
-`azure.storage.tokenDuration`
-: The duration of the SAS token generated by Nextflow when the `sasToken` option is *not* specified (default: `48h`).
-
-(config-charliecloud)=
-
-## `charliecloud`
-
-The `charliecloud` scope controls how [Charliecloud](https://hpc.github.io/charliecloud/) containers are executed by Nextflow.
-
-The following settings are available:
-
-`charliecloud.cacheDir`
-: The directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
-
-`charliecloud.enabled`
-: Execute tasks with Charliecloud containers (default: `false`).
-
-`charliecloud.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`charliecloud.pullTimeout`
-: The amount of time the Charliecloud pull can last, exceeding which the process is terminated (default: `20 min`).
-
-`charliecloud.registry`
-: The registry from where images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`charliecloud.runOptions`
-: Specify extra command line options supported by the `ch-run` command.
-
-`charliecloud.temp`
-: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
-
-`charliecloud.writableInputMounts`
-: When `false`, mount input directories as read-only (default: `true`).
-
-`charliecloud.writeFake`
-: Run containers from storage in writeable mode using overlayfs (default: `true`).
-: This option requires unprivileged `overlayfs` (Linux kernel >= 5.11). For full support, tempfs with xattrs in the user namespace (Linux kernel >= 6.6) is required. See [charliecloud documentation](https://hpc.github.io/charliecloud/ch-run.html#ch-run-overlay) for details.
-
-(config-conda)=
-
-## `conda`
-
-The `conda` scope controls the creation of Conda environments by the Conda package manager.
-
-The following settings are available:
-
-`conda.cacheDir`
-: The path where Conda environments are stored. It should be accessible from all compute nodes when using a shared file system.
-
-`conda.channels`
-: The list of Conda channels that can be used to resolve Conda packages. Channel priority decreases from left to right.
-
-`conda.createOptions`
-: Extra command line options for the `conda create` command. See the [Conda documentation](https://docs.conda.io/projects/conda/en/latest/commands/create.html) for more information.
-
-`conda.createTimeout`
-: The amount of time to wait for the Conda environment to be created before failing (default: `20 min`).
-
-`conda.enabled`
-: Execute tasks with Conda environments (default: `false`).
-
-`conda.useMamba`
-: Use [Mamba](https://github.com/mamba-org/mamba) instead of `conda` to create Conda environments (default: `false`).
-
-`conda.useMicromamba`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Use [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) instead of `conda` to create Conda environments (default: `false`).
-
-(config-dag)=
-
-## `dag`
-
-The `dag` scope controls the workflow diagram generated by Nextflow.
-
-The following settings are available:
-
-`dag.depth`
-: :::{versionadded} 23.10.0
-  :::
-: *Supported by the HTML and Mermaid renderers.*
-: Controls the maximum depth at which to render sub-workflows (default: no limit).
-
-`dag.direction`
-: :::{versionadded} 23.10.0
-  :::
-: *Supported by the Graphviz, DOT, HTML and Mermaid renderers.*
-: Controls the direction of the DAG, can be `'LR'` (left-to-right) or `'TB'` (top-to-bottom) (default: `'TB'`).
-
-`dag.enabled`
-: When `true` enables the generation of the DAG file (default: `false`).
-
-`dag.file`
-: Graph file name (default: `'dag-<timestamp>.html'`).
-
-`dag.overwrite`
-: When `true` overwrites any existing DAG file with the same name (default: `false`).
-
-`dag.verbose`
-: :::{versionadded} 23.10.0
-  :::
-: *Only supported by the HTML and Mermaid renderers.*
-: When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`).
-
-(config-docker)=
-
-## `docker`
-
-The `docker` scope controls how [Docker](https://www.docker.com) containers are executed by Nextflow.
-
-The following settings are available:
-
-`docker.enabled`
-: Enable Docker execution (default: `false`).
-
-`docker.engineOptions`
-: Specify additional options supported by the Docker engine i.e. `docker [OPTIONS]`.
-
-`docker.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`docker.fixOwnership`
-: Fix ownership of files created by the Docker container (default: `false`).
-
-`docker.legacy`
-: Use command line options removed since Docker 1.10.0 (default: `false`).
-
-`docker.mountFlags`
-: Add the specified flags to the volume mounts e.g. `'ro,Z'`.
-
-`docker.registry`
-: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`docker.registryOverride`
-: :::{versionadded} 25.06.0-edge
-  :::
-: When `true`, forces the override of the registry name in fully qualified container image names with the registry specified by `docker.registry` (default: `false`).
-: This setting allows you to redirect container image pulls from their original registry to a different registry, such as a private mirror or proxy.
-
-`docker.remove`
-: Clean up the container after the execution (default: `true`). See the [Docker documentation](https://docs.docker.com/engine/reference/run/#clean-up---rm) for details.
-
-`docker.runOptions`
-: Specify extra command line options supported by the `docker run` command. See the [Docker documentation](https://docs.docker.com/engine/reference/run/) for details.
-
-`docker.sudo`
-: Executes Docker run command as `sudo` (default: `false`).
-
-`docker.temp`
-: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
-
-`docker.tty`
-: Allocates a pseudo-tty (default: `false`).
-
-`docker.writableInputMounts`
-: When `false`, mount input directories as read-only (default: `true`).
-
-(config-env)=
-
-## `env`
-
-The `env` scope allows the definition one or more variables that will be exported into the environment where workflow tasks are executed.
-
-Simply prefix your variable names with the `env` scope or surround them by curly brackets, as shown below:
-
-```groovy
-env.ALPHA = 'some value'
-env.BETA = "$HOME/some/path"
-
-env {
-     DELTA = 'one more'
-     GAMMA = "/my/path:$PATH"
-}
-```
-
-:::{note}
-In the above example, variables like `$HOME` and `$PATH` are evaluated when the workflow is launched. If you want these variables to be evaluated during task execution, escape them with `\$`. This difference is important for variables like `$PATH`, which may be different in the workflow environment versus the task environment.
-:::
-
-:::{warning}
-The `env` scope provides environment variables to *tasks*, not Nextflow itself. Nextflow environment variables such as `NXF_VER` should be set in the environment in which Nextflow is launched.
-:::
-
-(config-executor)=
-
-## `executor`
-
-The `executor` scope controls various executor behaviors.
-
-The following settings are available:
-
-`executor.account`
-: :::{versionadded} 24.04.0
-  :::
-: *Used only by the {ref}`slurm-executor`, {ref}`lsf-executor`, {ref}`pbs-executor` and {ref}`pbspro-executor` executors.*
-: The project or organization account that should be charged for running the pipeline jobs.
-
-`executor.cpus`
-: *Used only by the local executor.*
-: The maximum number of CPUs made available by the underlying system.
-
-`executor.dumpInterval`
-: Determines how often to log the executor status (default: `5 min`).
-
-`executor.exitReadTimeout`
-: *Used only by grid executors.*
-: Determines how long to wait for the `.exitcode` file to be created after the task has completed, before returning an error status (default: `270 sec`).
-
-`executor.jobName`
-: *Used only by grid executors and Google Batch.*
-: Determines the name of jobs submitted to the underlying cluster executor:
-  ```groovy
-  executor.jobName = { "$task.name - $task.hash" }
-  ```
-: The job name should satisfy the validation constraints of the underlying scheduler.
-
-`executor.killBatchSize`
-: Determines the number of jobs that can be killed in a single command execution (default: `100`).
-
-`executor.memory`
-: *Used only by the local executor.*
-: The maximum amount of memory made available by the underlying system.
-
-`executor.name`
-: The name of the executor to be used (default: `local`).
-
-`executor.perCpuMemAllocation`
-: :::{versionadded} 23.07.0-edge
-  :::
-: *Used only by the {ref}`slurm-executor` executor.*
-: When `true`, memory allocations for SLURM jobs are specified as `--mem-per-cpu <task.memory / task.cpus>` instead of `--mem <task.memory>`.
-
-`executor.perJobMemLimit`
-: *Used only by the {ref}`lsf-executor` executor.*
-: Enables the *per-job* memory limit mode for LSF jobs.
-
-`executor.perTaskReserve`
-: *Used only by the {ref}`lsf-executor` executor.*
-: Enables the *per-task* memory reserve mode for LSF jobs.
-
-`executor.pollInterval`
-: Determines how often to check for process termination. Default varies for each executor.
-
-`executor.queueGlobalStatus`
-: :::{versionadded} 23.01.0-edge
-  :::
-: Determines how job status is retrieved. When `false` only the queue associated with the job execution is queried. When `true` the job status is queried globally i.e. irrespective of the submission queue (default: `false`).
-
-`executor.queueSize`
-: The number of tasks the executor will handle in a parallel manner. A queue size of zero corresponds to no limit. Default varies for each executor.
-
-`executor.queueStatInterval`
-: *Used only by grid executors.*
-: Determines how often to fetch the queue status from the scheduler (default: `1 min`).
-
-`executor.submitRateLimit`
-: Determines the max rate of job submission per time unit, for example `'10sec'` (10 jobs per second) or `'50/2min'` (50 jobs every 2 minutes) (default: unlimited).
-
-`executor.retry.delay`
-: :::{versionadded} 22.03.0-edge
-  :::
-: *Used only by grid executors.*
-: Delay when retrying failed job submissions (default: `500ms`).
-
-`executor.retry.jitter`
-: :::{versionadded} 22.03.0-edge
-  :::
-: *Used only by grid executors.*
-: Jitter value when retrying failed job submissions (default: `0.25`).
-
-`executor.retry.maxAttempts`
-: :::{versionadded} 22.03.0-edge
-  :::
-: *Used only by grid executors.*
-: Max attempts when retrying failed job submissions (default: `3`).
-
-`executor.retry.maxDelay`
-: :::{versionadded} 22.03.0-edge
-  :::
-: *Used only by grid executors.*
-: Max delay when retrying failed job submissions (default: `30s`).
-
-`executor.retry.reason`
-: :::{versionadded} 22.03.0-edge
-  :::
-: :::{versionchanged} 25.10.0
-  This option was renamed from `executor.submit.retry.reason` to `executor.retry.reason`.
-  :::
-: *Used only by grid executors.*
-: Regex pattern that when verified causes a failed submit operation to be re-tried (default: `Socket timed out`).
-
-### Executor-specific defaults
-
-Some executor settings have different default values depending on the executor.
-
-| Executor       | `queueSize` | `pollInterval` |
-| -------------- | ----------- | -------------- |
-| AWS Batch      | `1000`      | `10s`          |
-| Azure Batch    | `1000`      | `10s`          |
-| Google Batch   | `1000`      | `10s`          |
-| Grid Executors | `100`       | `5s`           |
-| Kubernetes     | `100`       | `5s`           |
-| Local          | N/A         | `100ms`        |
-
-### Executor-specific configuration
-
-Executor config settings can be applied to specific executors by prefixing the executor name with the symbol `$` and using it as special scope. For example:
-
-```groovy
-// block syntax
-executor {
-  $sge {
-      queueSize = 100
-      pollInterval = '30sec'
-  }
-
-  $local {
-      cpus = 8
-      memory = '32 GB'
-  }
-}
-
-// dot syntax
-executor.$sge.queueSize = 100
-executor.$sge.pollInterval = '30sec'
-executor.$local.cpus = 8
-executor.$local.memory = '32 GB'
-```
-
-(config-fusion)=
-
-## `fusion`
-
-The `fusion` scope provides advanced configuration for the use of the {ref}`Fusion file system <fusion-page>`.
-
-The following settings are available:
-
-`fusion.cacheSize`
-: :::{versionadded} 23.11.0-edge
-  :::
-: The maximum size of the local cache used by the Fusion client.
-
-`fusion.containerConfigUrl`
-: The URL of the container layer that provides the Fusion client.
-
-`fusion.enabled`
-: Enable the Fusion file system (default: `false`).
-
-`fusion.exportStorageCredentials`
-: Export access credentials required by the underlying object storage as environment variables (e.g., `AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY`, and `AWS_SESSION_TOKEN` for AWS S3) to task execution environments (default: `false`).
-
-  :::{note}
-  This configuration does not mount or provide access to credential files. For example, AWS credentials like `~/.aws/credentials`, `~/.aws/config`, and SSO cache files are not mounted. AWS SSO users must export credentials to environment variables:
-  
-  ```bash
-  eval "$(aws configure export-credentials --format env)"
-  ```
-  :::
-
-  :::{warning}
-  This option leaks credentials is the task launcher script. It should only be used for testing and development purposes.
-  :::
-
-`fusion.logLevel`
-: The log level of the Fusion client.
-
-`fusion.logOutput`
-: The output location of the Fusion log.
-
-`fusion.privileged`
-: :::{versionadded} 23.10.0
-  :::
-: Enable privileged containers for Fusion (default: `true`).
-: Non-privileged use is supported only on Kubernetes with the [k8s-fuse-plugin](https://github.com/nextflow-io/k8s-fuse-plugin) or a similar FUSE device plugin.
-
-`fusion.snapshots`
-: :::{versionadded} 25.03.0-edge
-  :::
-: *Currently only supported for AWS Batch*
-: Enable Fusion snapshotting (preview, default: `false`). This feature allows Fusion to automatically restore a job when it is interrupted by a spot reclamation.
-
-`fusion.tags`
-: The pattern that determines how tags are applied to files created via the Fusion client (default: `[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`). Set to `false` to disable tags.
-
-(config-google)=
-
-## `google`
-
-The `google` scope allows you to configure the interactions with Google Cloud, including Google Cloud Batch and Google Cloud Storage.
-
-The following settings are available:
-
-`google.enableRequesterPaysBuckets`
-: Use the given Google Cloud project ID as the billing project for storage access (default: `false`). Required when accessing data from [requester pays](https://cloud.google.com/storage/docs/requester-pays) buckets.
-
-`google.httpConnectTimeout`
-: :::{versionadded} 23.06.0-edge
-  :::
-: The HTTP connection timeout for Cloud Storage API requests (default: `'60s'`).
-
-`google.httpReadTimeout`
-: :::{versionadded} 23.06.0-edge
-  :::
-: The HTTP read timeout for Cloud Storage API requests (default: `'60s'`).
-
-`google.location`
-: The Google Cloud location where jobs are executed (default: `us-central1`).
-
-`google.project`
-: The Google Cloud project ID to use for pipeline execution.
-
-`google.batch.allowedLocations`
-: :::{versionadded} 22.12.0-edge
-  :::
-: The set of [allowed locations](https://cloud.google.com/batch/docs/reference/rest/v1/projects.locations.jobs#locationpolicy) for VMs to be provisioned (default: no restriction).
-
-`google.batch.autoRetryExitCodes`
-: :::{versionadded} 24.07.0-edge
-  :::
-: The list of exit codes that should be automatically retried by Google Batch when `google.batch.maxSpotAttempts` is greater than 0 (default: `[50001]`).
-: See [Google Batch documentation](https://cloud.google.com/batch/docs/troubleshooting#reserved-exit-codes) for the complete list of retryable exit codes.
-
-`google.batch.bootDiskImage`
-: :::{versionadded} 24.08.0-edge
-  :::
-: The image URI of the virtual machine boot disk, e.g `batch-debian` (default: none).
-: See [Google documentation](https://cloud.google.com/batch/docs/vm-os-environment-overview#vm-os-image-options) for details.
-
-`google.batch.bootDiskSize`
-: The size of the virtual machine boot disk, e.g `50.GB` (default: none).
-
-`google.batch.cpuPlatform`
-: The [minimum CPU Platform](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications), e.g. `'Intel Skylake'` (default: none).
-
-`google.batch.gcsfuseOptions`
-: :::{versionadded} 25.03.0-edge
-  :::
-: List of custom mount options for `gcsfuse` (default: `['-o rw', '-implicit-dirs']`).
-
-`google.batch.maxSpotAttempts`
-: :::{versionadded} 23.11.0-edge
-  :::
-: :::{versionchanged} 24.08.0-edge
-  The default value was changed from `5` to `0`.
-  :::
-: Max number of execution attempts of a job interrupted by a Compute Engine Spot reclaim event (default: `0`).
-: See also: `google.batch.autoRetryExitCodes`
-
-`google.batch.network`
-: The URL of an existing network resource to which the VM will be attached.
-
-: You can specify the network as a full or partial URL. For example, the following are all valid URLs:
-
-  - `https://www.googleapis.com/compute/v1/projects/{project}/global/networks/{network}`
-  - `projects/{project}/global/networks/{network}`
-  - `global/networks/{network}`
-
-`google.batch.networkTags`
-: The [network tags](https://cloud.google.com/vpc/docs/add-remove-network-tags) to be applied to the instances created by Google Batch jobs (e.g., `['allow-ssh', 'allow-http']`).
-: Network tags are ignored when using instance templates.
-
-`google.batch.serviceAccountEmail`
-: The Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
-: This service account will only be used for tasks submitted by Nextflow, not for Nextflow itself. See {ref}`google-credentials` for more information on Google Cloud credentials.
-
-`google.batch.spot`
-: Enable the use of spot virtual machines (default: `false`).
-
-`google.batch.subnetwork`
-: The URL of an existing subnetwork resource in the network to which the VM will be attached.
-
-: You can specify the subnetwork as a full or partial URL. For example, the following are all valid URLs:
-
-  - `https://www.googleapis.com/compute/v1/projects/{project}/regions/{region}/subnetworks/{subnetwork}`
-  - `projects/{project}/regions/{region}/subnetworks/{subnetwork}`
-  - `regions/{region}/subnetworks/{subnetwork}`
-
-`google.batch.usePrivateAddress`
-: Do not provision public IP addresses for VMs, such that they only have an internal IP address (default: `false`).
-: When this option is enabled, jobs can only load Docker images from Google Container Registry, and cannot use external services other than Google APIs.
-
-`google.storage.retryPolicy.maxAttempts`
-: :::{versionadded} 23.11.0-edge
-  :::
-: Max attempts when retrying failed API requests to Cloud Storage (default: `10`).
-
-`google.storage.retryPolicy.maxDelay`
-: :::{versionadded} 23.11.0-edge
-  :::
-: Max delay when retrying failed API requests to Cloud Storage (default: `'90s'`).
-
-`google.storage.retryPolicy.multiplier`
-: :::{versionadded} 23.11.0-edge
-  :::
-: Delay multiplier when retrying failed API requests to Cloud Storage (default: `2.0`).
-
-(config-k8s)=
-
-## `k8s`
-
-The `k8s` scope controls the deployment and execution of workflow applications in a Kubernetes cluster.
-
-The following settings are available:
-
-`k8s.autoMountHostPaths`
-: Automatically mount host paths into the task pods (default: `false`). Only intended for development purposes when using a single node.
-
-`k8s.cleanup`
-: When `true`, successful pods are automatically deleted (default: `true`).
-
-`k8s.client`
-: Map of options for the Kubernetes HTTP client.
-: If this option is specified, it will be used instead of `.kube/config`.
-: The following options are available:
-  - `server`
-  - `token`
-  - `tokenFile`
-  - `verifySsl`
-  - `sslCert`
-  - `sslCertFile`
-  - `clientCert`
-  - `clientCertFile`
-  - `clientKey`
-  - `clientKeyFile`
-
-`k8s.computeResourceType`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Whether to use Kubernetes `Pod` or `Job` resource type to carry out Nextflow tasks (default: `Pod`).
-
-`k8s.context`
-: The Kubernetes [configuration context](https://kubernetes.io/docs/tasks/access-application-cluster/configure-access-multiple-clusters/) to use.
-
-`k8s.cpuLimits`
-: :::{versionadded} 24.04.0
-  :::
-: When `true`, set both the pod CPUs `request` and `limit` to the value specified by the `cpus` directive, otherwise set only the `request` (default: `false`).
-: This setting is useful when a K8s cluster requires a CPU limit to be defined through a [LimitRange](https://kubernetes.io/docs/concepts/policy/limit-range/).
-
-`k8s.fetchNodeName`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Include the hostname of each task in the execution trace (default: `false`).
-
-`k8s.fuseDevicePlugin`
-: :::{versionadded} 24.01.0-edge
-  :::
-: The FUSE device plugin to be used when enabling Fusion in unprivileged mode (default: `['nextflow.io/fuse': 1]`).
-
-`k8s.httpConnectTimeout`
-: :::{versionadded} 22.10.0
-  :::
-: The Kubernetes HTTP client request connection timeout e.g. `'60s'`.
-
-`k8s.httpReadTimeout`
-: :::{versionadded} 22.10.0
-  :::
-: The Kubernetes HTTP client request connection read timeout e.g. `'60s'`.
-
-`k8s.imagePullPolicy`
-: The strategy for pulling container images. Can be `IfNotPresent`, `Always`, `Never`.
-
-`k8s.launchDir`
-: The path where the workflow is launched and the user data is stored (default: `<volume-claim-mount-path>/<user-name>`). Must be a path in a shared K8s persistent volume.
-
-`k8s.namespace`
-: The Kubernetes namespace to use (default: `default`).
-
-`k8s.pod`
-: Additional pod configuration options such as environment variables, config maps, secrets, etc. Allows the same settings as the {ref}`process-pod` process directive.
-: When using the `kuberun` command, this setting also applies to the submitter pod.
-
-`k8s.projectDir`
-: The path where Nextflow projects are downloaded (default: `<volume-claim-mount-path>/projects`). Must be a path in a shared K8s persistent volume.
-
-`k8s.runAsUser`
-: The user ID to be used to run the containers. Shortcut for the `securityContext` option.
-
-`k8s.securityContext`
-: The [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) to use for all pods.
-
-`k8s.serviceAccount`
-: The Kubernetes [service account name](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/) to use.
-
-`k8s.storageClaimName`
-: The name of the persistent volume claim where the shared work directory is stored.
-
-`k8s.storageMountPath`
-: The mount path for the persistent volume claim (default: `/workspace`).
-
-`k8s.storageSubPath`
-: The path in the persistent volume to be mounted (default: `/`).
-
-`k8s.workDir`
-: The path of the shared work directory (default: `<user-dir>/work`). Must be a path in a shared K8s persistent volume.
-
-`k8s.debug.yaml`
-: Save the pod spec for each task to `.command.yaml` in the task directory (default: `false`).
-
-`k8s.retryPolicy.delay`
-: Delay when retrying failed API requests (default: `250ms`).
-
-`k8s.retryPolicy.jitter`
-: Jitter value when retrying failed API requests (default: `0.25`).
-
-`k8s.retryPolicy.maxAttempts`
-: Max attempts when retrying failed API requests (default: `4`).
-
-`k8s.retryPolicy.maxDelay`
-: Max delay when retrying failed API requests (default: `90s`).
-
-(config-lineage)=
-
-## `lineage`
-
-The `lineage` scope controls the generation of {ref}`cli-lineage` metadata.
-
-The following settings are available:
-
-`lineage.enabled`
-: Enable generation of lineage metadata (default: `false`).
-
-`lineage.store.location`
-: The location of the lineage metadata store (default: `./.lineage`).
-
-(config-mail)=
-
-## `mail`
-
-The `mail` scope controls the mail server used to send email notifications.
-
-The following settings are available:
-
-`mail.debug`
-: Enable Java Mail logging for debugging purposes (default: `false`).
-
-`mail.from`
-: Default email sender address.
-
-`mail.smtp.host`
-: Host name of the mail server.
-
-`mail.smtp.password`
-: User password to connect to the mail server.
-
-`mail.smtp.port`
-: Port number of the mail server.
-
-`mail.smtp.user`
-: User name to connect to the mail server.
-
-`mail.smtp.proxy.host`
-: Host name of an HTTP web proxy server that will be used for connections to the mail server.
-
-`mail.smtp.proxy.port`
-: Port number for the HTTP web proxy server.
-
-`mail.smtp.*`
-: Any SMTP configuration property supported by the [Java Mail API](https://javaee.github.io/javamail/), which Nextflow uses to send emails. See the table of available properties [here](https://javaee.github.io/javamail/docs/api/com/sun/mail/smtp/package-summary.html#properties).
-
-(config-manifest)=
-
-## `manifest`
-
-The `manifest` scope allows you to define some metadata that is useful when publishing or running your pipeline.
-
-The following settings are available:
-
-`manifest.author`
-: :::{deprecated} 24.09.0-edge
-  Use `manifest.contributors` instead.
-  :::
-: Project author name (use a comma to separate multiple names).
-
-`manifest.contributors`
-: :::{versionadded} 24.09.0-edge
-  :::
-: List of project contributors. Should be a list of maps.
-
-: The following fields are supported in the contributor map:
-
-  `name`
-  : The contributor name.
-
-  `affiliation`
-  : The contributor affiliated organization.
-
-  `email`
-  : The contributor email address.
-
-  `github`
-  : The contributor GitHub URL.
-
-  `contribution`
-  : List of contribution types, each element can be one of `'author'`, `'maintainer'`, or `'contributor'`.
-
-  `orcid`
-  : The contributor [ORCID](https://orcid.org/) URL.
-
-`manifest.defaultBranch`
-: Git repository default branch (default: `master`).
-
-`manifest.description`
-: Free text describing the workflow project.
-
-`manifest.docsUrl`
-: Project documentation URL.
-
-`manifest.doi`
-: Project related publication DOI identifier.
-
-`manifest.gitmodules`
-: Controls whether git sub-modules should be cloned with the main repository.
-: Can be either a boolean value, a list of submodule names, or a comma-separated string of submodule names.
-
-`manifest.homePage`
-: Project home page URL.
-
-`manifest.icon`
-: Project related icon location (Relative path or URL).
-
-`manifest.license`
-: Project license.
-
-`manifest.mainScript`
-: Project main script (default: `main.nf`).
-
-`manifest.name`
-: Project short name.
-
-`manifest.nextflowVersion`
-: Minimum required Nextflow version.
-
-: This setting may be useful to ensure that a specific version is used:
-
-  ```groovy
-  manifest.nextflowVersion = '1.2.3'        // exact match
-  manifest.nextflowVersion = '1.2+'         // 1.2 or later (excluding 2 and later)
-  manifest.nextflowVersion = '>=1.2'        // 1.2 or later
-  manifest.nextflowVersion = '>=1.2, <=1.5' // any version in the 1.2 .. 1.5 range
-  manifest.nextflowVersion = '!>=1.2'       // with ! prefix, stop execution if current version does not match required version.
-  ```
-
-: See {ref}`stdlib-types-versionnumber` for details.
-
-`manifest.organization`
-: Project organization.
-
-`manifest.recurseSubmodules`
-: Pull submodules recursively from the Git repository.
-
-`manifest.version`
-: Project version number.
-
-(config-nextflow)=
-
-## `nextflow`
-
-:::{versionchanged} 24.10.0
-The `nextflow.publish.retryPolicy` settings were moved to `workflow.output.retryPolicy`.
-:::
-
-:::{versionchanged} 25.06.0-edge
-The `workflow.output.retryPolicy` settings were moved to `nextflow.retryPolicy`.
-:::
-
-`retryPolicy.delay`
-: Delay used for retryable operations (default: `350ms`).
-
-`retryPolicy.jitter`
-: Jitter value used for retryable operations (default: `0.25`).
-
-`retryPolicy.maxAttempts`
-: Max attempts used for retryable operations (default: `5`).
-
-`retryPolicy.maxDelay`
-: Max delay used for retryable operations (default: `90s`).
-
-(config-notification)=
-
-## `notification`
-
-The `notification` scope controls the automatic sending of an email notification on workflow completion.
-
-The following settings are available:
-
-`notification.attributes`
-: Map of variables that can be used in the template file.
-
-`notification.enabled`
-: Send an email notification when the workflow execution completes (default: `false`).
-
-`notification.from`
-: Sender address for the email notification.
-
-`notification.template`
-: Path of a template file containing the contents of the email notification.
-
-`notification.to`
-: Recipient address for the email notification. Multiple addresses can be specified as a comma-separated list.
-
-(config-podman)=
-
-## `podman`
-
-The `podman` scope controls how [Podman](https://podman.io/) containers are executed by Nextflow.
-
-The following settings are available:
-
-`podman.enabled`
-: Execute tasks with Podman containers (default: `false`).
-
-`podman.engineOptions`
-: Specify additional options supported by the Podman engine i.e. `podman [OPTIONS]`.
-
-`podman.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`podman.mountFlags`
-: Add the specified flags to the volume mounts e.g. `'ro,Z'`.
-
-`podman.registry`
-: The registry from where container images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`podman.remove`
-: Clean-up the container after the execution (default: `true`).
-
-`podman.runOptions`
-: Specify extra command line options supported by the `podman run` command.
-
-`podman.temp`
-: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
-
-(config-report)=
-
-## `report`
-
-The `report` scope allows you to configure the workflow {ref}`execution-report`.
-
-The following settings are available:
-
-`report.enabled`
-: Create the execution report on workflow completion (default: `false`).
-
-`report.file`
-: The path of the created execution report file (default: `'report-<timestamp>.html'`).
-
-`report.overwrite`
-: Overwrite any existing report file with the same name (default: `false`).
-
-(config-sarus)=
-
-## `sarus`
-
-The `sarus` scope controls how [Sarus](https://sarus.readthedocs.io) containers are executed by Nextflow.
-
-The following settings are available:
-
-`sarus.enabled`
-: Execute tasks with Sarus containers (default: `false`).
-
-`sarus.envWhitelist`
-: Comma-separated list of environment variable names to be included in the container environment.
-
-`sarus.runOptions`
-: Specify extra command line options supported by the `sarus run` command.
-: See the [Sarus user guide](https://sarus.readthedocs.io/en/stable/user/user_guide.html) for details.
-
-`sarus.tty`
-: Allocates a pseudo-tty (default: `false`).
-
-(config-shifter)=
-
-## `shifter`
-
-The `shifter` scope controls how [Shifter](https://docs.nersc.gov/programming/shifter/overview/) containers are executed by Nextflow.
-
-The following settings are available:
-
-`shifter.enabled`
-: Execute tasks with Shifter containers (default: `false`).
-
-`shifter.envWhitelist`
-: Comma-separated list of environment variable names to be included in the container environment.
-
-(config-singularity)=
-
-## `singularity`
-
-The `singularity` scope controls how [Singularity](https://sylabs.io/singularity/) containers are executed by Nextflow.
-
-The following settings are available:
-
-`singularity.autoMounts`
-: :::{versionchanged} 23.09.0-edge
-  Default value was changed from `false` to `true`.
-  :::
-: Automatically mount host paths in the executed container (default: `true`). It requires the `user bind control` feature to be enabled in your Singularity installation.
-
-`singularity.cacheDir`
-: The directory where remote Singularity images are stored. When using a compute cluster, it must be a shared folder accessible to all compute nodes.
-
-`singularity.enabled`
-: Execute tasks with Singularity containers (default: `false`).
-
-`singularity.engineOptions`
-: Specify additional options supported by the Singularity engine i.e. `singularity [OPTIONS]`.
-
-`singularity.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`singularity.libraryDir`
-: Directory where remote Singularity images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
-
-`singularity.noHttps`
-: Pull the Singularity image with http protocol (default: `false`).
-
-`singularity.ociAutoPull`
-: :::{versionadded} 23.12.0-edge
-  :::
-: *Requires Singularity 3.11 or later*
-: When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow (default: `false`).
-
-  :::{note}
-  Leave `ociAutoPull` disabled if willing to build a Singularity native image with Wave (see the {ref}`wave-singularity` section).
-  :::
-
-`singularity.ociMode`
-: :::{versionadded} 23.12.0-edge
-  :::
-: *Requires Singularity 4 or later*
-: Enable OCI-mode, that allows running native OCI compliant container image with Singularity using `crun` or `runc` as low-level runtime (default: `false`).
-: See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
-
-  :::{note}
-  Leave `ociMode` disabled if you are willing to build a Singularity native image with Wave (see the {ref}`wave-singularity` section).
-  :::
-
-`singularity.pullTimeout`
-: The amount of time the Singularity pull can last, after which the process is terminated (default: `20 min`).
-
-`singularity.registry`
-: :::{versionadded} 22.12.0-edge
-  :::
-: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`singularity.runOptions`
-: Specify extra command line options supported by `singularity exec`.
-
-(config-spack)=
-
-## `spack`
-
-The `spack` scope controls the creation of a Spack environment by the Spack package manager.
-
-The following settings are available:
-
-`spack.cacheDir`
-: The path where Spack environments are stored. It should be accessible from all compute nodes when using a shared file system.
-
-`spack.checksum`
-: Enable checksum verification of source tarballs (default: `true`).
-: Only disable when requesting a package version not yet encoded in the corresponding Spack recipe.
-
-`spack.createTimeout`
-: The amount of time to wait for the Spack environment to be created before failing (default: `60 min`).
-
-`spack.enabled`
-: Execute tasks with Spack environments (default: `false`).
-
-`spack.parallelBuilds`
-: The maximum number of parallel package builds (default: the number of available CPUs).
-
-(config-timeline)=
-
-## `timeline`
-
-The `timeline` scope controls the execution timeline report generated by Nextflow.
-
-The following settings are available:
-
-`timeline.enabled`
-: Create the timeline report on workflow completion file (default: `false`).
-
-`timeline.file`
-: Timeline file name (default: `'timeline-<timestamp>.html'`).
-
-`timeline.overwrite`
-: Overwrite any existing timeline file with the same name (default: `false`).
-
-(config-tower)=
-
-## `tower`
-
-The `tower` scope controls the settings for [Seqera Platform](https://seqera.io) (formerly Tower Cloud).
-
-The following settings are available:
-
-`tower.accessToken`
-: The unique access token for your Seqera Platform account.
-: Your `accessToken` can be obtained from your Seqera Platform instance in the [Tokens page](https://cloud.seqera.io/tokens).
-
-`tower.computeEnvId`
-: The compute environment ID in your Seqera Platform account used to launch pipelines (default: the primary compute environment in the selected workspace).
-
-`tower.enabled`
-: Enable workflow monitoring with Seqera Platform (default: `false`).
-
-`tower.endpoint`
-: The endpoint of your Seqera Platform instance (default: `https://api.cloud.seqera.io`).
-
-`tower.workspaceId`
-: The workspace ID in Seqera Platform in which to save the run (default: the launching user's personal workspace).
-: The workspace ID can also be specified using the environment variable `TOWER_WORKSPACE_ID` (config file has priority over the environment variable).
-
-(config-trace)=
-
-## `trace`
-
-The `trace` scope controls the layout of the execution trace file generated by Nextflow.
-
-The following settings are available:
-
-`trace.enabled`
-: Create the execution trace file on workflow completion (default: `false`).
-
-`trace.fields`
-: Comma-separated list of {ref}`trace fields <trace-fields>` to include in the report.
-
-`trace.file`
-: Trace file name (default: `'trace-<timestamp>.txt'`).
-
-`trace.overwrite`
-: Overwrite any existing trace file with the same name (default: `false`).
-
-`trace.raw`
-: Report trace metrics as raw numbers where applicable, i.e. report duration values in milliseconds and memory values in bytes (default: `false`).
-
-`trace.sep`
-: Character used to separate values in each row (default: `\t`).
-
-(config-wave)=
-
-## `wave`
-
-The `wave` scope provides advanced configuration for the use of {ref}`Wave containers <wave-page>`.
-
-The following settings are available:
-
-`wave.enabled`
-: Enable the use of Wave containers (default: `false`).
-
-`wave.endpoint`
-: The Wave service endpoint (default: `https://wave.seqera.io`).
-
-`wave.freeze`
-: :::{versionadded} 23.07.0-edge
-  :::
-: Enable Wave container freezing (default: `false`). Wave will provision a non-ephemeral container image that will be pushed to a container repository of your choice.
-: The target registry must be specified using the `wave.build.repository` setting. It is also recommended to specify a custom cache repository using `wave.build.cacheRepository`.
-: :::{note}
-  The container registry authentication must be managed by the underlying infrastructure.
-  :::
-
-`wave.mirror`
-: :::{versionadded} 24.09.1-edge
-  :::
-: Enable Wave container mirroring (default: `false`). Wave will mirror (i.e. copy) the containers in your pipeline to a container registry of your choice, so that pipeline tasks can pull the containers from this registry instead of the original one.
-: The mirrored containers will have the same name, digest, and metadata.
-: The target registry must be specified using the `wave.build.repository` setting.
-: This option is only compatible with `wave.strategy = 'container'`. It cannot be used with `wave.freeze`.
-: :::{note}
-  The container registry authentication must be managed by the underlying infrastructure.
-  :::
-
-`wave.strategy`
-: The strategy to be used when resolving multiple Wave container requirements (default: `'container,dockerfile,conda'`).
-
-`wave.build.cacheRepository`
-: The container repository used to cache image layers built by the Wave service.
-: The corresponding credentials must be provided in your Seqera Platform account.
-
-`wave.build.compression.mode`
-: :::{versionadded} 25.05.0-edge
-  :::
-: The compression algorithm that should be used when building the container. Allowed values are: `gzip`, `estargz` and `zstd` (default: `gzip`).
-
-`wave.build.compression.level`
-: :::{versionadded} 25.05.0-edge
-  :::
-: Level of compression used when building a container depending the chosen algorithm: gzip, estargz (0-9) and zstd (0-22).
-
-`wave.build.compression.force`
-: :::{versionadded} 25.05.0-edge
-  :::
-: Forcefully apply compression option to all layers, including already existing layers (default: `false`).
-
-`wave.build.conda.basePackages`
-: One or more Conda packages to be always added in the resulting container (default: `conda-forge::procps-ng`).
-
-`wave.build.conda.commands`
-: One or more commands to be added to the Dockerfile used to build a Conda based image.
-
-`wave.build.conda.mambaImage`
-: The Mamba container image is used to build Conda based container. This is expected to be [micromamba-docker](https://github.com/mamba-org/micromamba-docker) image.
-
-`wave.build.repository`
-: The container repository where images built by Wave are uploaded.
-: The corresponding credentials must be provided in your Seqera Platform account.
-
-`wave.httpClient.connectTimeout`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The connection timeout for the Wave HTTP client (default: `30s`).
-
-`wave.httpClient.maxRate`
-: :::{versionadded} 25.01.0-edge
-  :::
-: The maximum request rate for the Wave HTTP client (default: `1/sec`).
-
-`wave.retryPolicy.delay`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The initial delay when a failing HTTP request is retried (default: `450ms`).
-
-`wave.retryPolicy.jitter`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The jitter factor used to randomly vary retry delays (default: `0.25`).
-
-`wave.retryPolicy.maxAttempts`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The max number of attempts a failing HTTP request is retried (default: `5`).
-
-`wave.retryPolicy.maxDelay`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The max delay when a failing HTTP request is retried (default: `90s`).
-
-`wave.scan.allowedLevels`
-: :::{versionadded} 24.09.1-edge
-  :::
-: Comma-separated list of allowed vulnerability levels when scanning containers for security vulnerabilities in `required` mode.
-
-: Allowed values are: `low`, `medium`, `high`, `critical`.
-
-: This option requires `wave.scan.mode = 'required'`.
-
-`wave.scan.mode`
-: :::{versionadded} 24.09.1-edge
-  :::
-: Enable Wave container security scanning. Wave will scan the containers in your pipeline for security vulnerabilities.
-
-: The following options can be specified:
-
-  `'none'`
-  : No security scanning is performed.
-
-  `'async'`
-  : The containers used by your pipeline are scanned for security vulnerabilities. The task execution is carried out regardless of the security scan result.
-
-  `'required'`
-  : The containers used by your pipeline are scanned for security vulnerabilities. The task is only executed if the corresponding container is free of vulnerabilities.
-
-(config-workflow)=
-
-## `workflow`
-
-:::{versionadded} 24.10.0
-:::
-
-The `workflow` scope provides workflow execution options.
-
-The following settings are available:
-
-`workflow.failOnIgnore`
-: :::{versionadded} 24.05.0-edge
-  :::
-: When `true`, the pipeline will exit with a non-zero exit code if any failed tasks are ignored using the `ignore` {ref}`error strategy <process-error-strategy>` (default: `false`).
-
-`workflow.onComplete`
-: Specify a closure that will be invoked at the end of a workflow run (including failed runs). See {ref}`workflow-handlers` for more information.
-
-`workflow.onError`
-: Specify a closure that will be invoked if a workflow run is terminated. See {ref}`workflow-handlers` for more information.
-
-`workflow.output.contentType`
-: *Currently only supported for S3.*
-: Specify the media type, also known as [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/MIME_types), of published files (default: `false`). Can be a string (e.g. `'text/html'`), or `true` to infer the content type from the file extension.
-
-`workflow.output.copyAttributes`
-: :::{versionadded} 25.01.0-edge
-  :::
-: *Currently only supported for local and shared filesystems.*
-: Copy file attributes (such as the last modified timestamp) to the published file (default: `false`).
-
-`workflow.output.enabled`
-: Enable or disable publishing (default: `true`).
-
-`workflow.output.ignoreErrors`
-: When `true`, the workflow will not fail if a file can't be published for some reason (default: `false`).
-
-`workflow.output.mode`
-: The file publishing method (default: `'symlink'`).
-
-: The following options are available:
-
-  `'copy'`
-  : Copy each file into the output directory.
-
-  `'copyNoFollow'`
-  : Copy each file into the output directory without following symlinks, i.e. only the link is copied.
-
-  `'link'`
-  : Create a hard link in the output directory for each file.
-
-  `'move'`
-  : Move each file into the output directory.
-  : Should only be used for files which are not used by downstream processes in the workflow.
-
-  `'rellink'`
-  : Create a relative symbolic link in the output directory for each file.
-
-  `'symlink'`
-  : Create an absolute symbolic link in the output directory for each output file.
-
-`workflow.output.overwrite`
-: When `true` any existing file in the specified folder will be overwritten (default: `'standard'`).
-
-: The following options are available:
-
-  `false`
-  : Never overwrite existing files.
-
-  `true`
-  : Always overwrite existing files.
-
-  `'deep'`
-  : Overwrite existing files when the file content is different.
-
-  `'lenient'`
-  : Overwrite existing files when the file size is different.
-
-  `'standard'`
-  : Overwrite existing files when the file size or last modified timestamp is different.
-
-`workflow.output.storageClass`
-: *Currently only supported for S3.*
-: Specify the storage class for published files.
-
-`workflow.output.tags`
-: *Currently only supported for S3.*
-: Specify arbitrary tags for published files.
-
-: For example:
-  ```groovy
-  workflow.output.tags = [FOO: 'hello', BAR: 'world']
-  ```
diff --git a/docs/reference/config.mdx b/docs/reference/config.mdx
new file mode 100644
index 0000000000..bad8e8de6b
--- /dev/null
+++ b/docs/reference/config.mdx
@@ -0,0 +1,2214 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Configuration options
+
+This page lists all of the available settings in the [Nextflow configuration][config-page].
+
+## Unscoped options
+
+The following settings are available:
+
+##### `bucketDir`
+
+The remote work directory used by hybrid workflows. Equivalent to the `-bucket-dir` option of the `run` command.
+
+##### `cleanup`
+
+Delete all files associated with a run in the work directory when the run completes successfully (default: `false`).
+
+:::warning
+This option will prevent the use of the *resume* feature on subsequent executions of that pipeline run.
+:::
+
+:::warning
+This option is not supported for remote work directories, such as Amazon S3, Google Cloud Storage, and Azure Blob Storage.
+:::
+
+##### `dumpHashes`
+
+If `true`, dump task hash keys in the log file, for debugging purposes. Equivalent to the `-dump-hashes` option of the `run` command.
+
+##### `outputDir`
+
+<AddedInVersion version="24.10.0">
+</AddedInVersion>
+
+The pipeline output directory. Equivalent to the `-output-dir` option of the `run` command.
+
+##### `resume`
+
+Enable the use of previously cached task executions. Equivalent to the `-resume` option of the `run` command.
+
+##### `workDir`
+
+The pipeline work directory. Equivalent to the `-work-dir` option of the `run` command.
+
+## `apptainer`
+
+The `apptainer` scope controls how [Apptainer](https://apptainer.org) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `apptainer.autoMounts`
+
+Automatically mount host paths in the executed container (default: `true`). It requires the `user bind control` feature to be enabled in your Apptainer installation.
+
+##### `apptainer.cacheDir`
+
+The directory where remote Apptainer images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+##### `apptainer.enabled`
+
+Execute tasks with Apptainer containers (default: `false`).
+
+##### `apptainer.engineOptions`
+
+Specify additional options supported by the Apptainer engine i.e. `apptainer [OPTIONS]`.
+
+##### `apptainer.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `apptainer.libraryDir`
+
+Directory where remote Apptainer images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+##### `apptainer.noHttps`
+
+Pull the Apptainer image with http protocol (default: `false`).
+
+##### `apptainer.ociAutoPull`
+
+<AddedInVersion version="23.12.0-edge">
+</AddedInVersion>
+
+When enabled, OCI (and Docker) container images are pulled and converted to the SIF format by the Apptainer run command, instead of Nextflow (default: `false`).
+
+:::note
+Leave `ociAutoPull` disabled if you are willing to build a Singularity/Apptainer native image with Wave (see the [Singularity][wave-singularity] section).
+:::
+
+
+##### `apptainer.pullTimeout`
+
+The amount of time the Apptainer pull can last, exceeding which the process is terminated (default: `20 min`).
+
+##### `apptainer.registry`
+
+The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `apptainer.runOptions`
+
+Specify extra command line options supported by `apptainer exec`.
+
+See the [Apptainer][container-apptainer] page to learn more about how to use Apptainer containers with Nextflow.
+
+## `aws`
+
+The `aws` scope controls the interactions with AWS, including AWS Batch and S3.
+
+The following settings are available:
+
+##### `aws.accessKey`
+
+AWS account access key.
+
+##### `aws.profile`
+
+<AddedInVersion version="22.12.0-edge">
+</AddedInVersion>
+
+AWS profile from `~/.aws/credentials`.
+
+##### `aws.region`
+
+AWS region (e.g. `us-east-1`).
+
+##### `aws.secretKey`
+
+AWS account secret key.
+
+##### `aws.batch.cliPath`
+
+The path where the AWS command line tool is installed in the host AMI.
+
+##### `aws.batch.delayBetweenAttempts`
+
+Delay between download attempts from S3 (default: `10 sec`).
+
+##### `aws.batch.executionRole`
+
+The AWS Batch [Execution Role](https://docs.aws.amazon.com/batch/latest/userguide/execution-IAM-role.html) ARN that needs to be used to execute the Batch Job. It is mandatory when using AWS Fargate.
+
+##### `aws.batch.jobRole`
+
+The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
+
+##### `aws.batch.logsGroup`
+
+<AddedInVersion version="22.09.0-edge">
+</AddedInVersion>
+
+The name of the logs group used by Batch Jobs (default: `/aws/batch/job`).
+
+##### `aws.batch.maxParallelTransfers`
+
+Max parallel upload/download transfer operations *per job* (default: `4`).
+
+##### `aws.batch.maxSpotAttempts`
+
+<AddedInVersion version="22.04.0">
+</AddedInVersion>
+
+<ChangedInVersion version="24.08.0-edge">
+The default value was changed from `5` to `0`.
+</ChangedInVersion>
+
+Max number of execution attempts of a job interrupted by a EC2 Spot reclaim event (default: `0`)
+
+##### `aws.batch.maxTransferAttempts`
+
+Max number of downloads attempts from S3 (default: `1`).
+
+##### `aws.batch.platformType`
+
+The compute platform type used by AWS Batch. Can be either `ec2` or `fargate`. Set to `fargate` to use [AWS Fargate](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html).
+
+##### `aws.batch.retryMode`
+
+The [retry mode](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-retries.html) used to handle rate-limiting by AWS APIs. Can be one of `standard`, `legacy`, `adaptive`, or `built-in` (default: `standard`).
+
+##### `aws.batch.schedulingPriority`
+
+<AddedInVersion version="23.01.0-edge">
+</AddedInVersion>
+
+The scheduling priority for all tasks when using [fair-share scheduling](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/) (default: `0`).
+
+##### `aws.batch.shareIdentifier`
+
+<AddedInVersion version="22.09.0-edge">
+</AddedInVersion>
+
+The share identifier for all tasks when using [fair-share scheduling](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/).
+
+##### `aws.batch.terminateUnschedulableJobs`
+
+<AddedInVersion version="25.03.0-edge">
+</AddedInVersion>
+
+When `true`, jobs that cannot be scheduled due to lack of resources or misconfiguration are terminated and handled as task failures (default: `false`).
+
+##### `aws.batch.volumes`
+
+List of container mounts. Mounts can be specified as simple e.g. `/some/path` or canonical format e.g. `/host/path:/mount/path[:ro|rw]`.
+
+##### `aws.client.anonymous`
+
+Allow the access of public S3 buckets without providing AWS credentials (default: `false`). Any service that does not accept unsigned requests will return a service access error.
+
+##### `aws.client.connectionTimeout`
+
+The amount of time to wait (in milliseconds) when initially establishing a connection before timing out (default: `10000`).
+
+##### `aws.client.endpoint`
+
+The AWS S3 API entry point e.g. `https://s3-us-west-1.amazonaws.com`. The endpoint must include the protocol prefix e.g. `https://`.
+
+##### `aws.client.maxConcurrency`
+
+<AddedInVersion version="25.06.0-edge" />
+
+The maximum number of concurrent S3 transfers used by the S3 transfer manager. By default, this setting is determined by `aws.client.targetThroughputInGbps`. Modifying this value can affect the amount of memory used for S3 transfers.
+
+##### `aws.client.maxConnections`
+
+The maximum number of open HTTP connections used by the S3 client (default: `50`).
+
+##### `aws.client.maxDownloadHeapMemory`
+
+The maximum size for the heap memory buffer used by concurrent downloads. It must be at least 10 times the `minimumPartSize` (default:`400 MB`).
+
+##### `aws.client.maxErrorRetry`
+
+The maximum number of retry attempts for failed retryable requests (default: `-1`).
+
+##### `aws.client.maxNativeMemory`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The maximum native memory used by the S3 transfer manager. By default, this setting is determined by `aws.client.targetThroughputInGbps`.
+
+##### `aws.client.minimumPartSize`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The minimum part size used for multipart S3 transfers (default: `8 MB`).
+
+##### `aws.client.multipartThreshold`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The object size threshold used for multipart S3 transfers (default: same as `aws.cllient.minimumPartSize`).
+
+##### `aws.client.protocol`
+
+<AddedInVersion version="25.06.0-edge" />
+
+The protocol to use when connecting to AWS. Can be `http` or `https` (default: `'https'`).
+
+##### `aws.client.proxyHost`
+
+The proxy host to connect through.
+
+##### `aws.client.proxyPassword`
+
+The password to use when connecting through a proxy.
+
+##### `aws.client.proxyPort`
+
+The port to use when connecting through a proxy.
+
+##### `aws.client.proxyScheme`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The protocol scheme to use when connecting through a proxy. Can be `http` or `https` (default: `'http'`).
+
+##### `aws.client.proxyUsername`
+
+The user name to use when connecting through a proxy.
+
+##### `aws.client.requesterPays`
+
+<AddedInVersion version="24.05.0-edge">
+</AddedInVersion>
+
+Use [Requester Pays](https://docs.aws.amazon.com/AmazonS3/latest/userguide/RequesterPaysBuckets.html) for S3 buckets (default: `false`).
+
+##### `aws.client.s3Acl`
+
+Specify predefined bucket permissions, also known as [canned ACL](https://docs.aws.amazon.com/AmazonS3/latest/userguide/acl-overview.html#canned-acl). Can be one of `Private`, `PublicRead`, `PublicReadWrite`, `AuthenticatedRead`, `LogDeliveryWrite`, `BucketOwnerRead`, `BucketOwnerFullControl`, or `AwsExecRead`.
+
+##### `aws.client.s3PathStyleAccess`
+
+Use the path-based access model to access objects in S3-compatible storage systems (default: `false`).
+
+##### `aws.client.signerOverride`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The name of the signature algorithm to use for signing requests made by the client.
+
+##### `aws.client.socketSendBufferSizeHint`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The Size hint (in bytes) for the low level TCP send buffer (default: `0`).
+
+##### `aws.client.socketRecvBufferSizeHint`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The Size hint (in bytes) for the low level TCP receive buffer (default: `0`).
+
+##### `aws.client.socketTimeout`
+
+The amount of time to wait (in milliseconds) for data to be transferred over an established, open connection before the connection is timed out (default: `50000`).
+
+##### `aws.client.storageClass`
+
+The S3 storage class applied to stored objects, one of \[`STANDARD`, `STANDARD_IA`, `ONEZONE_IA`, `INTELLIGENT_TIERING`\] (default: `STANDARD`).
+
+##### `aws.client.storageEncryption`
+
+The S3 server side encryption to be used when saving objects on S3. Can be `AES256` or `aws:kms` (default: none).
+
+##### `aws.client.storageKmsKeyId`
+
+<AddedInVersion version="25.05.0-edge">
+</AddedInVersion>
+
+The AWS KMS key Id to be used to encrypt files stored in the target S3 bucket.
+
+##### `aws.client.targetThroughputInGbps`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The target network throughput (in Gbps) used for S3 uploads and downloads (default: `10`).
+
+The number of threads used by the S3 transfer manager (default: `10`).
+
+##### `aws.client.userAgent`
+
+<DeprecatedInVersion version="25.06.0-edge">
+</DeprecatedInVersion>
+
+The HTTP user agent header passed with all HTTP requests.
+
+##### `aws.client.uploadChunkSize`
+
+<DeprecatedInVersion version="25.06.0-edge">
+</DeprecatedInVersion>
+
+The size of a single part in a multipart upload (default: `100 MB`).
+
+##### `aws.client.uploadMaxAttempts`
+
+<DeprecatedInVersion version="25.06.0-edge">
+</DeprecatedInVersion>
+
+The maximum number of upload attempts after which a multipart upload returns an error (default: `5`).
+
+##### `aws.client.uploadMaxThreads`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The maximum number of threads used for multipart upload (default: `10`).
+
+##### `aws.client.uploadRetrySleep`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The time to wait after a failed upload attempt to retry the part upload (default: `500ms`).
+
+##### `aws.client.uploadStorageClass`
+
+The S3 storage class applied to stored objects. Can be `STANDARD`, `STANDARD_IA`, `ONEZONE_IA`, or `INTELLIGENT_TIERING` (default: `STANDARD`).
+
+## `azure`
+
+The `azure` scope allows you to configure the interactions with Azure, including Azure Batch and Azure Blob Storage.
+
+The following settings are available:
+
+##### `azure.activeDirectory.servicePrincipalId`
+
+The service principal client ID. Defaults to environment variable `AZURE_CLIENT_ID`.
+
+##### `azure.activeDirectory.servicePrincipalSecret`
+
+The service principal client secret. Defaults to environment variable `AZURE_CLIENT_SECRET`.
+
+##### `azure.activeDirectory.tenantId`
+
+The Azure tenant ID. Defaults to environment variable `AZURE_TENANT_ID`.
+
+##### `azure.azcopy.blobTier`
+
+The blob [access tier](https://learn.microsoft.com/en-us/azure/storage/blobs/access-tiers-overview) used by `azcopy` to upload files to Azure Blob Storage. Valid options are `None`, `Hot`, or `Cool` (default: `None`).
+
+##### `azure.azcopy.blockSize`
+
+The block size (in MB) used by `azcopy` to transfer files between Azure Blob Storage and compute nodes (default: `4`).
+
+##### `azure.batch.accountKey`
+
+The batch service account key. Defaults to environment variable `AZURE_BATCH_ACCOUNT_KEY`.
+
+##### `azure.batch.accountName`
+
+The batch service account name. Defaults to environment variable `AZURE_BATCH_ACCOUNT_NAME`.
+
+##### `azure.batch.allowPoolCreation`
+
+Enable the automatic creation of batch pools specified in the Nextflow configuration file (default: `false`).
+
+##### `azure.batch.autoPoolMode`
+
+Enable the automatic creation of batch pools depending on the pipeline resources demand (default: `true`).
+
+##### `azure.batch.copyToolInstallMode`
+
+The mode in which the `azcopy` tool is installed by Nextflow (default: `'node'`).
+
+The following options are available:
+
+###### `'node'`
+
+The `azcopy` tool is installed once during the pool creation.
+
+###### `'task'`
+
+The `azcopy` tool is installed for each task execution.
+
+###### `'off'`
+
+The `azcopy` tool is not installed.
+
+##### `azure.batch.deleteJobsOnCompletion`
+
+<ChangedInVersion version="24.08.0-edge">
+Default value was changed from `true` to `false`.
+</ChangedInVersion>
+
+Delete all jobs when the workflow completes (default: `false`).
+
+##### `azure.batch.deletePoolsOnCompletion`
+
+Delete all compute node pools when the workflow completes (default: `false`).
+
+##### `azure.batch.deleteTasksOnCompletion`
+
+<AddedInVersion version="23.08.0-edge">
+</AddedInVersion>
+
+Delete each task when it completes (default: `true`).
+Although this setting is enabled by default, failed tasks will not be deleted unless it is explicitly enabled. This way, the default behavior is that successful tasks are deleted while failed tasks are preserved for debugging purposes.
+
+##### `azure.batch.endpoint`
+
+The batch service endpoint e.g. `https://nfbatch1.westeurope.batch.azure.com`.
+
+##### `azure.batch.jobMaxWallClockTime`
+
+<AddedInVersion version="25.04.0">
+</AddedInVersion>
+
+The maximum elapsed time that jobs may run, measured from the time they are created (default: `30d`).
+
+If jobs do not complete within this time limit, the Batch service terminates them and any tasks still running.
+
+##### `azure.batch.location`
+
+The name of the batch service region, e.g. `westeurope` or `eastus2`. Not needed when the endpoint is specified.
+
+#####`azure.batch.poolIdentityClientId`
+
+<AddedInVersion version="25.05.0-edge" />
+
+The client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) that is available on all Azure Batch node pools. This identity is used by Fusion to authenticate to Azure storage. If set to `'auto'`, Fusion will use the first available managed identity.
+
+##### `azure.batch.pools.<name>.autoScale`
+
+Enable autoscaling feature for the pool identified with `<name>`.
+
+##### `azure.batch.pools.<name>.fileShareRootPath`
+
+The internal root mount point when mounting File Shares. Must be `/mnt/resource/batch/tasks/fsmounts` for CentOS nodes or `/mnt/batch/tasks/fsmounts` for Ubuntu nodes (default: CentOS).
+
+##### `azure.batch.pools.<name>.lowPriority`
+
+Enable the use of low-priority VMs (default: `false`).
+
+:::warning
+As of September 30, 2025, Low Priority VMs will no longer be supported in Azure Batch accounts that use Batch Managed mode for pool allocation.
+You may continue to use this setting to configure Spot VMs in Batch accounts configured with User Subscription mode.
+:::
+
+##### `azure.batch.pools.<name>.maxVmCount`
+
+The max number of virtual machines when using auto scaling.
+
+##### `azure.batch.pools.<name>.mountOptions`
+
+The mount options for mounting the file shares (default: `-o vers=3.0,dir_mode=0777,file_mode=0777,sec=ntlmssp`).
+
+##### `azure.batch.pools.<name>.offer`
+
+The offer type of the virtual machine type used by the pool identified with `<name>` (default: `centos-container`).
+
+##### `azure.batch.pools.<name>.privileged`
+
+Enable the task to run with elevated access. Ignored if `runAs` is set (default: `false`).
+
+##### `azure.batch.pools.<name>.publisher`
+
+The publisher of virtual machine type used by the pool identified with `<name>` (default: `microsoft-azure-batch`).
+
+##### `azure.batch.pools.<name>.runAs`
+
+The username under which the task is run. The user must already exist on each node of the pool.
+
+##### `azure.batch.pools.<name>.scaleFormula`
+
+The [scale formula](https://docs.microsoft.com/en-us/azure/batch/batch-automatic-scaling) for the pool identified with `<name>`.
+
+##### `azure.batch.pools.<name>.scaleInterval`
+
+The interval at which to automatically adjust the Pool size according to the autoscale formula. Must be at least 5 minutes and at most 168 hours (default: `10 mins`).
+
+##### `azure.batch.pools.<name>.schedulePolicy`
+
+The scheduling policy for the pool identified with `<name>`. Can be either `spread` or `pack` (default: `spread`).
+
+##### `azure.batch.pools.<name>.sku`
+
+The ID of the Compute Node agent SKU which the pool identified with `<name>` supports (default: `batch.node.centos 8`).
+
+##### `azure.batch.pools.<name>.startTask.privileged`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+Enable the `startTask` to run with elevated access (default: `false`).
+
+##### `azure.batch.pools.<name>.startTask.script`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+The `startTask` that is executed as the node joins the Azure Batch node pool.
+
+##### `azure.batch.pools.<name>.virtualNetwork`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+The subnet ID of a virtual network in which to create the pool.
+
+##### `azure.batch.pools.<name>.vmCount`
+
+The number of virtual machines provisioned by the pool identified with `<name>`.
+
+##### `azure.batch.pools.<name>.vmType`
+
+Specify the virtual machine type used by the pool identified with `<name>`.
+
+##### `azure.batch.terminateJobsOnCompletion`
+
+<AddedInVersion version="23.05.0-edge">
+</AddedInVersion>
+
+When the workflow completes, set all jobs to terminate on task completion (default: `true`).
+
+##### `azure.managedIdentity.clientId`
+
+The client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview). Defaults to environment variable `AZURE_MANAGED_IDENTITY_USER`.
+
+##### `azure.managedIdentity.system`
+
+ When `true`, use the system-assigned [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) to authenticate Azure resources. Defaults to environment variable `AZURE_MANAGED_IDENTITY_SYSTEM`.
+
+##### `azure.registry.password`
+
+The password to connect to a private container registry.
+
+##### `azure.registry.server`
+
+The container registry from which to pull the Docker images (default: `docker.io`).
+
+##### `azure.registry.userName`
+
+The username to connect to a private container registry.
+
+##### `azure.retryPolicy.delay`
+
+Delay when retrying failed API requests (default: `250ms`).
+
+##### `azure.retryPolicy.jitter`
+
+Jitter value when retrying failed API requests (default: `0.25`).
+
+##### `azure.retryPolicy.maxAttempts`
+
+Max attempts when retrying failed API requests (default: `10`).
+
+##### `azure.retryPolicy.maxDelay`
+
+Max delay when retrying failed API requests (default: `90s`).
+
+##### `azure.storage.accountKey`
+
+The blob storage account key. Defaults to environment variable `AZURE_STORAGE_ACCOUNT_KEY`.
+
+##### `azure.storage.accountName`
+
+The blob storage account name. Defaults to environment variable `AZURE_STORAGE_ACCOUNT_NAME`.
+
+##### `azure.storage.fileShares.<name>.mountOptions`
+
+The file share mount options.
+
+##### `azure storage.fileShares.<name>.mountPath`
+
+The file share mount path.
+
+##### `azure.storage.sasToken`
+
+The blob storage shared access signature (SAS) token, which can be provided instead of an account key. Defaults to environment variable `AZURE_STORAGE_SAS_TOKEN`.
+
+##### `azure.storage.tokenDuration`
+
+The duration of the SAS token generated by Nextflow when the `sasToken` option is *not* specified (default: `48h`).
+
+## `charliecloud`
+
+The `charliecloud` scope controls how [Charliecloud](https://hpc.github.io/charliecloud/) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `charliecloud.cacheDir`
+
+The directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+##### `charliecloud.enabled`
+
+Execute tasks with Charliecloud containers (default: `false`).
+
+##### `charliecloud.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `charliecloud.pullTimeout`
+
+The amount of time the Charliecloud pull can last, exceeding which the process is terminated (default: `20 min`).
+
+##### `charliecloud.registry`
+
+The registry from where images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `charliecloud.runOptions`
+
+Specify extra command line options supported by the `ch-run` command.
+
+##### `charliecloud.temp`
+
+Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
+
+##### `charliecloud.writableInputMounts`
+
+When `false`, mount input directories as read-only (default: `true`).
+
+##### `charliecloud.writeFake`
+
+Run containers from storage in writeable mode using overlayfs (default: `true`).
+
+This option requires unprivileged `overlayfs` (Linux kernel >= 5.11). For full support, tempfs with xattrs in the user namespace (Linux kernel >= 6.6) is required. See [charliecloud documentation](https://hpc.github.io/charliecloud/ch-run.html#ch-run-overlay) for details.
+
+## `conda`
+
+The `conda` scope controls the creation of Conda environments by the Conda package manager.
+
+The following settings are available:
+
+##### `conda.cacheDir`
+
+The path where Conda environments are stored. It should be accessible from all compute nodes when using a shared file system.
+
+##### `conda.channels`
+
+The list of Conda channels that can be used to resolve Conda packages. Channel priority decreases from left to right.
+
+##### `conda.createOptions`
+
+Extra command line options for the `conda create` command. See the [Conda documentation](https://docs.conda.io/projects/conda/en/latest/commands/create.html) for more information.
+
+##### `conda.createTimeout`
+
+The amount of time to wait for the Conda environment to be created before failing (default: `20 min`).
+
+##### `conda.enabled`
+
+Execute tasks with Conda environments (default: `false`).
+
+##### `conda.useMamba`
+
+Use [Mamba](https://github.com/mamba-org/mamba) instead of `conda` to create Conda environments (default: `false`).
+
+<AddedInVersion version="25.05.0-edge">
+</AddedInVersion>
+
+Use [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) instead of `conda` to create Conda environments (default: `false`).
+
+See [Conda][conda-page] for more information about using Conda environments with Nextflow.
+
+## `dag`
+
+The `dag` scope controls the workflow diagram generated by Nextflow.
+
+The following settings are available:
+
+##### `dag.enabled`
+
+When `true` enables the generation of the DAG file (default: `false`).
+
+##### `dag.depth`
+
+<AddedInVersion version="23.10.0">
+</AddedInVersion>
+
+*Supported by the HTML and Mermaid renderers.*
+
+Controls the maximum depth at which to render sub-workflows (default: no limit).
+
+##### `dag.direction`
+
+<AddedInVersion version="23.10.0">
+</AddedInVersion>
+
+*Supported by Graphviz, DOT, HTML and Mermaid renderers.*
+
+Controls the direction of the DAG, can be `'LR'` (left-to-right) or `'TB'` (top-to-bottom) (default: `'TB'`).
+
+##### `dag.enabled`
+
+When `true` enables the generation of the DAG file (default: `false`).
+
+##### `dag.file`
+
+Graph file name (default: `'dag-<timestamp>.html'`).
+
+##### `dag.overwrite`
+
+When `true` overwrites any existing DAG file with the same name (default: `false`).
+
+##### `dag.verbose`
+
+<AddedInVersion version="23.10.0">
+</AddedInVersion>
+
+*Only supported by the HTML and Mermaid renderers.*
+
+When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`).
+
+## `docker`
+
+The `docker` scope controls how [Docker](https://www.docker.com) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `docker.enabled`
+
+Enable Docker execution (default: `false`).
+
+##### `docker.engineOptions`
+
+Specify additional options supported by the Docker engine i.e. `docker [OPTIONS]`.
+
+##### `docker.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `docker.fixOwnership`
+
+Fix ownership of files created by the Docker container (default: `false`).
+
+##### `docker.legacy`
+
+Use command line options removed since Docker 1.10.0 (default: `false`).
+
+##### `docker.mountFlags`
+
+Add the specified flags to the volume mounts e.g. `'ro,Z'`.
+
+##### `docker.registry`
+
+The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `docker.registryOverride`
+
+<AddedInVersion version="25.06.0-edge" />
+
+When `true`, forces the override of the registry name in fully qualified container image names with the registry specified by `docker.registry` (default: `false`).
+
+This setting allows you to redirect container image pulls from their original registry to a different registry, such as a private mirror or proxy.
+
+##### `docker.remove`
+
+Clean up the container after the execution (default: `true`). See the [Docker documentation](https://docs.docker.com/engine/reference/run/#clean-up---rm) for details.
+
+##### `docker.runOptions`
+
+Specify extra command line options supported by the `docker run` command. See the [Docker documentation](https://docs.docker.com/engine/reference/run/) for details.
+
+##### `docker.sudo`
+
+Executes Docker run command as `sudo` (default: `false`).
+
+##### `docker.temp`
+
+Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
+
+##### `docker.tty`
+
+Allocates a pseudo-tty (default: `false`).
+
+##### `docker.writableInputMounts`
+
+When `false`, mount input directories as read-only (default: `true`).
+
+## `env`
+
+The `env` scope allows the definition one or more variables that will be exported into the environment where workflow tasks are executed.
+
+Simply prefix your variable names with the `env` scope or surround them by curly brackets, as shown below:
+
+```groovy
+env.ALPHA = 'some value'
+env.BETA = "$HOME/some/path"
+
+env {
+     DELTA = 'one more'
+     GAMMA = "/my/path:$PATH"
+}
+```
+
+:::note
+In the above example, variables like `$HOME` and `$PATH` are evaluated when the workflow is launched. If you want these variables to be evaluated during task execution, escape them with `\$`. This difference is important for variables like `$PATH`, which may be different in the workflow environment versus the task environment.
+:::
+
+:::warning
+The `env` scope provides environment variables to *tasks*, not Nextflow itself. Nextflow environment variables such as `NXF_VER` should be set in the environment in which Nextflow is launched.
+:::
+
+## `executor`
+
+The `executor` scope controls various executor behaviors.
+
+The following settings are available:
+
+##### `executor.account`
+
+<AddedInVersion version="24.04.0">
+</AddedInVersion>
+
+*Used only by the [SLURM][slurm-executor], [LSF][lsf-executor], [PBS][pbs-executor] and [PBS Pro][pbspro-executor] executors.*
+The project or organization account that should be charged for running the pipeline jobs.
+
+##### `executor.cpus`
+
+*Used only by the local executor.*
+
+The maximum number of CPUs made available by the underlying system.
+
+##### `executor.dumpInterval`
+
+Determines how often to log the executor status (default: `5 min`).
+
+##### `executor.exitReadTimeout`
+
+*Used only by grid executors.*
+
+Determines how long to wait for the `.exitcode` file to be created after the task has completed, before returning an error status (default: `270 sec`).
+
+##### `executor.jobName`
+
+*Used only by grid executors and Google Batch.*
+
+Determines the name of jobs submitted to the underlying cluster executor:
+
+```groovy
+executor.jobName = { "$task.name - $task.hash" }
+```
+
+The job name should satisfy the validation constraints of the underlying scheduler.
+
+##### `executor.killBatchSize`
+
+Determines the number of jobs that can be killed in a single command execution (default: `100`).
+
+##### `executor.memory`
+
+*Used only by the local executor.*
+
+The maximum amount of memory made available by the underlying system.
+
+##### `executor.name`
+
+The name of the executor to be used (default: `local`).
+
+##### `executor.perCpuMemAllocation`
+
+<AddedInVersion version="23.07.0-edge">
+</AddedInVersion>
+
+*Used only by the [SLURM][slurm-executor] executor.*
+
+When `true`, memory allocations for SLURM jobs are specified as `--mem-per-cpu <task.memory / task.cpus>` instead of `--mem <task.memory>`.
+
+##### `executor.perJobMemLimit`
+
+*Used only by the [LSF][lsf-executor] executor.*
+
+Specifies Platform LSF *per-job* memory limit mode (default: `false`).
+
+##### `executor.perTaskReserve`
+
+*Used only by the [LSF][lsf-executor] executor.*
+
+Enables the *per-task* memory reserve mode for LSF jobs.
+
+##### `executor.pollInterval`
+
+Determines how often to check for process termination. Default varies for each executor.
+
+##### `executor.queueGlobalStatus`
+
+<AddedInVersion version="23.01.0-edge">
+</AddedInVersion>
+
+Determines how job status is retrieved. When `false` only the queue associated with the job execution is queried. When `true` the job status is queried globally i.e. irrespective of the submission queue (default: `false`).
+
+##### `executor.queueSize`
+
+The number of tasks the executor will handle in a parallel manner. A queue size of zero corresponds to no limit. Default varies for each executor.
+
+##### `executor.queueStatInterval`
+
+*Used only by grid executors.*
+
+Determines how often to fetch the queue status from the scheduler (default: `1 min`).
+
+##### `executor.submitRateLimit`
+
+Determines the max rate of job submission per time unit, for example `'10sec'` (10 jobs per second) or `'50/2min'` (50 jobs every 2 minutes) (default: unlimited).
+
+##### `executor.retry.delay`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+*Used only by grid executors.*
+
+Delay when retrying failed job submissions (default: `500ms`).
+
+##### `executor.retry.jitter`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+*Used only by grid executors.*
+
+Jitter value when retrying failed job submissions (default: `0.25`).
+
+##### `executor.retry.maxAttempt`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+*Used only by grid executors.*
+
+Max attempts when retrying failed job submissions (default: `3`).
+
+##### `executor.retry.maxDelay`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+*Used only by grid executors.*
+
+Max delay when retrying failed job submissions (default: `30s`).
+
+##### `executor.retry.reason`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+<ChangedInVersion version="23.03.0-edge">
+This option was renamed from `executor.submit.retry.reason` to `executor.retry.reason`.
+</ChangedInVersion>
+
+*Used only by grid executors.*
+
+Regex pattern that when verified causes a failed submit operation to be re-tried (default: `Socket timed out`).
+
+### Executor-specific defaults
+
+Some executor settings have different default values depending on the executor.
+
+| Executor       | `queueSize` | `pollInterval` |
+| -------------- | ----------- | -------------- |
+| AWS Batch      | `1000`      | `10s`          |
+| Azure Batch    | `1000`      | `10s`          |
+| Google Batch   | `1000`      | `10s`          |
+| Grid Executors | `100`       | `5s`           |
+| Kubernetes     | `100`       | `5s`           |
+| Local          | N/A         | `100ms`        |
+
+### Executor-specific configuration
+
+Executor config settings can be applied to specific executors by prefixing the executor name with the symbol `$` and using it as special scope. For example:
+
+```groovy
+// block syntax
+executor {
+  $sge {
+      queueSize = 100
+      pollInterval = '30sec'
+  }
+
+  $local {
+      cpus = 8
+      memory = '32 GB'
+  }
+}
+
+// dot syntax
+executor.$sge.queueSize = 100
+executor.$sge.pollInterval = '30sec'
+executor.$local.cpus = 8
+executor.$local.memory = '32 GB'
+```
+
+## `fusion`
+
+The `fusion` scope provides advanced configuration for the use of the [Fusion file system][fusion-page].
+
+The following settings are available:
+
+##### `fusion.cacheSize`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+The maximum size of the local cache used by the Fusion client.
+
+##### `fusion.containerConfigUrl`
+
+The URL of the container layer that provides the Fusion client.
+
+##### `fusion.enabled`
+
+Enable the Fusion file system (default: `false`).
+
+##### `fusion.exportStorageCredentials`
+
+Export access credentials required by the underlying object storage as environment variables (e.g., `AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY`, and `AWS_SESSION_TOKEN` for AWS S3) to task execution environments (default: `false`).
+
+:::note
+This configuration does not mount or provide access to credential files. For example, AWS credentials like `~/.aws/credentials`, `~/.aws/config`, and SSO cache files are not mounted. AWS SSO users must export credentials to environment variables:
+
+```bash
+eval "$(aws configure export-credentials --format env)"
+```
+:::
+
+:::warning
+This option leaks credentials is the task launcher script. It should only be used for testing and development purposes.
+:::
+
+##### `fusion.logLevel`
+
+The log level of the Fusion client.
+
+##### `fusion.logOutput`
+
+The output location of the Fusion log.
+
+##### `fusion.privileged`
+
+<AddedInVersion version="23.10.0-edge">
+</AddedInVersion>
+
+Enable privileged containers for Fusion (default: `true`)
+Non-privileged use is supported only on Kubernetes with the [k8s-fuse-plugin](https://github.com/nextflow-io/k8s-fuse-plugin) or a similar FUSE device plugin
+
+##### `fusion.snapshots`
+
+<AddedInVersion version="25.03.0-edge">
+</AddedInVersion>
+
+*Currently only supported for AWS Batch*
+
+Enable Fusion snapshotting (preview, default: `false`). This feature allows Fusion to automatically restore a job when it is interrupted by a spot reclamation.
+
+##### `fusion.tags`
+
+The pattern that determines how tags are applied to files created via the Fusion client (default: `[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`). Set to `false` to disable tags.
+
+## `google`
+
+The `google` scope allows you to configure the interactions with Google Cloud, including Google Cloud Batch and Google Cloud Storage.
+
+The following settings are available:
+
+##### `google.enableRequesterPaysBuckets`
+
+Use the given Google Cloud project ID as the billing project for storage access (default: `false`). Required when accessing data from [requester pays](https://cloud.google.com/storage/docs/requester-pays) buckets.
+
+##### `google.httpConnectTimeout`
+
+<AddedInVersion version="23.06.0-edge">
+</AddedInVersion>
+
+The HTTP connection timeout for Cloud Storage API requests (default: `'60s'`).
+
+##### `google.httpReadTimeout`
+
+<AddedInVersion version="23.06.0-edge">
+</AddedInVersion>
+
+The HTTP read timeout for Cloud Storage API requests (default: `'60s'`).
+
+##### `google.location`
+
+The Google Cloud location where jobs are executed (default: `us-central1`).
+
+##### `google.project`
+
+The Google Cloud project ID to use for pipeline execution.
+
+##### `google.batch.allowedLocations`
+
+<AddedInVersion version="22.12.0-edge">
+</AddedInVersion>
+
+The set of [allowed locations](https://cloud.google.com/batch/docs/reference/rest/v1/projects.locations.jobs#locationpolicy) for VMs to be provisioned (default: no restriction).
+
+##### `google.batch.autoRetryExitCodes`
+
+<AddedInVersion version="24.07.0-edge">
+</AddedInVersion>
+
+The list of exit codes that should be automatically retried by Google Batch when `google.batch.maxSpotAttempts` is greater than 0 (default: `[50001]`).
+See [Google Batch documentation](https://cloud.google.com/batch/docs/troubleshooting#reserved-exit-codes) for the complete list of exit codes.
+
+##### `google.batch.bootDiskImage`
+
+<AddedInVersion version="24.08.0-edge">
+</AddedInVersion>
+
+The image URI of the virtual machine boot disk, e.g `batch-debian` (default: none).
+See [Google documentation](https://cloud.google.com/batch/docs/vm-os-environment-overview#vm-os-image-options) for details.
+
+##### `google.batch.bootDiskSize`
+
+The size of the virtual machine boot disk, e.g `50.GB` (default: none).
+
+##### `google.batch.cpuPlatform`
+
+The [minimum CPU Platform](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications), e.g. `'Intel Skylake'` (default: none).
+
+##### `google.batch.gcsfuseOptions`
+
+<AddedInVersion version="25.03.0-edg">
+</AddedInVersion>
+
+List of custom mount options for `gcsfuse` (default: `['-o rw', '-implicit-dirs']`).
+
+##### `google.batch.maxSpotAttempts`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+<ChangedInVersion version="24.08.0-edge">
+The default value was changed from `5` to `0`.
+</ChangedInVersion>
+
+Max number of execution attempts of a job interrupted by a Compute Engine Spot reclaim event (default: `0`).
+See also: `google.batch.autoRetryExitCodes`
+
+##### `google.batch.network`
+
+The URL of an existing network resource to which the VM will be attached.
+
+Specify the network as a full or partial URL. For example, the following are all valid URLs:
+
+- `https://www.googleapis.com/compute/v1/projects/\{project\}/global/networks/\{network\}`
+- `projects/\{project\}/global/networks/\{network\}`
+- `global/networks/\{network\}`
+
+##### `google.batch.networkTags`
+
+The [network tags](https://cloud.google.com/vpc/docs/add-remove-network-tags) to be applied to the instances created by Google Batch jobs (e.g., `['allow-ssh', 'allow-http']`).
+
+Network tags are ignored when using instance templates.
+
+##### `google.batch.serviceAccountEmail`
+
+The Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
+
+This service account will only be used for tasks submitted by Nextflow, not for Nextflow itself. See [Credentials][google-credentials] for more information on Google Cloud credentials.
+
+##### `google.batch.spot`
+
+Enable the use of spot virtual machines (default: `false`).
+
+##### `google.batch.subnetwork`
+
+The URL of an existing subnetwork resource in the network to which the VM will be attached.
+
+You can specify the subnetwork as a full or partial URL. For example, the following are all valid URLs:
+
+- `https://www.googleapis.com/compute/v1/projects/\{project\}/regions/\{region\}/subnetworks/\{subnetwork\}`
+- `projects/\{project\}/regions/\{region}/subnetworks/\{subnetwork\}`
+- `regions/\{regio\n}/subnetworks/\{subnetwork\}`
+
+##### `google.batch.usePrivateAddress`
+
+Do not provision public IP addresses for VMs, such that they only have an internal IP address (default: `false`).
+
+When this option is enabled, jobs can only load Docker images from Google Container Registry, and cannot use external services other than Google APIs.
+
+##### `google.storage.retryPolicy.maxAttempts`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+Max attempts when retrying failed API requests to Cloud Storage (default: `10`).
+
+##### `google.storage.retryPolicy.maxDelay`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+Max delay when retrying failed API requests to Cloud Storage (default: `'90s'`).
+
+##### `google.storage.retryPolicy.multiplier`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+Delay multiplier when retrying failed API requests to Cloud Storage (default: `2.0`).
+
+## `k8s`
+
+The `k8s` scope controls the deployment and execution of workflow applications in a Kubernetes cluster.
+
+The following settings are available:
+
+##### `k8s.autoMountHostPaths`
+
+Automatically mount host paths into the task pods (default: `false`). Only intended for development purposes when using a single node.
+
+##### `k8s.cleanup`
+
+When `true`, successful pods are automatically deleted (default: `true`).
+
+##### `k8s.client`
+
+Map of options for the Kubernetes HTTP client.
+If this option is specified, it will be used instead of `.kube/config`.
+
+The following options are available:
+
+- `server`
+- `token`
+- `tokenFile`
+- `verifySsl`
+- `sslCert`
+- `sslCertFile`
+- `clientCert`
+- `clientCertFile`
+- `clientKey`
+- `clientKeyFile`
+
+##### `k8s.computeResourceType`
+
+<AddedInVersion version="22.05.0-edge">
+</AddedInVersion>
+
+Whether to use Kubernetes `Pod` or `Job` resource type to carry out Nextflow tasks (default: `Pod`).
+
+##### `k8s.context`
+
+The Kubernetes [configuration context](https://kubernetes.io/docs/tasks/access-application-cluster/configure-access-multiple-clusters/) to use.
+
+##### `k8s.cpuLimits`
+
+<AddedInVersion version="24.04.0-edge">
+</AddedInVersion>
+
+When `true`, set both the pod CPUs `request` and `limit` to the value specified by the `cpus` directive, otherwise set only the `request` (default: `false`).
+
+This setting is useful when a K8s cluster requires a CPU limit to be defined through a [LimitRange](https://kubernetes.io/docs/concepts/policy/limit-range/).
+
+##### `k8s.fetchNodeName`
+
+<AddedInVersion version="22.05.0-edge">
+</AddedInVersion>
+
+Include the hostname of each task in the execution trace (default: `false`).
+
+##### `k8s.fuseDevicePlugin`
+
+<AddedInVersion version="24.01.0-edge">
+</AddedInVersion>
+
+The FUSE device plugin to be used when enabling Fusion in unprivileged mode (default: `['nextflow.io/fuse': 1]`).
+
+##### `k8s.httpConnectTimeout`
+
+<AddedInVersion version="22.10.0">
+</AddedInVersion>
+
+The Kubernetes HTTP client request connection timeout e.g. `'60s'`.
+
+##### `k8s.httpReadTimeout`
+
+<AddedInVersion version="22.10.0">
+</AddedInVersion>
+
+The Kubernetes HTTP client request connection read timeout e.g. `'60s'`.
+
+##### `k8s.imagePullPolicy`
+
+The strategy for pulling container images. Can be `IfNotPresent`, `Always`, `Never`.
+
+##### `k8s.launchDir`
+
+The path where the workflow is launched and the user data is stored (default: `<volume-claim-mount-path>/<user-name>`). Must be a path in a shared K8s persistent volume.
+
+##### `k8s.namespace`
+
+The Kubernetes namespace to use (default: `default`).
+
+##### `k8s.pod`
+
+Additional pod configuration options such as environment variables, config maps, secrets, etc. Allows the same settings as the [pod][process-pod] process directive.
+
+When using the `kuberun` command, this setting also applies to the submitter pod.
+
+##### `k8s.projectDir`
+
+The path where Nextflow projects are downloaded (default: `<volume-claim-mount-path>/projects`). Must be a path in a shared K8s persistent volume.
+
+##### `k8s.runAsUser`
+
+The user ID to be used to run the containers. Shortcut for the `securityContext` option.
+
+##### `k8s.securityContext`
+
+The [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) to use for all pods.
+
+##### `k8s.serviceAccount`
+
+The Kubernetes [service account name](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/) to use.
+
+##### `k8s.storageClaimName`
+
+The name of the persistent volume claim where the shared work directory is stored.
+
+##### `k8s.storageMountPath`
+
+The mount path for the persistent volume claim (default: `/workspace`).
+
+##### `k8s.storageSubPath`
+
+The path in the persistent volume to be mounted (default: `/`).
+
+##### `k8s.workDir`
+
+The path of the shared work directory (default: `<user-dir>/work`). Must be a path in a shared K8s persistent volume.
+
+##### `k8s.debug.yaml`
+
+Save the pod spec for each task to `.command.yaml` in the task directory (default: `false`).
+
+##### `k8s.retryPolicy.delay`
+
+Delay when retrying failed API requests (default: `250ms`).
+
+##### `k8s.retryPolicy.jitter`
+
+Jitter value when retrying failed API requests (default: `0.25`).
+
+##### `k8s.retryPolicy.maxAttempts`
+
+Max attempts when retrying failed API requests (default: `4`).
+
+##### `k8s.retryPolicy.maxDelay`
+
+Max delay when retrying failed API requests (default: `90s`).
+
+## `lineage`
+
+The `lineage` scope controls the generation of [lineage][cli-lineage] metadata.
+
+The following settings are available:
+
+##### `lineage.enabled`
+
+Enable generation of lineage metadata (default: `false`).
+
+##### `lineage.store.location`
+
+The location of the lineage metadata store (default: `./.lineage`).
+
+## `mail`
+
+The `mail` scope controls the mail server used to send email notifications.
+
+The following settings are available:
+
+##### `mail.debug`
+
+Enable Java Mail logging for debugging purposes (default: `false`).
+
+##### `mail.from`
+
+Default email sender address.
+
+##### `mail.smtp.host`
+
+Host name of the mail server.
+
+##### `mail.smtp.password`
+
+User password to connect to the mail server.
+
+##### `mail.smtp.port`
+
+Port number of the mail server.
+
+##### `mail.smtp.user`
+
+User name to connect to the mail server.
+
+##### `mail.smtp.proxy.host`
+
+Host name of an HTTP web proxy server that will be used for connections to the mail server.
+
+##### `mail.smtp.proxy.port`
+
+Port number for the HTTP web proxy server.
+
+##### `mail.smtp.*`
+
+Any SMTP configuration property supported by the [Java Mail API](https://javaee.github.io/javamail/), which Nextflow uses to send emails. See the table of available properties [here](https://javaee.github.io/javamail/docs/api/com/sun/mail/smtp/package-summary.html#properties).
+
+## `manifest`
+
+The `manifest` scope allows you to define some metadata that is useful when publishing or running your pipeline.
+
+The following settings are available:
+
+##### `manifest.author`
+
+<DeprecatedInVersion version="24.09.0-edge">
+Use `manifest.contributors` instead.
+</DeprecatedInVersion>
+
+Project author name (use a comma to separate multiple names).
+
+##### `manifest.contributors`
+
+<AddedInVersion version="24.09.0-edge">
+</AddedInVersion>
+
+List of project contributors. Should be a list of maps.
+
+The following fields are supported in the contributor map:
+
+###### `name`
+
+The contributor's name.
+
+###### `affiliation`
+
+The contributor's affiliated organization.
+
+###### `email`
+
+The contributor's email address.
+
+###### `github`
+
+The contributor's GitHub URL.
+
+###### `contribution`
+
+List of contribution types, each element can be one of `'author'`, `'maintainer'`, or `'contributor'`.
+
+###### `orcid`
+
+The contributor's [ORCID](https://orcid.org/) URL.
+
+##### `manifest.defaultBranch`
+
+Git repository default branch (default: `master`).
+
+##### `manifest.description`
+
+Free text describing the workflow project.
+
+##### `manifest.docsUrl`
+
+Project documentation URL.
+
+##### `manifest.doi`
+
+Project related publication DOI identifier.
+
+##### `manifest.gitmodules`
+
+Controls whether git sub-modules should be cloned with the main repository.
+Can be either a boolean value, a list of submodule names, or a comma-separated string of submodule names.
+
+##### `manifest.homePage`
+
+Project home page URL.
+
+##### `manifest.icon`
+
+Project related icon location (Relative path or URL).
+
+##### `manifest.license`
+
+Project license.
+
+##### `manifest.mainScript`
+
+Project main script (default: `main.nf`).
+
+##### `manifest.name`
+
+Project short name.
+
+##### `manifest.nextflowVersion`
+
+Minimum required Nextflow version.
+
+This setting may be useful to ensure that a specific version is used:
+
+```groovy
+manifest.nextflowVersion = '1.2.3'        // exact match
+manifest.nextflowVersion = '1.2+'         // 1.2 or later (excluding 2 and later)
+manifest.nextflowVersion = '>=1.2'        // 1.2 or later
+manifest.nextflowVersion = '>=1.2, <=1.5' // any version in the 1.2 .. 1.5 range
+manifest.nextflowVersion = '!>=1.2'       // with ! prefix, stop execution if current version does not match required version.
+```
+
+##### `manifest.organization`
+
+Project organization.
+
+##### `manifest.recurseSubmodules`
+
+Pull submodules recursively from the Git repository.
+
+##### `manifest.version`
+
+Project version number.
+
+## `nextflow`
+
+<ChangedInVersion version="24.10.0">
+The `nextflow.publish.retryPolicy` settings were moved to `workflow.output.retryPolicy`.
+</ChangedInVersion>
+
+<ChangedInVersion version="25.06.0-edge">
+The `workflow.output.retryPolicy` settings were moved to `nextflow.retryPolicy`.
+</ChangedInVersion>
+
+##### `retryPolicy.delay`
+
+Delay used for retryable operations (default: `350ms`).
+
+##### `retryPolicy.jitter`
+
+Jitter value used for retryable operations (default: `0.25`).
+
+##### `retryPolicy.maxAttempts`
+
+Max attempts used for retryable operations (default: `5`).
+
+##### `retryPolicy.maxDelay`
+
+Max delay used for retryable operations (default: `90s`).
+
+## `notification`
+
+The `notification` scope controls the automatic sending of an email notification on workflow completion.
+
+The following settings are available:
+
+##### `notification.attributes`
+
+Map of variables that can be used in the template file.
+
+##### `notification.enabled`
+
+Send an email notification when the workflow execution completes (default: `false`).
+
+##### `notification.from`
+
+Sender address for the email notification.
+
+##### `notification.template`
+
+Path of a template file containing the contents of the email notification.
+
+##### `notification.to`
+
+Recipient address for the email notification. Multiple addresses can be specified as a comma-separated list.
+
+## `podman`
+
+The `podman` scope controls how [Podman](https://podman.io/) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `podman.enabled`
+
+Execute tasks with Podman containers (default: `false`).
+
+##### `podman.engineOptions`
+
+Specify additional options supported by the Podman engine i.e. `podman [OPTIONS]`.
+
+##### `podman.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `podman.mountFlags`
+
+Add the specified flags to the volume mounts e.g. `'ro,Z'`.
+
+##### `podman.registry`
+
+The registry from where container images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `podman.remove`
+
+Clean-up the container after the execution (default: `true`).
+
+##### `podman.runOptions`
+
+Specify extra command line options supported by the `podman run` command.
+
+##### `podman.temp`
+
+Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
+
+## `report`
+The `report` scope allows you to configure the workflow [Execution report][execution-report].
+
+The following settings are available:
+
+##### `report.enabled`
+
+Create the execution report on workflow completion (default: `false`).
+
+##### `report.file`
+
+The path of the created execution report file (default: `'report-<timestamp>.html'`).
+
+##### `report.overwrite`
+
+Overwrite any existing report file with the same name (default: `false`).
+
+## `sarus`
+
+The `sarus` scope controls how [Sarus](https://sarus.readthedocs.io) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `sarus.enabled`
+
+Execute tasks with Sarus containers (default: `false`).
+
+##### `sarus.envWhitelist`
+
+Comma-separated list of environment variable names to be included in the container environment.
+
+##### `sarus.runOptions`
+
+Specify extra command line options supported by the `sarus run` command.
+
+For details see the [Sarus user guide](https://sarus.readthedocs.io/en/stable/user/user_guide.html).
+
+##### `sarus.tty`
+
+Allocates a pseudo-tty (default: `false`).
+
+See the [Sarus][container-sarus] page to learn more about how to use Sarus containers with Nextflow.
+
+## `shifter`
+
+The `shifter` scope controls how [Shifter](https://docs.nersc.gov/programming/shifter/overview/) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `shifter.enabled`
+
+Execute tasks with Shifter containers (default: `false`).
+
+##### `shifter.envWhitelist`
+
+Comma-separated list of environment variable names to be included in the container environment.
+
+## `singularity`
+
+The `singularity` scope controls how [Singularity](https://sylabs.io/singularity/) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `singularity.autoMounts`
+
+<ChangedInVersion version="23.09.0-edge">
+Default value was changed from `false` to `true`.
+</ChangedInVersion>
+
+Automatically mount host paths in the executed container (default: `true`). It requires the `user bind control` feature to be enabled in your Singularity installation.
+
+##### `singularity.cacheDir`
+
+The directory where remote Singularity images are stored. When using a compute cluster, it must be a shared folder accessible to all compute nodes.
+
+##### `singularity.enabled`
+
+Execute tasks with Singularity containers (default: `false`).
+
+##### `singularity.engineOptions`
+
+Specify additional options supported by the Singularity engine i.e. `singularity [OPTIONS]`.
+
+##### `singularity.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `singularity.libraryDir`
+
+Directory where remote Singularity images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+##### `singularity.noHttps`
+
+Pull the Singularity image with http protocol (default: `false`).
+
+##### `singularity.ociAutoPull`
+
+<AddedInVersion version="23.12.0-edge">
+</AddedInVersion>
+
+*Requires Singularity 3.11 or later*
+
+When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow (default: `false`).
+
+:::note
+Leave `ociAutoPull` disabled if willing to build a Singularity native image with Wave. See [Build Singularity native images][wave-singularity] for more information.
+:::
+
+##### `singularity.ociMode`
+
+<AddedInVersion version="23.12.0-edge">
+</AddedInVersion>
+
+*Requires Singularity 4 or later*
+
+nable OCI-mode, that allows running native OCI compliant container image with Singularity using `crun` or `runc` as low-level runtime (default: `false`). See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
+
+:::note
+Leave `ociMode` disabled if you are willing to build a Singularity native image with Wave. See the [Build Singularity native images][wave-singularit] section for more information.
+:::
+
+##### `singularity.pullTimeout`
+
+The amount of time the Singularity pull can last, after which the process is terminated (default: `20 min`).
+
+##### `singularity.registry`
+
+<AddedInVersion version="22.12.0-edge">
+</AddedInVersion>
+
+The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `singularity.runOptions`
+
+Specify extra command line options supported by `singularity exec`.
+
+## `spack`
+
+The `spack` scope controls the creation of a Spack environment by the Spack package manager.
+
+The following settings are available:
+
+##### `spack.cacheDir`
+
+The path where Spack environments are stored. It should be accessible from all compute nodes when using a shared file system.
+
+##### `spack.checksum`
+
+Enable checksum verification of source tarballs (default: `true`).
+Only disable when requesting a package version not yet encoded in the corresponding Spack recipe.
+
+##### `spack.createTimeout`
+
+The amount of time to wait for the Spack environment to be created before failing (default: `60 min`).
+
+##### `spack.enabled`
+
+Execute tasks with Spack environments (default: `false`).
+
+##### `spack.parallelBuilds`
+
+The maximum number of parallel package builds (default: the number of available CPUs).
+
+## `timeline`
+
+The `timeline` scope controls the execution timeline report generated by Nextflow.
+
+The following settings are available:
+
+##### `timeline.enabled`
+
+Create the timeline report on workflow completion file (default: `false`).
+
+##### `timeline.file`
+
+Timeline file name (default: `'timeline-<timestamp>.html'`).
+
+##### `timeline.overwrite`
+
+Overwrite any existing timeline file with the same name (default: `false`).
+
+## `tower`
+
+The `tower` scope controls the settings for [Seqera Platform](https://seqera.io) (formerly Tower Cloud).
+
+The following settings are available:
+
+##### `tower.accessToken`
+
+The unique access token for your Seqera Platform account.
+
+Your `accessToken` can be obtained from your Seqera Platform instance in the [Tokens page](https://cloud.seqera.io/tokens).
+
+##### `tower.computeEnvId`
+
+The compute environment ID in your Seqera Platform account used to launch pipelines (default: the primary compute environment in the selected workspace).
+
+##### `tower.enabled`
+
+Enable workflow monitoring with Seqera Platform (default: `false`).
+
+##### `tower.endpoint`
+
+The endpoint of your Seqera Platform instance (default: `https://api.cloud.seqera.io`).
+
+##### `tower.workspaceId`
+
+The workspace ID in Seqera Platform in which to save the run (default: the launching user's personal workspace).
+
+The workspace ID can also be specified using the environment variable `TOWER_WORKSPACE_ID` (config file has priority over the environment variable).
+
+## `trace`
+
+The `trace` scope controls the layout of the execution trace file generated by Nextflow.
+
+The following settings are available:
+
+##### `trace.enabled`
+
+Create the execution trace file on workflow completion (default: `false`).
+
+##### `trace.fields`
+
+Comma-separated list of [trace fields][trace-fields] to include in the report.
+
+##### `trace.file`
+
+Trace file name (default: `'trace-<timestamp>.txt'`).
+
+##### `trace.overwrite`
+Overwrite any existing trace file with the same name (default: `false`).
+
+##### `trace.raw`
+
+Report trace metrics as raw numbers where applicable, i.e. report duration values in milliseconds and memory values in bytes (default: `false`).
+
+##### `trace.sep`
+
+Character used to separate values in each row (default: `\t`).
+
+## `wave`
+
+The `wave` scope provides advanced configuration for the use of [Wave containers][wave-page].
+
+The following settings are available:
+
+##### `wave.enabled`
+
+Enable the use of Wave containers (default: `false`).
+
+##### `wave.endpoint`
+
+The Wave service endpoint (default: `https://wave.seqera.io`).
+
+##### `wave.freeze`
+
+<AddedInVersion version="23.07.0-edge" />
+
+Enable Wave container freezing (default: `false`). Wave will provision a non-ephemeral container image that will be pushed to a container repository of your choice.
+
+The target registry must be specified using the `wave.build.repository` setting. It is also recommended to specify a custom cache repository using `wave.build.cacheRepository`.
+
+:::note
+The container registry authentication must be managed by the underlying infrastructure.
+:::
+
+##### `wave.mirror`
+
+<AddedInVersion version="23.07.0-edge" />
+
+Enable Wave container mirroring (default: `false`). Wave will mirror (i.e. copy) the containers in your pipeline to a container registry of your choice, so that pipeline tasks can pull the containers from this registry instead of the original one.
+
+The mirrored containers will have the same name, digest, and metadata.
+
+The target registry must be specified using the `wave.build.repository` setting.
+
+This option is only compatible with `wave.strategy = 'container'`. It cannot be used with `wave.freeze`.
+
+:::note
+The container registry authentication must be managed by the underlying infrastructure.
+:::
+
+##### `wave.strategy`
+
+The strategy to be used when resolving multiple Wave container requirements (default: `'container,dockerfile,conda'`).
+
+##### `wave.build.cacheRepository`
+
+The container repository used to cache image layers built by the Wave service.
+The corresponding credentials must be provided in your Seqera Platform account.
+
+##### `wave.build.compression.mode`
+
+<AddedInVersion version="25.05.0-edge" />
+
+The compression algorithm that should be used when building the container. Allowed values are: `gzip`, `estargz` and `zstd` (default: `gzip`).
+
+##### `wave.build.compression.level`
+
+<AddedInVersion version="25.05.0-edge" />
+
+Level of compression used when building a container depending the chosen algorithm: gzip, estargz (0-9) and zstd (0-22).
+
+##### `wave.build.compression.force`
+
+<AddedInVersion version="25.05.0-edge" />
+
+Forcefully apply compression option to all layers, including already existing layers (default: `false`).
+
+##### `wave.build.conda.basePackages`
+
+One or more Conda packages to be always added in the resulting container (default: `conda-forge::procps-ng`).
+
+##### `wave.build.conda.commands`
+
+One or more commands to be added to the Dockerfile used to build a Conda based image.
+
+##### `wave.build.conda.mambaImage`
+
+The Mamba container image is used to build Conda based container. This is expected to be [micromamba-docker](https://github.com/mamba-org/micromamba-docker) image.
+
+##### `wave.build.repository`
+
+The container repository where images built by Wave are uploaded.
+The corresponding credentials must be provided in your Seqera Platform account.
+
+##### `wave.httpClient.connectTimeout`
+
+<AddedInVersion version="25.06.0-edge" />
+
+The connection timeout for the Wave HTTP client (default: `30s`).
+
+##### `wave.httpClient.maxRate`
+
+<AddedInVersion version="25.01.0-edge" />
+
+The maximum request rate for the Wave HTTP client (default: `1/sec`).
+
+##### `wave.retryPolicy.delay`
+
+<AddedInVersion version="22.06.0-edge" />
+
+The initial delay when a failing HTTP request is retried (default: `450ms`).
+
+##### `wave.retryPolicy.jitter`
+
+<AddedInVersion version="22.06.0-edge" />
+
+The jitter factor used to randomly vary retry delays (default: `0.25`).
+
+##### `wave.retryPolicy.maxAttempts`
+
+<AddedInVersion version="22.06.0-edge" />
+
+The max number of attempts a failing HTTP request is retried (default: `5`).
+
+##### `wave.retryPolicy.maxDelay`
+
+<AddedInVersion version="22.06.0-edge" />
+
+The max delay when a failing HTTP request is retried (default: `90s`).
+
+##### `wave.scan.allowedLevels`
+
+<AddedInVersion version="24.09.1-edge" />
+
+Comma-separated list of allowed vulnerability levels when scanning containers for security vulnerabilities in `required` mode.
+
+Allowed values are: `low`, `medium`, `high`, `critical`.
+
+This option requires `wave.scan.mode = 'required'`.
+
+##### `wave.scan.mode`
+
+<AddedInVersion version="24.09.1-edge" />
+
+Enable Wave container security scanning. Wave will scan the containers in your pipeline for security vulnerabilities.
+
+The following options can be specified:
+
+###### `'none'`
+
+No security scanning is performed.
+
+###### `'async'`
+
+The containers used by your pipeline are scanned for security vulnerabilities. The task execution is carried out regardless of the security scan result.
+
+###### `'required'`
+
+The containers used by your pipeline are scanned for security vulnerabilities. The task is only executed if the corresponding container is free of vulnerabilities.
+
+## `workflow`
+
+<AddedInVersion version="24.10.0" />
+
+The `workflow` scope provides workflow execution options.
+
+The following settings are available:
+
+##### `workflow.failOnIgnore`
+
+<AddedInVersion version="24.05.0-edge" />
+
+When `true`, the pipeline will exit with a non-zero exit code if any failed tasks are ignored using the `ignore` [error strategy][process-error-strategy] (default: `false`).
+
+##### `workflow.onComplete`
+
+Specify a closure that will be invoked at the end of a workflow run (including failed runs). See [Workflow handlers][workflow-handlers] for more information.
+
+##### `workflow.onError`
+
+Specify a closure that will be invoked if a workflow run is terminated. See [Workflow handlers][workflow-handlers] for more information.
+
+##### `workflow.output.contentType`
+
+*Currently only supported for S3.*
+
+Specify the media type, also known as [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/MIME_types), of published files (default: `false`). Can be a string (e.g. `'text/html'`), or `true` to infer the content type from the file extension.
+
+##### `workflow.output.copyAttributes`
+
+<AddedInVersion version="25.01.0-edge" />
+
+*Currently only supported for local and shared filesystems.*
+
+Copy file attributes (such as the last modified timestamp) to the published file (default: `false`).
+
+##### `workflow.output.enabled`
+
+Enable or disable publishing (default: `true`).
+
+##### `workflow.output.ignoreErrors`
+
+When `true`, the workflow will not fail if a file can't be published for some reason (default: `false`).
+
+#####`workflow.output.mode`
+
+The file publishing method (default: `'symlink'`).
+
+The following options are available:
+
+###### `'copy'`
+
+Copy each file into the output directory.
+
+###### `'copyNoFollow'`
+
+Copy each file into the output directory without following symlinks, i.e. only the link is copied.
+
+###### `'link'`
+
+Create a hard link in the output directory for each file.
+
+###### `'move'`
+
+Move each file into the output directory.
+
+Should only be used for files which are not used by downstream processes in the workflow.
+
+###### `'rellink'`
+
+Create a relative symbolic link in the output directory for each file.
+
+###### `'symlink'`
+
+Create an absolute symbolic link in the output directory for each output file.
+
+##### `workflow.output.overwrite`
+
+When `true` any existing file in the specified folder will be overwritten (default: `'standard'`).
+
+The following options are available:
+
+###### `false`
+
+Never overwrite existing files.
+
+###### `true`
+
+Always overwrite existing files.
+
+###### `'deep'`
+
+Overwrite existing files when the file content is different.
+
+###### `'lenient'`
+
+Overwrite existing files when the file size is different.
+
+###### `'standard'`
+
+Overwrite existing files when the file size or last modified timestamp is different.
+
+##### `workflow.output.storageClass`
+
+*Currently only supported for S3.*
+
+Specify the storage class for published files.
+
+`workflow.output.tags`
+
+*Currently only supported for S3.*
+
+Specify arbitrary tags for published files.
+
+For example:
+
+```groovy
+workflow.output.tags = [FOO: 'hello', BAR: 'world']
+```
+
+[amazons3-page]: /nextflow_docs/nextflow_repo/docs/amazons3.mdx
+[aws-page]: /nextflow_docs/nextflow_repo/docs/aws.mdx
+[azure-page]: /nextflow_docs/nextflow_repo/docs/azure.mdx
+[config-mail]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#mail
+[azure-managed-identities]: /nextflow_docs/nextflow_repo/docs/azure.mdx#managed-identities
+[cli-lineage]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lineage
+[config-page]: /nextflow_docs/nextflow_repo/docs/config.mdx
+[config-workflow]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#workflow
+[ontainer-apptainer]: /nextflow_docs/nextflow_repo/docs/container.mdx#apptainer
+[container-charliecloud]: /nextflow_docs/nextflow_repo/docs/container.mdx#charliecloud
+[container-docker]: /nextflow_docs/nextflow_repo/docs/container.mdx#docker
+[container-podman]: /nextflow_docs/nextflow_repo/docs/container.mdx#podman
+[container-sarus]: /nextflow_docs/nextflow_repo/docs/container.mdx#sarus
+[container-shifter]: /nextflow_docs/nextflow_repo/docs/container.mdx#shifter
+[container-shifter]: /nextflow_docs/nextflow_repo/docs/container.mdx#singularity
+[execution-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#execution-report
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[google-credentials]: /nextflow_docs/nextflow_repo/docs/google.mdx#credentials
+[google-page]: /nextflow_docs/nextflow_repo/docs/google.mdx
+[k8s-page]: /nextflow_docs/nextflow_repo/docs/kubernetes.mdx
+[lsf-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#lsf
+[pbs-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#pbstorque
+[pbspro-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#pbs-pro
+[process-error-strategy]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#errorstrategy
+[process-pod]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#pod
+[sharing-page]: /nextflow_docs/nextflow_repo/docs/sharing.mdx
+[slurm-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#slurm
+[trace-fields]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-fields
+[trace-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
+[wave-singularity]: /nextflow_docs/nextflow_repo/docs/wave.mdx#build-singularity-native-images
+[workflow-diagram]: /nextflow_docs/nextflow_repo/docs/reports.mdx#workflow-diagram
+[workflow-handlers]: /nextflow_docs/nextflow_repo/docs/notifications.mdx#workflow-handlers
diff --git a/docs/reference/env-vars.md b/docs/reference/env-vars.md
deleted file mode 100644
index 45d4a7b23c..0000000000
--- a/docs/reference/env-vars.md
+++ /dev/null
@@ -1,304 +0,0 @@
-(config-env-vars)=
-
-# Environment variables
-
-The following environment variables control the configuration of the Nextflow runtime and the underlying Java virtual machine.
-
-## Java settings
-
-`JAVA_CMD`
-: Defines the path location of the Java binary command used to launch Nextflow.
-
-`JAVA_HOME`
-: Defines the path location of the Java VM installation used to run Nextflow.
-
-(nxf-env-vars)=
-
-## Nextflow settings
-
-`NXF_ANSI_LOG`
-: Enables/disables ANSI console output (default `true` when ANSI terminal is detected).
-
-`NXF_ANSI_SUMMARY`
-: Enables/disables ANSI completion summary: `true\|false` (default: print summary if execution last more than 1 minute).
-
-`NXF_ASSETS`
-: Defines the directory where downloaded pipeline repositories are stored (default: `$NXF_HOME/assets`)
-
-`NXF_CACHE_DIR`
-: :::{versionadded} 24.02.0-edge
-  :::
-: Defines the base cache directory when using the default cache store (default: `"$launchDir/.nextflow"`).
-
-`NXF_CHARLIECLOUD_CACHEDIR`
-: Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
-
-`NXF_CLOUDCACHE_PATH`
-: :::{versionadded} 23.07.0-edge
-  :::
-: Defines the base cache path when using the cloud cache store.
-
-`NXF_CLOUD_DRIVER`
-: Defines the default cloud driver to be used if not specified in the config file or as command line option, either `aws` or `google`.
-
-`NXF_CONDA_CACHEDIR`
-: Directory where Conda environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
-
-`NXF_CONDA_ENABLED`
-: :::{versionadded} 22.08.0-edge
-  :::
-: Enable the use of Conda recipes defined by using the {ref}`process-conda` directive. (default: `false`).
-
-`NXF_CONTAINER_ENTRYPOINT_OVERRIDE`
-: :::{deprecated} 22.10.0
-  :::
-: When `true`, override the container entrypoint with `/bin/bash` (default: `false`).
-
-`NXF_DATE_FORMAT`
-: :::{versionadded} 25.07.0-edge
-  :::
-: Defines the format for date and time representations in notifications and reports. Supports custom formats (e.g., `yyyy-MM-dd HH:mm:ss`) or `iso` for ISO 8601 format with timezone (default: `dd-MMM-yyyy HH:mm:ss`).
-
-`NXF_DEFAULT_DSL`
-: :::{versionadded} 22.03.0-edge
-  :::
-: Defines the DSL version that should be used in not specified otherwise in the script of config file (default: `2`)
-
-`NXF_DISABLE_CHECK_LATEST`
-: :::{versionadded} 23.09.0-edge
-  :::
-: Nextflow automatically checks for a newer version of itself unless this option is enabled (default: `false`).
-
-`NXF_DISABLE_JOBS_CANCELLATION`
-: :::{versionadded} 21.12.0-edge
-  :::
-: Disables the cancellation of child jobs on workflow execution termination.
-
-`NXF_DISABLE_PARAMS_TYPE_DETECTION`
-: :::{versionadded} 23.07.0-edge
-  :::
-: Disables the automatic type detection of command line parameters.
-
-`NXF_DISABLE_WAVE_SERVICE`
-: :::{versionadded} 23.08.0-edge
-  :::
-: Disables the requirement for Wave service when enabling the Fusion file system.
-
-`NXF_ENABLE_AWS_SES`
-: :::{versionadded} 23.06.0-edge
-  :::
-: Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default: `false`)
-
-`NXF_ENABLE_FS_SYNC`
-: :::{versionadded} 23.10.0
-  :::
-: When enabled the job script will execute Linux `sync` command on job completion. This may be useful to synchronize the job state over shared file systems (default: `false`)
-
-`NXF_ENABLE_SECRETS`
-: :::{versionadded} 21.09.0-edge
-  :::
-: Enable Nextflow secrets features (default: `true`)
-
-`NXF_ENABLE_STRICT`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Enable Nextflow *strict* execution mode (default: `false`)
-
-`NXF_ENABLE_VIRTUAL_THREADS`
-: :::{versionadded} 23.05.0-edge
-  :::
-: Enable the use of virtual threads in the Nextflow runtime (default: `false`)
-
-`NXF_EXECUTOR`
-: Defines the default process executor, e.g. `sge`
-
-`NXF_FILE_ROOT`
-: :::{versionadded} 23.05.0-edge
-  :::
-: The file storage path against which relative file paths are resolved.
-: For example, with `NXF_FILE_ROOT=/some/root/path`, the use of `file('hello')` will be resolved to the absolute path `/some/root/path/hello`. A remote root path can be specified using the usual protocol prefix, e.g. `NXF_FILE_ROOT=s3://my-bucket/data`. Files defined using an absolute path are not affected by this setting.
-
-`NXF_HOME`
-: Nextflow home directory (default: `$HOME/.nextflow`).
-
-`NXF_JAVA_HOME`
-: Defines the path location of the Java VM installation used to run Nextflow. This variable overrides the `JAVA_HOME` variable if defined.
-
-`NXF_JVM_ARGS`
-: :::{versionadded} 21.12.1-edge
-  :::
-: Allows the setting Java VM options. This is similar to `NXF_OPTS` however it's only applied the JVM running Nextflow and not to any java pre-launching commands.
-
-`NXF_LOG_FILE`
-: The filename of the Nextflow log (default: `.nextflow.log`)
-
-`NXF_OFFLINE`
-: When `true` prevents Nextflow from automatically downloading and updating remote project repositories (default: `false`).
-: :::{versionchanged} 23.09.0-edge
-  This option also disables the automatic version check (see `NXF_DISABLE_CHECK_LATEST`).
-  :::
-: :::{versionchanged} 23.11.0-edge
-  This option also prevents plugins from being downloaded. Plugin versions must be specified in offline mode, or else Nextflow will fail.
-  :::
-
-`NXF_OPTS`
-: Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of `-Dkey[=value]` properties.
-
-`NXF_ORG`
-: Default `organization` prefix when looking for a hosted repository (default: `nextflow-io`).
-
-`NXF_PARAMS_FILE`
-: :::{versionadded} 20.10.0
-  :::
-: Defines the path location of the pipeline parameters file .
-
-`NXF_PID_FILE`
-: Name of the file where the process PID is saved when Nextflow is launched in background.
-
-`NXF_PLUGINS_ALLOWED`
-: :::{versionadded} 25.04.0
-  :::
-: Comma separated list of plugin IDs that can be used in a workflow executions e.g. `NXF_PLUGINS_ALLOWED=nf-amazon,nf-tower,nf-wave`. Use empty string to disallow all plugins.
-
-`NXF_PLUGINS_DEFAULT`
-: Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: `true`).
-
-`NXF_PLUGINS_DIR`
-: The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins`).
-
-`NXF_PLUGINS_REGISTRY_URL`
-: :::{versionadded} 25.08.0-edge
-  :::
-: Specifies the URL of the plugin registry used to download and resolve plugins. This allows using custom or private plugin registries instead of the default public registry.
-
-`NXF_PLUGINS_TEST_REPOSITORY`
-: :::{versionadded} 23.04.0
-  :::
-: Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry.
-
-`NXF_PUBLISH_FAIL_ON_ERROR`
-: :::{versionadded} 24.04.3
-  :::
-: Defines the default behavior of `publishDir.failOnError` setting. See {ref}`publishDir<process-publishdir>` directive for more information.
-
-`NXF_RETRY_POLICY_DELAY`
-: :::{versionadded} 25.06.0-edge
-  :::
-: Delay used for HTTP retryable operations (default: `350ms`).
-
-`NXF_RETRY_POLICY_JITTER`
-: :::{versionadded} 25.06.0-edge
-  :::
-: Jitter value used for HTTP retryable operations (default: `0.25`).
-
-`NXF_RETRY_POLICY_MAX_ATTEMPTS`
-: :::{versionadded} 25.06.0-edge
-  :::
-: Max number of attempts used for HTTP retryable operations (default: `5`).
-
-`NXF_RETRY_POLICY_MAX_DELAY`
-: :::{versionadded} 25.06.0-edge
-  :::
-: Max delay used for HTTP retryable operations (default: `90s`).
-
-`NXF_RETRY_POLICY_MULTIPLIER`
-: :::{versionadded} 25.08.0-edge
-  :::
-: Delay multiplier used for HTTP retryable operations (default: `2.0`).
-
-`NXF_SCM_FILE`
-: :::{versionadded} 20.10.0
-  :::
-: Defines the path location of the SCM config file .
-
-`NXF_SINGULARITY_CACHEDIR`
-: Directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
-
-`NXF_SINGULARITY_LIBRARYDIR`
-: :::{versionadded} 21.09.0-edge
-  :::
-: Directory where remote Singularity images are retrieved. It should be a directory accessible to all compute nodes.
-
-`NXF_SPACK_CACHEDIR`
-: Directory where Spack environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
-
-`NXF_SPACK_ENABLED`
-: :::{versionadded} 23.02.0-edge
-  :::
-: Enable the use of Spack recipes defined by using the {ref}`process-spack` directive. (default: `false`).
-
-`NXF_SYNTAX_PARSER`
-: :::{versionadded} 25.02.0-edge
-  :::
-: Set to `'v2'` to use the {ref}`strict syntax <strict-syntax-page>` for Nextflow scripts and config files (default: `'v1'`).
-
-`NXF_TEMP`
-: Directory where temporary files are stored
-
-`NXF_TRACE`
-: Enable trace level logging for the specified packages. Equivalent to the `-trace` command-line option.
-
-`NXF_VER`
-: Defines which version of Nextflow to use.
-
-`NXF_WORK`
-: Directory where working files are stored (usually your *scratch* directory)
-
-`NXF_WRAPPER_STAGE_FILE_THRESHOLD`
-: :::{versionadded} 23.05.0-edge
-  :::
-: Defines the minimum size of the `.command.run` staging script for it to be written to a separate `.command.stage` file (default: `'1 MB'`).
-: This setting is useful for executors that impose a size limit on job scripts.
-
-## Seqera Platform settings
-
-`TOWER_ACCESS_TOKEN`
-: Specifies the access token for authenticating with Seqera Platform. Can also be configured using the `tower.accessToken` config option.
-
-`TOWER_API_ENDPOINT`
-: Specifies the Seqera Platform API endpoint (default: `https://api.cloud.seqera.io`). Can also be configured using the `tower.endpoint` config option.
-
-`TOWER_AUTH_DOMAIN`
-: :::{versionadded} 25.10.0
-  :::
-: Specifies the Auth0 domain for authenticating with Seqera Platform when connecting to a custom endpoint. When specified, this value takes precedence over the built-in mappings for known Seqera endpoints. Must be used in conjunction with `TOWER_AUTH_CLIENT_ID`.
-
-`TOWER_AUTH_CLIENT_ID`
-: :::{versionadded} 25.10.0
-  :::
-: Specifies the Auth0 client ID for authenticating with a custom Seqera Platform endpoint. Must be used in conjunction with `TOWER_AUTH_DOMAIN`.
-
-`TOWER_REFRESH_TOKEN`
-: Specifies the refresh token for maintaining authentication with Seqera Platform. Can also be configured using the `tower.refreshToken` config option.
-
-`TOWER_WORKSPACE_ID`
-: Specifies the Seqera Platform workspace ID. Can also be configured using the `tower.workspaceId` config option.
-
-## Other settings
-
-`FTP_PROXY`
-: :::{versionadded} 21.06.0-edge
-  :::
-: Defines the FTP proxy server. Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `ftp://user:password@proxy-host.com:port`.
-
-`HTTP_PROXY`
-: Defines the HTTP proxy server.
-: :::{versionadded} 21.06.0-edge
-  Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `http://user:password@proxy-host.com:port`.
-  :::
-
-`HTTPS_PROXY`
-: Defines the HTTPS proxy server.
-: :::{versionadded} 21.06.0-edge
-  Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `https://user:password@proxy-host.com:port`.
-  :::
-
-`NO_COLOR`
-: Disables ANSI color codes in Nextflow log output. When this variable is set, Nextflow prints plain text logs following the [NO_COLOR standard](https://no-color.org/).
-: If both `NO_COLOR` and `NXF_ANSI_LOG` are set, `NXF_ANSI_LOG` takes precedence.
-
-`NO_PROXY`
-: Defines one or more host names that should not use the proxy server. Separate multiple names using a comma character.
-
-`TERMINAL_WIDTH`
-: Forces the terminal width of ANSI-formatted log output. Overrides automatic terminal width detection and uses the specified width for line wrapping when set to an integer value.
diff --git a/docs/reference/env-vars.mdx b/docs/reference/env-vars.mdx
new file mode 100644
index 0000000000..bcc44fdacd
--- /dev/null
+++ b/docs/reference/env-vars.mdx
@@ -0,0 +1,399 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Environment variables
+
+The following environment variables control the configuration of the Nextflow runtime and the underlying Java virtual machine.
+
+## Java settings
+
+##### `JAVA_CMD`
+
+Defines the path location of the Java binary command used to launch Nextflow.
+
+##### `JAVA_HOME`
+
+Defines the path location of the Java VM installation used to run Nextflow.
+
+## Nextflow settings
+
+##### `NXF_ANSI_LOG`
+
+Enables/disables ANSI console output (default `true` when ANSI terminal is detected).
+
+##### `NXF_ANSI_SUMMARY`
+
+Enables/disables ANSI completion summary`true\|false` (defaultprint summary if execution last more than 1 minute).
+
+##### `NXF_ASSETS`
+
+Defines the directory where downloaded pipeline repositories are stored (default`$NXF_HOME/assets`)
+
+##### `NXF_CACHE_DIR`
+
+<AddedInVersion version="24.02.0-edge" />
+
+Defines the base cache directory when using the default cache store (default`"$launchDir/.nextflow"`).
+
+##### `NXF_CHARLIECLOUD_CACHEDIR`
+
+Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+##### `NXF_CLOUDCACHE_PATH`
+
+<AddedInVersion version="23.07.0-edge" />
+
+Defines the base cache path when using the cloud cache store.
+
+##### `NXF_CLOUD_DRIVER`
+
+Defines the default cloud driver to be used if not specified in the config file or as command line option, either `aws` or `google`.
+
+##### `NXF_CONDA_CACHEDIR`
+
+Directory where Conda environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+##### `NXF_CONDA_ENABLED`
+
+<AddedInVersion version="22.08.0-edge" />
+
+Enable the use of Conda recipes defined by using the [conda][process-conda] directive. (default`false`).
+
+##### `NXF_CONTAINER_ENTRYPOINT_OVERRIDE`
+
+<DeprecatedInVersion version="22.10.0" />
+
+When `true`, override the container entrypoint with `/bin/bash` (default: `false`).
+
+##### `NXF_DATE_FORMAT`
+
+<AddedInVersion version="25.07.0-edge">
+</AddedInVersion>
+
+Defines the format for date and time representations in notifications and reports. Supports custom formats (e.g., `yyyy-MM-dd HH:mm:ss`) or `iso` for ISO 8601 format with timezone (default: `dd-MMM-yyyy HH:mm:ss`).
+
+##### `NXF_DEFAULT_DSL`
+
+<AddedInVersion version="22.03.0-edge" />
+
+Defines the DSL version that should be used in not specified otherwise in the script of config file (default`2`)
+
+##### `NXF_DISABLE_CHECK_LATEST`
+
+<AddedInVersion version="23.09.0-edge" />
+
+Nextflow automatically checks for a newer version of itself unless this option is enabled (default`false`).
+
+##### `NXF_DISABLE_JOBS_CANCELLATION`
+
+<AddedInVersion version="21.12.0-edge" />
+
+Disables the cancellation of child jobs on workflow execution termination.
+
+##### `NXF_DISABLE_PARAMS_TYPE_DETECTION`
+
+<AddedInVersion version="23.07.0-edge" />
+
+Disables the automatic type detection of command line parameters.
+
+##### `NXF_DISABLE_WAVE_SERVICE`
+
+<AddedInVersion version="23.08.0-edge" />
+
+Disables the requirement for Wave service when enabling the Fusion file system.
+
+##### `NXF_ENABLE_AWS_SES`
+
+<AddedInVersion version="23.06.0-edge" />
+
+Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default`false`)
+
+##### `NXF_ENABLE_FS_SYNC`
+
+<AddedInVersion version="23.10.0" />
+
+When enabled the job script will execute Linux `sync` command on job completion. This may be useful to synchronize the job state over shared file systems (default`false`)
+
+##### `NXF_ENABLE_SECRETS`
+
+<AddedInVersion version="21.09.0-edge" />
+
+Enable Nextflow secrets features (default`true`)
+
+##### `NXF_ENABLE_STRICT`
+
+<AddedInVersion version="22.05.0-edge" />
+
+Enable Nextflow *strict* execution mode (default`false`)
+
+##### `NXF_ENABLE_VIRTUAL_THREADS`
+
+<AddedInVersion version="23.05.0-edge" />
+
+Enable the use of virtual threads in the Nextflow runtime (default`false`)
+
+##### `NXF_EXECUTOR`
+
+Defines the default process executor, e.g. `sge`
+
+##### `NXF_FILE_ROOT`
+
+<AddedInVersion version="23.05.0-edge" />
+
+The file storage path against which relative file paths are resolved.
+
+For example, with `NXF_FILE_ROOT=/some/root/path`, the use of `file('hello')` will be resolved to the absolute path `/some/root/path/hello`. A remote root path can be specified using the usual protocol prefix, e.g. `NXF_FILE_ROOT=s3://my-bucket/data`. Files defined using an absolute path are not affected by this setting.
+
+##### `NXF_HOME`
+
+Nextflow home directory (default`$HOME/.nextflow`).
+
+##### `NXF_JAVA_HOME`
+
+Defines the path location of the Java VM installation used to run Nextflow. This variable overrides the `JAVA_HOME` variable if defined.
+
+##### `NXF_JVM_ARGS`
+
+<AddedInVersion version="21.12.1-edge" />
+
+Allows the setting Java VM options. This is similar to `NXF_OPTS` however it's only applied the JVM running Nextflow and not to any java pre-launching commands.
+
+##### `NXF_LOG_FILE`
+
+The filename of the Nextflow log (default`.nextflow.log`)
+
+##### `NXF_OFFLINE`
+
+When `true` prevents Nextflow from automatically downloading and updating remote project repositories (default`false`).
+
+<ChangedInVersion version="23.09.0-edge">
+This option also disables the automatic version check (see `NXF_DISABLE_CHECK_LATEST`).
+</ChangedInVersion>
+
+<ChangedInVersion version="23.11.0-edge">
+This option also prevents plugins from being downloaded. Plugin versions must be specified in offline mode, or else Nextflow will fail.
+</ChangedInVersion>
+
+##### `NXF_OPTS`
+
+Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of `-Dkey[=value]` properties.
+
+##### `NXF_ORG`
+
+Default `organization` prefix when looking for a hosted repository (default`nextflow-io`).
+
+##### `NXF_PARAMS_FILE`
+
+<AddedInVersion version="20.10.0" />
+
+Defines the path location of the pipeline parameters file .
+
+##### `NXF_PID_FILE`
+
+Name of the file where the process PID is saved when Nextflow is launched in background.
+
+##### `NXF_PLUGINS_ALLOWED`
+
+<AddedInVersion version="25.04.0" />
+
+Comma separated list of plugin IDs that can be used in a workflow executions e.g. `NXF_PLUGINS_ALLOWED=nf-amazon,nf-tower,nf-wave`. Use empty string to disallow all plugins.
+
+##### `NXF_PLUGINS_DEFAULT`
+
+Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default`true`).
+
+##### `NXF_PLUGINS_DIR`
+
+The path where the plugin archives are loaded and stored (default`$NXF_HOME/plugins`).
+
+##### `NXF_PLUGINS_REGISTRY_URL`
+
+<AddedInVersion version="25.08.0-edge" />
+
+Specifies the URL of the plugin registry used to download and resolve plugins. This allows using custom or private plugin registries instead of the default public registry.
+
+##### `NXF_PLUGINS_TEST_REPOSITORY`
+
+<AddedInVersion version="23.04.0" />
+
+Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry.
+
+##### `NXF_PUBLISH_FAIL_ON_ERROR`
+
+<AddedInVersion version="24.04.3" />
+
+Defines the default behavior of `publishDir.failOnError` setting. See the [publishDir][process-publishdir] directive for more information.
+
+##### `NXF_RETRY_POLICY_DELAY`
+
+
+<AddedInVersion version="25.06.0-edge" />
+
+Delay used for HTTP retryable operations (default: `350ms`).
+
+##### `NXF_RETRY_POLICY_JITTER`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Jitter value used for HTTP retryable operations (default: `0.25`).
+
+##### `NXF_RETRY_POLICY_MAX_ATTEMPTS`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Max number of attempts used for HTTP retryable operations (default: `5`).
+
+##### `NXF_RETRY_POLICY_MAX_DELAY`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Max delay used for HTTP retryable operations (default: `90s`).
+
+##### `NXF_RETRY_POLICY_DELAY`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Delay used for HTTP retryable operations (default: `350ms`).
+
+##### `NXF_RETRY_POLICY_JITTER`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Jitter value used for HTTP retryable operations (default: `0.25`).
+
+##### `NXF_RETRY_POLICY_MAX_ATTEMPTS`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Max number of attempts used for HTTP retryable operations (default: `5`).
+
+##### `NXF_RETRY_POLICY_MAX_DELAY`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Max delay used for HTTP retryable operations (default: `90s`).
+
+##### `NXF_RETRY_POLICY_MULTIPLIER`
+
+<AddedInVersion version="25.08.0-edge" />
+
+Delay multiplier used for HTTP retryable operations (default: `2.0`).
+
+##### `NXF_SCM_FILE`
+
+<AddedInVersion version="20.10.0" />
+
+Defines the path location of the SCM config file .
+
+##### `NXF_SINGULARITY_CACHEDIR`
+
+Directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+##### `NXF_SINGULARITY_LIBRARYDIR`
+
+<AddedInVersion version="21.09.0-edge" />
+
+Directory where remote Singularity images are retrieved. It should be a directory accessible to all compute nodes.
+
+##### `NXF_SPACK_CACHEDIR`
+
+Directory where Spack environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+##### `NXF_SPACK_ENABLED`
+
+<AddedInVersion version="23.02.0-edge" />
+
+Enable the use of Spack recipes defined by using the [spack][process-spack] directive. (default`false`).
+
+##### `NXF_SYNTAX_PARSER`
+
+<AddedInVersion version="25.02.0-edge" />
+
+Set to `'v2'` to use the [strict syntax][strict-syntax-page] for Nextflow scripts and config files (default`'v1'`).
+
+##### `NXF_TEMP`
+
+Directory where temporary files are stored
+
+##### `NXF_TRACE`
+
+Enable trace level logging for the specified packages. Equivalent to the `-trace` command-line option.
+
+##### `NXF_VER`
+
+Defines which version of Nextflow to use.
+
+##### `NXF_WORK`
+
+Directory where working files are stored (usually your *scratch* directory)
+
+##### `NXF_WRAPPER_STAGE_FILE_THRESHOLD`
+
+<AddedInVersion version="23.05.0-edge" />
+
+Defines the minimum size of the `.command.run` staging script for it to be written to a separate `.command.stage` file (default`'1 MB'`).
+This setting is useful for executors that impose a size limit on job scripts.
+
+## Seqera Platform settings
+
+##### `TOWER_ACCESS_TOKEN`
+
+Access token for authenticating with Seqera Platform. Can also be configured using the `tower.accessToken` config option.
+
+##### `TOWER_API_ENDPOINT`
+
+Seqera Platform API endpoint (default: `https://api.cloud.seqera.io`). Can also be configured using the `tower.endpoint` config option.
+
+##### `TOWER_AUTH_DOMAIN`
+
+<VersionAdded version="25.10.0" />
+
+Auth0 domain for authenticating with Seqera Platform when connecting to a custom endpoint. When specified, this value takes precedence over the built-in mappings for known Seqera endpoints. Must be used in conjunction with `TOWER_AUTH_CLIENT_ID`.
+
+##### `TOWER_AUTH_CLIENT_ID`
+
+<AddedInVersion version="25.10.0" />
+
+Auth0 client ID for authenticating with a custom Seqera Platform endpoint. Must be used in conjunction with `TOWER_AUTH_DOMAIN`.
+
+##### `TOWER_REFRESH_TOKEN`
+
+Refresh token for maintaining authentication with Seqera Platform. Can also be configured using the `tower.refreshToken` config option.
+
+##### `TOWER_WORKSPACE_ID`
+
+Seqera Platform workspace ID. Can also be configured using the `tower.workspaceId` config option.
+
+## Other settings
+
+##### `FTP_PROXY`
+
+<AddedInVersion version="21.06.0-edge" />
+
+Defines the FTP proxy server. Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `ftp://user:password@proxy-host.com:port`.
+
+##### `HTTP_PROXY`
+
+Defines the HTTP proxy server.
+
+<AddedInVersion version="21.06.0-edge">
+Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `http://user:password@proxy-host.com:port`.
+</AddedInVersion>
+
+##### `NO_COLOR`
+
+Disables ANSI color codes in Nextflow log output. When this variable is set, Nextflow prints plain text logs following the [NO_COLOR standard](https://no-color.org/).
+
+If both `NO_COLOR` and `NXF_ANSI_LOG` are set, `NXF_ANSI_LOG` takes precedence.
+
+##### `NO_PROXY`
+
+Defines one or more host names that should not use the proxy server. Separate multiple names using a comma character.
+
+##### `TERMINAL_WIDTH`
+
+Forces the terminal width of ANSI-formatted log output. Overrides automatic terminal width detection and uses the specified width for line wrapping when set to an integer value.
+
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
+[process-spack]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#spack
+[process-publishdir]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#publishdir
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
diff --git a/docs/reference/feature-flags.md b/docs/reference/feature-flags.md
deleted file mode 100644
index 33591d250f..0000000000
--- a/docs/reference/feature-flags.md
+++ /dev/null
@@ -1,73 +0,0 @@
-(config-feature-flags)=
-
-# Feature flags
-
-Feature flags enable experimental or other opt-in features. They must be specified in the pipeline script.
-
-:::{warning}
-Feature flags with the `nextflow.preview` prefix can cause pipelines run with newer versions of Nextflow to fail due to breaking changes. Always consult the {ref}`migration notes <migrations-page>` before updating to a new Nextflow version.
-:::
-
-`nextflow.enable.configProcessNamesValidation`
-: :::{deprecated} 25.10.0
-  Use the {ref}`strict syntax <strict-syntax-page>` instead. It validates process selectors without producing false warnings.
-  :::
-: When `true`, prints a warning for every `withName:` process selector that doesn't match a process in the pipeline (default: `true`).
-
-`nextflow.enable.dsl`
-: :::{deprecated} 25.04.0
-  :::
-: Defines the DSL version to use (`1` or `2`).
-
-`nextflow.enable.moduleBinaries`
-: When `true`, enables the use of modules with binary scripts. See {ref}`module-binaries` for more information.
-
-`nextflow.enable.strict`
-: When `true`, executes the pipeline in "strict" mode, which introduces the following rules:
-
-  - When reading a params file, Nextflow will fail if a dynamic param value references an undefined variable
-
-  - When merging params from a config file with params from the command line, Nextflow will fail if a param is specified from both sources but with different types
-
-  - When using the `join` operator, the `failOnDuplicate` option is `true` regardless of any user setting
-
-  - When using the `join` operator, the `failOnMismatch` option is `true` (unless `remainder` is also `true`) regardless of any user setting
-
-  - When using the `publishDir` process directive, the `failOnError` option is `true` regardless of any user setting
-
-  - In a process definition, Nextflow will fail if an input or output tuple has only one element
-
-  - In a process definition, Nextflow will fail if an output emit name is not a valid identifier (i.e. it should match the pattern `/[A-Za-z_][A-Za-z0-9_]*/`)
-
-  - During a process execution, Nextflow will fail if a received input tuple does not have the same number of elements as was declared
-
-  - During a process execution, Nextflow will fail if the `storeDir` directive is used with non-file outputs
-
-  - Nextflow will fail if a pipeline param is referenced before it is defined
-
-  - Nextflow will fail if multiple functions and/or processes with the same name are defined in a module script
-
-`nextflow.preview.output`
-: :::{versionadded} 24.04.0
-  :::
-: :::{deprecated} 25.10.0
-  This feature flag is no longer supported. Workflow outputs are out of preview.
-  :::
-: When `true`, enables the use of {ref}`workflow outputs <workflow-output-def>`.
-
-`nextflow.preview.recursion`
-: *Experimental: may change in a future release.*
-: When `true`, enables {ref}`process and workflow recursion <workflow-recursion>`.
-
-`nextflow.preview.topic`
-: :::{versionadded} 24.04.0
-  :::
-: :::{deprecated} 25.04.0
-  This feature flag is no longer supported. Topic channels are out of preview.
-  :::
-: When `true`, enables the use of {ref}`topic channels <channel-topic>`.
-
-`nextflow.preview.types`
-: :::{versionadded} 25.10.0
-  :::
-: When `true`, enables the use of {ref}`typed processes <process-typed-page>`. Must be enabled in every script that uses typed processes. Legacy processes cannot be defined in scripts with this flag enabled.
diff --git a/docs/reference/feature-flags.mdx b/docs/reference/feature-flags.mdx
new file mode 100644
index 0000000000..5f4081ac04
--- /dev/null
+++ b/docs/reference/feature-flags.mdx
@@ -0,0 +1,93 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Feature flags
+
+Feature flags enable experimental or other opt-in features. They must be specified in the pipeline script.
+
+:::warning
+Feature flags with the `nextflow.preview` prefix can cause pipelines run with newer versions of Nextflow to fail due to breaking changes. Always consult the [migration notes][migrations-page] before updating to a new Nextflow version.
+:::
+
+##### `nextflow.enable.configProcessNamesValidation`
+
+<DeprecatedInVersion version="25.10.0">
+Use the [strict syntax][strict-syntax-page] instead. It validates process selectors without producing false warnings.
+</DeprecatedInVersion>
+
+When `true`, prints a warning for every `withName:` process selector that doesn't match a process in the pipeline (default: `true`).
+
+##### `nextflow.enable.dsl`
+
+<DeprecatedInVersion version="25.04.0">
+
+Defines the DSL version to use (`1` or `2`).
+
+##### `nextflow.enable.moduleBinaries`
+
+When `true`, enables the use of modules with binary scripts. See [Module binaries][module-binaries] for more information.
+
+##### `nextflow.enable.strict`
+
+When `true`, executes the pipeline in "strict" mode, which introduces the following rules:
+
+- When reading a params file, Nextflow will fail if a dynamic param value references an undefined variable
+
+- When merging params from a config file with params from the command line, Nextflow will fail if a param is specified from both sources but with different types
+
+- When using the `join` operator, the `failOnDuplicate` option is `true` regardless of any user setting
+
+- When using the `join` operator, the `failOnMismatch` option is `true` (unless `remainder` is also `true`) regardless of any user setting
+
+- When using the `publishDir` process directive, the `failOnError` option is `true` regardless of any user setting
+
+- In a process definition, Nextflow will fail if an input or output tuple has only one element
+
+- In a process definition, Nextflow will fail if an output emit name is not a valid identifier (i.e. it should match the pattern `/[A-Za-z_][A-Za-z0-9_]*/`)
+
+- During a process execution, Nextflow will fail if a received input tuple does not have the same number of elements as was declared
+
+- During a process execution, Nextflow will fail if the `storeDir` directive is used with non-file outputs
+
+- Nextflow will fail if a pipeline param is referenced before it is defined
+
+- Nextflow will fail if multiple functions and/or processes with the same name are defined in a module script
+
+##### `nextflow.preview.output`
+
+<AddedInVersion version="24.04.0"/>
+
+<DeprecatedInVersion version="25.10.0">
+This feature flag is no longer supported. Workflow outputs are out of preview.
+</DeprecatedInVersion>
+
+When `true`, enables the use of {ref}`workflow outputs <workflow-output-def>`.
+
+##### `nextflow.preview.recursion`
+
+*Experimental: may change in a future release.*
+
+When `true`, enables [process and workflow recursion][workflow-recursion].
+
+##### `nextflow.preview.topic`
+
+<AddedInVersion version="24.04.0"/>
+
+<DeprecatedInVersion version="25.04.0">
+This feature flag is no longer supported. Topic channels are out of preview.
+</DeprecatedInVersion>
+
+When `true`, enables the use of [topic channels][channel-topic].
+
+##### `nextflow.preview.types`
+
+<AddedInVersion version="25.10.0"/>
+
+When `true`, enables the use of [typed processes][process-typed-page]. Must be enabled in every script that uses typed processes. Legacy processes cannot be defined in scripts with this flag enabled.
+
+[channel-topic]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#topic
+[migrations-page]: /nextflow_docs/nextflow_repo/docs/migrations/index.mdx
+[module-binaries]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-binaries
+[process-typed-page]: /nextflow_docs/nextflow_repo/docs/process-typed.mdx#process-typed-page
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-recursion]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#process-and-workflow-recursion
diff --git a/docs/reference/operator.md b/docs/reference/operator.md
deleted file mode 100644
index aacf2a79f9..0000000000
--- a/docs/reference/operator.md
+++ /dev/null
@@ -1,1714 +0,0 @@
-(operator-page)=
-
-# Operators
-
-(operator-branch)=
-
-## branch
-
-:::{versionadded} 19.08.0-edge
-:::
-
-*Returns: multiple channels*
-
-The `branch` operator forwards each item from a source channel to one of multiple output channels, based on a selection criteria.
-
-The selection criteria is a {ref}`closure <script-closure>` that defines, for each output channel, a unique label followed by a boolean expression. When an item is received, it is routed to the first output channel whose expression evaluates to `true`. For example:
-
-```{literalinclude} ../snippets/branch.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/branch.out
-:language: console
-```
-
-:::{note}
-The above output may be printed in any order since the two `view` operations are executed asynchronously.
-:::
-
-A fallback condition can be specified using `true` as the last branch condition:
-
-```{literalinclude} ../snippets/branch-with-fallback.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/branch-with-fallback.out
-:language: console
-```
-
-The value emitted to each branch can be customized with an expression statement (or statements) after the branch condition:
-
-```{literalinclude} ../snippets/branch-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/branch-with-mapper.out
-:language: console
-```
-
-:::{tip}
-When the `return` keyword is omitted, the value of the last expression statement is implicitly returned.
-:::
-
-The `branchCriteria()` method can be used to create a branch criteria as a variable that can be passed as an argument to any number of `branch` operations, as shown below:
-
-```{literalinclude} ../snippets/branch-criteria.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/branch-criteria.out
-:language: console
-```
-
-## buffer
-
-*Returns: channel*
-
-The `buffer` operator collects items from a source channel into subsets and emits each subset separately.
-
-This operator has multiple variants:
-
-`buffer( closingCondition )`
-
-: Emits each subset when `closingCondition` is satisfied. The closing condition can be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
-
-  ```{literalinclude} ../snippets/buffer-with-closing.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/buffer-with-closing.out
-  :language: console
-  ```
-
-`buffer( openingCondition, closingCondition )`
-
-: Creates a new subset when `openingCondition` is satisfied and emits the subset when is `closingCondition` is satisfied. The opening and closing conditions can each be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
-
-  ```{literalinclude} ../snippets/buffer-with-opening-closing.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/buffer-with-opening-closing.out
-  :language: console
-  ```
-
-`buffer( size: n, remainder: true | false )`
-
-: Emits a new subset for every `n` items. Remaining items are discarded. For example:
-
-  ```{literalinclude} ../snippets/buffer-with-size.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/buffer-with-size.out
-  :language: console
-  ```
-
-  The `remainder` option can be used to emit any remaining items as a partial subset:
-
-  ```{literalinclude} ../snippets/buffer-with-size-remainder.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/buffer-with-size-remainder.out
-  :language: console
-  ```
-
-`buffer( size: n, skip: m, remainder: true | false )`
-
-: Emits a new subset for every `n` items, skipping `m` items before collecting each subset. For example:
-
-  ```{literalinclude} ../snippets/buffer-with-size-skip.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/buffer-with-size-skip.out
-  :language: console
-  ```
-
-  The `remainder` option can be used to emit any remaining items as a partial subset.
-
-See also: [collate](#collate)
-
-## collate
-
-*Returns: channel*
-
-The `collate` operator collects items from a source channel into groups of *N* items.
-
-This operator has multiple variants:
-
-`collate( size, remainder = true )`
-
-: Collects items into groups of `size` items:
-
-  ```{literalinclude} ../snippets/collate.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/collate.out
-  :language: console
-  ```
-
-  By default, any remaining items are emitted as a partial group. You can specify `false` as the second parameter to discard them instead:
-
-  ```{literalinclude} ../snippets/collate-with-no-remainder.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/collate-with-no-remainder.out
-  :language: console
-  ```
-
-  :::{note}
-  This version of `collate` is equivalent to `buffer( size: n, remainder: true | false )`.
-  :::
-
-`collate( size, step, remainder = true )`
-
-: Collects items into groups of `size` items using a *sliding window* that moves by `step` items at a time:
-
-  ```{literalinclude} ../snippets/collate-with-step.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/collate-with-step.out
-  :language: console
-  ```
-
-  You can specify `false` as the third parameter to discard any remaining items.
-
-See also: [buffer](#buffer)
-
-(operator-collect)=
-
-## collect
-
-*Returns: dataflow value*
-
-The `collect` operator collects all items from a source channel into a list and emits it as a single item:
-
-```{literalinclude} ../snippets/collect.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/collect.out
-:language: console
-```
-
-An optional {ref}`closure <script-closure>` can be used to transform each item before it is collected:
-
-```{literalinclude} ../snippets/collect-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/collect-with-mapper.out
-:language: console
-```
-
-Available options:
-
-`flat`
-: When `true`, nested list structures are flattened and their items are collected individually (default: `true`).
-
-`sort`
-: When `true`, the collected items are sorted by their natural ordering (default: `false`). Can also be a {ref}`closure <script-closure>` or a [Comparator](https://docs.oracle.com/javase/8/docs/api/java/util/Comparator.html) which defines how items are compared during sorting.
-
-See also: [toList](#tolist), [toSortedList](#tosortedlist)
-
-## collectFile
-
-*Returns: channel*
-
-The `collectFile` operator collects the items from a source channel and saves them to one or more files, emitting the collected file(s).
-
-This operator has multiple variants:
-
-`collectFile( name: '...', [options] )`
-
-: Collects the items and saves them to a single file specified by the `name` option:
-
-  ```{literalinclude} ../snippets/collectfile.nf
-  :language: nextflow
-  ```
-
-`collectFile( closure, [options] )`
-
-: Collects the items into groups and saves each group to a file, using a grouping criteria. The grouping criteria is a {ref}`closure <script-closure>` that maps each item to a pair, where the first element is the file name for the group and the second element is the content to be appended to that file. For example:
-
-  ```{literalinclude} ../snippets/collectfile-closure.nf
-  :language: nextflow
-  ```
-
-  ```{literalinclude} ../snippets/collectfile-closure.out
-  :language: console
-  ```
-
-  When the items from the source channel are files, the grouping criteria can be omitted. In this case, the items will be grouped by their source filename.
-
-The following example shows how to use a closure to collect and sort all sequences in a FASTA file from shortest to longest:
-
-```nextflow
-channel.fromPath('/data/sequences.fa')
-    .splitFasta( record: [id: true, sequence: true] )
-    .collectFile( name: 'result.fa', sort: { v -> v.size() } ) {
-        v -> v.sequence
-    }
-    .view { fa -> fa.text }
-```
-
-:::{warning}
-The `collectFile` operator needs to store files in a temporary directory that is automatically deleted on workflow completion. For performance reasons, this directory is located in the machine's local storage, and it should have as much free space as the data that is being collected. The `tempDir` option can be used to specify a different temporary directory.
-:::
-
-Available options:
-
-`cache`
-: Controls the caching ability of the `collectFile` operator when using the *resume* feature. It follows the same semantic of the {ref}`process-cache` directive (default: `true`).
-
-`keepHeader`
-: Prepend the resulting file with the header fetched in the first collected file. The header size (ie. lines) can be specified by using the `skip` option (default: `0`), to determine how many lines to remove from all collected files except for the first (where no lines will be removed).
-
-`name`
-: Name of the file where all received values are stored.
-
-`newLine`
-: Appends a `newline` character automatically after each entry (default: `false`).
-
-`seed`
-: A value or a map of values used to initialize the files content.
-
-`skip`
-: Skip the first `n` lines e.g. `skip: 1` (default: `0`).
-
-`sort`
-: Defines sorting criteria of content in resulting file(s). Can be one of the following values:
-
-  - `false`: Disable content sorting. Entries are appended as they are produced.
-  - `true`: Order the content by the entry's natural ordering i.e. numerical for number, lexicographic for string, etc. See the [Java documentation](http://docs.oracle.com/javase/tutorial/collections/interfaces/order.html) for more information.
-  - `'index'`: Order the content by the incremental index number assigned to each entry while they are collected.
-  - `'hash'`: (default) Order the content by the hash number associated to each entry
-  - `'deep'`: Similar to the previous, but the hash number is created on actual entries content e.g. when the entry is a file the hash is created on the actual file content.
-  - A custom sorting criteria can be specified with a {ref}`Closure <script-closure>` or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
-
-  The file content is sorted in such a way that it does not depend on the order in which entries were added to it, which guarantees that it is consistent (i.e. does not change) across different executions with the same data.
-
-`storeDir`
-: Folder where the resulting file(s) are stored.
-
-`tempDir`
-: Folder where temporary files, used by the collecting process, are stored.
-
-(operator-combine)=
-
-## combine
-
-*Returns: channel*
-
-The `combine` operator produces the combinations (i.e. cross product, "Cartesian" product) of two source channels, or a channel and a list (as the right operand), emitting each combination separately.
-
-For example:
-
-```{literalinclude} ../snippets/combine.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/combine.out
-:language: console
-```
-
-The `by` option can be used to combine items that share a matching key. The value should be the zero-based index of the tuple, or a list of indices. For example:
-
-```{literalinclude} ../snippets/combine-by.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/combine-by.out
-:language: console
-```
-
-:::{note}
-The `combine` operator is similar to `cross` and `join`, making them easy to confuse. Their differences can be summarized as follows:
-
-- `combine` and `cross` both produce an *outer product* or *cross product*, whereas `join` produces an *inner product*.
-
-- `combine` filters pairs with a matching key only if the `by` option is used, whereas `cross` always filters pairs with a matching key.
-
-- `combine` with the `by` option merges and flattens each pair, whereas `cross` does not. Compare the examples for `combine` and `cross` to see this difference.
-:::
-
-See also: [cross](#cross), [join](#join)
-
-(operator-concat)=
-
-## concat
-
-*Returns: channel*
-
-The `concat` operator emits the items from two or more source channels into a single output channel. Each source channel is emitted in the order in which it was specified.
-
-In other words, given *N* channels, the items from the *i+1*-th channel are emitted only after all of the items from the *i*-th channel have been emitted.
-
-For example:
-
-```{literalinclude} ../snippets/concat.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/concat.out
-:language: console
-```
-
-See also: [mix](#mix)
-
-(operator-count)=
-
-## count
-
-*Returns: dataflow value*
-
-The `count` operator computes the total number of items in a source channel and emits it:
-
-```{literalinclude} ../snippets/count.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/count.out
-:language: console
-```
-
-An optional filter can be provided to select which items to count. The selection criteria can be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
-
-```{literalinclude} ../snippets/count-with-filter-number.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/count-with-filter-number.out
-:language: console
-```
-
-```{literalinclude} ../snippets/count-with-filter-regex.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/count-with-filter-regex.out
-:language: console
-```
-
-```{literalinclude} ../snippets/count-with-filter-closure.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/count-with-filter-closure.out
-:language: console
-```
-
-(operator-countfasta)=
-
-## countFasta
-
-*Returns: dataflow value*
-
-Counts the total number of records in a channel of FASTA files, equivalent to `splitFasta | count`. See [splitFasta](#splitfasta) for the list of available options.
-
-(operator-countfastq)=
-
-## countFastq
-
-*Returns: dataflow value*
-
-Counts the total number of records in a channel of FASTQ files, equivalent to `splitFastq | count`. See [splitFastq](#splitfastq) for the list of available options.
-
-(operator-countjson)=
-
-## countJson
-
-*Returns: dataflow value*
-
-Counts the total number of records in a channel of JSON files, equivalent to `splitJson | count`. See [splitJson](#splitjson) for the list of available options.
-
-(operator-countlines)=
-
-## countLines
-
-*Returns: dataflow value*
-
-Counts the total number of lines in a channel of text files, equivalent to `splitText | count`. See [splitLines](#splittext) for the list of available options.
-
-(operator-cross)=
-
-## cross
-
-*Returns: channel*
-
-The `cross` operator emits every pairwise combination of two channels for which the pair has a matching key.
-
-By default, the key is defined as the first entry in a list or map, or the value itself for any other data type. For example:
-
-```{literalinclude} ../snippets/cross.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/cross.out
-:language: console
-```
-
-An optional closure can be used to define the matching key for each item:
-
-```{literalinclude} ../snippets/cross-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/cross-with-mapper.out
-:language: console
-```
-
-There are two important caveats when using the `cross` operator:
-
-1. The operator is not *commutative*, i.e. `a.cross(b)` is not the same as `b.cross(a)`
-2. Each source channel should not emit any items with duplicate keys, i.e. each item should have a unique key.
-
-See also: [combine](#combine)
-
-## distinct
-
-*Returns: channel*
-
-The `distinct` operator forwards a source channel with *consecutively* repeated items removed, such that each emitted item is different from the preceding one:
-
-```{literalinclude} ../snippets/distinct.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/distinct.out
-:language: console
-```
-
-An optional {ref}`closure <script-closure>` can be used to transform each value before it is evaluated for distinct-ness:
-
-```{literalinclude} ../snippets/distinct-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/distinct-with-mapper.out
-:language: console
-```
-
-See also: [unique](#unique)
-
-(operator-dump)=
-
-## dump
-
-*Returns: channel*
-
-The `dump` operator prints each item in a source channel when the pipeline is executed with the `-dump-channels` command-line option, otherwise it does nothing. It is a useful way to inspect and debug channels quickly without having to modify the pipeline script.
-
-The `tag` option can be used to select which channels to dump:
-
-```{literalinclude} ../snippets/dump.nf
-:language: nextflow
-```
-
-Then, you can run your pipeline with `-dump-channels plus1` or `-dump-channels exp2` to dump the content of either channel. Multiple tag names can be specified as a comma-separated list.
-
-Available options:
-
-`pretty`
-: :::{versionadded} 22.10.0
-  :::
-: When `true`, format the output as pretty-printed JSON (default: `false`).
-
-`tag`
-: Associate the channel with a tag that can be specified with the `-dump-channels` option to select which channels to dump.
-
-(operator-filter)=
-
-## filter
-
-*Returns: channel*
-
-The `filter` operator emits the items from a source channel that satisfy a condition, discarding all other items. The filter condition can be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate.
-
-The following example filters a channel with a regular expression that only matches strings beginning with `a`:
-
-```{literalinclude} ../snippets/filter-regex.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/filter-regex.out
-:language: console
-```
-
-The following example filters a channel with the `Number` type qualifier so that only numbers are emitted:
-
-```{literalinclude} ../snippets/filter-type.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/filter-type.out
-:language: console
-```
-
-The following example filters a channel using a boolean predicate, which is a {ref}`closure <script-closure>` that returns a boolean value. In this case, the predicate is used to select only odd numbers:
-
-```{literalinclude} ../snippets/filter-closure.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/filter-closure.out
-:language: console
-```
-
-(operator-first)=
-
-## first
-
-*Returns: dataflow value*
-
-The `first` operator emits the first item in a source channel, or the first item that matches a condition. The condition can be a {ref}`regular expression<script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
-
-```{literalinclude} ../snippets/first.nf
-:language: nextflow
-```
-
-(operator-flatmap)=
-
-## flatMap
-
-*Returns: channel*
-
-The `flatMap` operator applies a *mapping function* to each item from a source channel.
-
-When the mapping function returns a list, each element in the list is emitted separately:
-
-```{literalinclude} ../snippets/flatmap-list.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/flatmap-list.out
-:language: console
-```
-
-When the mapping function returns a map, each key-value pair in the map is emitted separately:
-
-```{literalinclude} ../snippets/flatmap-map.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/flatmap-map.out
-:language: console
-```
-
-(operator-flatten)=
-
-## flatten
-
-*Returns: channel*
-
-The `flatten` operator flattens each item from a source channel that is a list or other collection, such that each element in each collection is emitted separately:
-
-```{literalinclude} ../snippets/flatten.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/flatten.out
-:language: console
-```
-
-As shown in the above example, deeply nested collections are also flattened.
-
-See also: [flatMap](#flatmap)
-
-(operator-grouptuple)=
-
-## groupTuple
-
-*Returns: channel*
-
-The `groupTuple` operator collects lists (i.e. *tuples*) from a source channel into groups based on a grouping key. A new tuple is emitted for each distinct key.
-
-To be more precise, the operator transforms a sequence of tuples like *(K, V, W, ..)* into a sequence of tuples like *(K, list(V), list(W), ..)*.
-
-For example:
-
-```{literalinclude} ../snippets/grouptuple.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/grouptuple.out
-:language: console
-```
-
-By default, the first element of each tuple is used as the grouping key. The `by` option can be used to specify a different index, or list of indices. For example, to group by the second element of each tuple:
-
-```{literalinclude} ../snippets/grouptuple-by.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/grouptuple-by.out
-:language: console
-```
-
-By default, if you don't specify a size, the `groupTuple` operator will not emit any groups until *all* inputs have been received. If possible, you should always try to specify the number of expected elements in each group using the `size` option, so that each group can be emitted as soon as it's ready. In cases where the size of each group varies based on the grouping key, you can use the built-in `groupKey()` function, which allows you to define a different expected size for each group:
-
-```{literalinclude} ../snippets/grouptuple-groupkey.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/grouptuple-groupkey.out
-:language: console
-```
-
-Available options:
-
-`by`
-: The zero-based index of the element to use as the grouping key. Can also be a list of indices, e.g. `by: [0,2]` (default: `[0]`).
-
-`remainder`
-: When `true`, incomplete tuples (i.e. groups with less than `size` items) are emitted as partial groups, otherwise they are discarded (default: `false`). This option can only be used with `size`.
-
-`size`
-: The required number of items for each group. When a group reaches the required size, it is emitted.
-
-`sort`
-: Defines the sorting criteria for the grouped items. Can be one of the following values:
-
-  - `false`: No sorting is applied (default).
-  - `true`: Order the grouped items by the item's natural ordering i.e. numerical for number, lexicographic for string, etc. See the [Java documentation](http://docs.oracle.com/javase/tutorial/collections/interfaces/order.html) for more information.
-  - `'hash'`: Order the grouped items by the hash number associated to each entry.
-  - `'deep'`: Similar to the previous, but the hash number is created on actual entries content e.g. when the item is a file, the hash is created on the actual file content.
-  - A custom sorting criteria used to order the nested list elements of each tuple. It can be a {ref}`Closure <script-closure>` or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
-
-(operator-ifempty)=
-
-## ifEmpty
-
-*Returns: channel*
-
-The `ifEmpty` operator emits a source channel, or a default value if the source channel is *empty* (doesn't emit any value):
-
-```{literalinclude} ../snippets/ifempty-1.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/ifempty-1.out
-:language: console
-```
-
-```{literalinclude} ../snippets/ifempty-2.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/ifempty-2.out
-:language: console
-```
-
-The default value can also be a {ref}`closure <script-closure>`, in which case the closure is evaluated and the result is emitted when the source channel is empty.
-
-See also: {ref}`channel-empty` channel factory
-
-(operator-join)=
-
-## join
-
-*Returns: channel*
-
-The `join` operator emits the inner product of two source channels using a matching key.
-
-To be more precise, the operator transforms a sequence of tuples like *(K, V1, V2, ..)* and *(K, W1, W1, ..)* into a sequence of tuples like *(K, V1, V2, .., W1, W2, ..)*.
-
-For example:
-
-```{literalinclude} ../snippets/join.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/join.out
-:language: console
-```
-
-By default, the first element of each item is used as the key. The `by` option can be used to specify a different index, or list of indices.
-
-By default, unmatched items are discarded. The `remainder` option can be used to emit them at the end:
-
-```{literalinclude} ../snippets/join-with-remainder.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/join-with-remainder.out
-:language: console
-```
-
-:::{note}
-The `join` operator is similar to an SQL *inner join*, or an SQL *outer join* when `remainder` is `true`. The only difference is that `join` does not support duplicate keys, whereas an SQL join produces the cross-product of duplicate keys. The `combine` operator with the `by` option is equivalent to an SQL join.
-:::
-
-Available options:
-
-`by`
-: The zero-based index of each item to use as the matching key. Can also be a list of indices, e.g. `by: [0, 2]` (default: `[0]`).
-
-`failOnDuplicate`
-: When `true`, an error is reported when the operator receives multiple items from the same channel with the same key (default: `false`). Value is set to `true` if {ref}`strict mode <config-feature-flags>` is enabled.
-
-`failOnMismatch`
-: When `true`, an error is reported when the operator receives an item from one channel for which there no matching item from the other channel (default: `false`). Value is set to `true` if {ref}`strict mode <config-feature-flags>` is enabled. This option cannot be used with `remainder`.
-
-`remainder`
-: When `true`, unmatched items are emitted at the end, otherwise they are discarded (default: `false`). 
-
-See also: [combine](#combine), [cross](#cross)
-
-(operator-last)=
-
-## last
-
-*Returns: dataflow value*
-
-The `last` operator emits the last item from a source channel:
-
-```{literalinclude} ../snippets/last.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/last.out
-:language: console
-```
-
-(operator-map)=
-
-## map
-
-*Returns: channel*
-
-The `map` operator applies a *mapping function* to each item from a source channel:
-
-```{literalinclude} ../snippets/map.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/map.out
-:language: console
-```
-
-:::{note}
-`null` values are not emitted by `map`.
-:::
-
-(operator-max)=
-
-## max
-
-*Returns: dataflow value*
-
-The `max` operator emits the item with the greatest value from a source channel:
-
-```{literalinclude} ../snippets/max.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/max.out
-:language: console
-```
-
-An optional {ref}`closure <script-closure>` can be used to control how the items are compared. The closure can be a *mapping function*, which transforms each item before it is compared, or a *comparator function*, which defines how to compare two items more generally.
-
-The following examples show how to find the longest string in a channel:
-
-```{literalinclude} ../snippets/max-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/max-with-mapper.out
-:language: console
-```
-
-```{literalinclude} ../snippets/max-with-comparator.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/max-with-comparator.out
-:language: console
-```
-
-(operator-merge)=
-
-## merge
-
-*Returns: channel*
-
-The `merge` operator joins the items from two or more channels into a new channel:
-
-```{literalinclude} ../snippets/merge.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/merge.out
-:language: console
-```
-
-An optional closure can be used to control how two items are merged:
-
-```{literalinclude} ../snippets/merge-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/merge-with-mapper.out
-:language: console
-```
-
-The `merge` operator may return a channel or value depending on the inputs:
-
-- If the first argument is a channel, the `merge` operator returns a channel merging as many values as are available for all inputs. Dataflow values are re-used for each merged value.
-
-- If the first argument is a dataflow value, the `merge` operator returns a dataflow value, merging the first value from each input, regardless of whether there are channel inputs with additional values.
-
-:::{danger}
-In general, the use of the `merge` operator is discouraged. Processes and channel operators are not guaranteed to emit items in the order that they were received, as they are executed concurrently. Therefore, if you try to merge output channels from different processes, the resulting channel may be different on each run, which will cause resumed runs to {ref}`not work properly <cache-nondeterministic-inputs>`.
-
-You should always use a matching key (e.g. sample ID) to merge multiple channels, so that they are combined in a deterministic way. For this purpose, you can use the [join](#join) operator.
-:::
-
-(operator-min)=
-
-## min
-
-*Returns: dataflow value*
-
-The `min` operator emits the item with the lowest value from a source channel:
-
-```{literalinclude} ../snippets/min.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/min.out
-:language: console
-```
-
-An optional {ref}`closure <script-closure>` can be used to control how the items are compared. The closure can be a *mapping function*, which transforms each item before it is compared, or a *comparator function*, which defines how to compare two items more generally.
-
-The following examples show how to find the shortest string in a channel:
-
-```{literalinclude} ../snippets/min-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/min-with-mapper.out
-:language: console
-```
-
-```{literalinclude} ../snippets/min-with-comparator.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/min-with-comparator.out
-:language: console
-```
-
-(operator-mix)=
-
-## mix
-
-*Returns: channel*
-
-The `mix` operator emits the items from two or more source channels into a single output channel:
-
-```{literalinclude} ../snippets/mix.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/mix.out
-:language: console
-```
-
-The items in the mixed output channel may appear in any order, regardless of which source channel they came from. Thus, the previous example could also output the following:
-
-```console
-z
-1
-a
-2
-b
-3
-```
-
-See also: [concat](#concat)
-
-(operator-multimap)=
-
-## multiMap
-
-:::{versionadded} 19.11.0-edge
-:::
-
-*Returns: multiple channels*
-
-The `multiMap` operator applies a set of mapping functions to a source channel, producing a separate output channel for each mapping function.
-
-The multi-map criteria is a {ref}`closure <script-closure>` that defines, for each output channel, a label followed by a mapping expression.
-
-For example:
-
-```{literalinclude} ../snippets/multimap.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/multimap.out
-:language: console
-```
-
-Multiple labels can share the same mapping expression using the following shorthand:
-
-```{literalinclude} ../snippets/multimap-shared.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/multimap-shared.out
-:language: console
-```
-
-The above example creates two channels as before, but now they both receive the same items.
-
-You can use the `multiMapCriteria()` method to create a multi-map criteria as a variable that can be passed as an argument to any number of `multiMap` operations, as shown below:
-
-```{literalinclude} ../snippets/multimap-criteria.nf
-:language: nextflow
-```
-
-:::{note}
-If you use `multiMap` to split a tuple or map into multiple channels, it is recommended that you retain a matching key (e.g. sample ID) with *each* new channel, so that you can re-combine these channels later on if needed. In general, you should not expect to be able to merge channels correctly without a matching key, due to the concurrent nature of Nextflow pipelines.
-:::
-
-(operator-randomsample)=
-
-## randomSample
-
-*Returns: channel*
-
-The `randomSample` operator emits a randomly-selected subset of items from a source channel:
-
-```{literalinclude} ../snippets/random-sample.nf
-:language: nextflow
-```
-
-The above snippet will print 10 randomly-selected numbers between 1 and 100 (without replacement).
-
-An optional second parameter can be used to set the initial *seed* for the random number generator, which ensures that the `randomSample` operator produces the same pseudo-random sequence across runs:
-
-```{literalinclude} ../snippets/random-sample-with-seed.nf
-:language: nextflow
-```
-
-The above example will print 10 randomly-selected numbers between 1 and 100 (without replacement). Each subsequent script execution will produce the same sequence.
-
-(operator-reduce)=
-
-## reduce
-
-*Returns: dataflow value*
-
-The `reduce` operator applies an *accumulator function* sequentially to each item in a source channel, and emits the final accumulated value. The accumulator function takes two parameters -- the accumulated value and the *i*-th emitted item -- and it should return the accumulated result, which is passed to the next invocation with the *i+1*-th item. This process is repeated for each item in the source channel.
-
-For example:
-
-```{literalinclude} ../snippets/reduce.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/reduce.out
-:language: console
-```
-
-By default, the first item is used as the initial accumulated value. You can optionally specify a different initial value as shown below:
-
-```{literalinclude} ../snippets/reduce-with-initial-value.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/reduce-with-initial-value.out
-:language: console
-```
-
-(operator-set)=
-
-## set
-
-*Returns: nothing*
-
-The `set` operator assigns a source channel to a variable, whose name is specified as a closure parameter:
-
-```nextflow
-channel.of(10, 20, 30).set { my_channel }
-```
-
-Using `set` is semantically equivalent to assigning a variable:
-
-```nextflow
-my_channel = channel.of(10, 20, 30)
-```
-
-See also: [tap](#tap)
-
-(operator-splitcsv)=
-
-## splitCsv
-
-*Returns: channel*
-
-The `splitCsv` operator parses and splits [CSV](http://en.wikipedia.org/wiki/Comma-separated_values) files or text from a source channel into records.
-
-For example:
-
-```{literalinclude} ../snippets/splitcsv.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/splitcsv.out
-:language: console
-```
-
-The above example shows hows CSV text is parsed and split into individual rows, where each row is simply a list of columns.
-
-When the CSV begins with a header line defining the column names, and the `header` option is `true`, each row is returned as a map instead:
-
-```{literalinclude} ../snippets/splitcsv-with-header.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/splitcsv-with-header.out
-:language: console
-```
-
-The `header` option can also just be a list of columns:
-
-```{literalinclude} ../snippets/splitcsv-with-columns.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/splitcsv-with-columns.out
-:language: console
-```
-
-Available options:
-
-`by`
-: When specified, group rows into *chunks* with the given size (default: none).
-
-`charset`
-: Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
-
-`decompress`
-: When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
-
-`elem`
-: The index of the element to split when the source items are lists or tuples (default: first file object or first element).
-
-`header`
-: When `true`, the first line is used as the columns names (default: `false`). Can also be a list of columns names.
-
-`limit`
-: Limits the number of records to retrieve for each source item (default: no limit).
-
-`quote`
-: The character used to quote values (default: `''` or `""`).
-
-`sep`
-: The character used to separate values (default: `,`)
-
-`skip`
-: Number of lines to ignore from the beginning when parsing the CSV text (default: `0`).
-
-`strip`
-: When `true`, remove leading and trailing blanks from values (default: `false`).
-
-(operator-splitfasta)=
-
-## splitFasta
-
-*Returns: channel*
-
-The `splitFasta` operator splits [FASTA](http://en.wikipedia.org/wiki/FASTA_format) files or text from a source channel into individual sequences.
-
-The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTA file and split it into chunks of 10 sequences each:
-
-```nextflow
-channel.fromPath('misc/sample.fa')
-    .splitFasta( by: 10 )
-    .view()
-```
-
-:::{warning}
-Chunks are stored in memory by default. When splitting large files, specify `file: true` to save the chunks into files in order to avoid running out of memory. See the list of options below for details.
-:::
-
-The `record` option can be used to split FASTA content into *records* instead of text chunks. Each record is a map that allows you to access the FASTA sequence data with ease. For example:
-
-```nextflow
-channel.fromPath('misc/sample.fa')
-    .splitFasta( record: [id: true, seqString: true] )
-    .filter { record -> record.id =~ /^ENST0.*/ }
-    .view { record -> record.seqString }
-```
-
-The above example loads the `misc/sample.fa` file, splits it into records containing the `id` and `seqString` fields (i.e. the sequence id and the sequence data), filters records by their ID, and finally prints the sequence string of each record.
-
-Available options:
-
-`by`
-: Defines the number of sequences in each chunk (default: `1`).
-
-`charset`
-: Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
-
-`compress`
-: When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
-
-`decompress`
-: When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
-
-`elem`
-: The index of the element to split when the source items are lists or tuples (default: first file object or first element).
-
-`file`
-: When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
-
-`limit`
-: Limits the number of sequences to retrieve for each source item (default: no limit).
-
-`record`
-: Parse each entry in the FASTA file into a record. The following fields are available:
-
-  - `id`: The FASTA sequence identifier, i.e. the word following the `>` symbol up to the first blank or newline character
-  - `header`: The first line in a FASTA sequence without the `>` character
-  - `desc`: The text in the FASTA header following the ID value
-  - `text`: The complete FASTA sequence including the header
-  - `seqString`: The sequence data as a single-line string, i.e. containing no newline characters
-  - `sequence`: The sequence data as a multi-line string, i.e. always ending with a newline character
-  - `width`: Define the length of a single line when the `sequence` field is used, after which the sequence data continues on a new line.
-
-`size`
-: Defines the size of the expected chunks as a memory unit, e.g. `1.MB`.
-
-See also: [countFasta](#countfasta)
-
-(operator-splitfastq)=
-
-## splitFastq
-
-*Returns: channel*
-
-The `splitFastq` operator splits [FASTQ](http://en.wikipedia.org/wiki/FASTQ_format) files or text from a source channel into individual sequences.
-
-The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTQ file and split it into chunks of 10 sequences each:
-
-```nextflow
-channel.fromPath('misc/sample.fastq')
-    .splitFastq( by: 10 )
-    .view()
-```
-
-:::{warning}
-Chunks are stored in memory by default. When splitting large files, specify `file: true` to save the chunks into files in order to avoid running out of memory. See the list of options below for details.
-:::
-
-The `record` option can be used to split FASTQ content into *records* instead of text chunks. Each record is a map that allows you to access the FASTQ sequence data with ease. For example:
-
-```nextflow
-channel.fromPath('misc/sample.fastq')
-    .splitFastq( record: true )
-    .view { record -> record.readHeader }
-```
-
-The `pe` option can be used to split paired-end FASTQ files. The source channel must emit tuples containing the file pairs. For example:
-
-```nextflow
-channel.fromFilePairs('/my/data/SRR*_{1,2}.fastq', flat: true)
-    .splitFastq(by: 100_000, pe: true, file: true)
-    .view()
-```
-
-:::{note}
-`channel.fromFilePairs()` requires the `flat: true` option in order to emit the file pairs as separate elements in the produced tuples.
-:::
-
-:::{note}
-This operator assumes that the order of the paired-end reads correspond with each other and that both files contain the same number of reads.
-:::
-
-Available options:
-
-`by`
-: Defines the number of sequences in each chunk (default: `1`).
-
-`charset`
-: Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
-
-`compress`
-: When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
-
-`decompress`
-: When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
-
-`elem`
-: The index of the element to split when the source items are lists or tuples (default: first file object or first element).
-
-`file`
-: When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
-
-`limit`
-: Limits the number of sequences to retrieve for each source item (default: no limit).
-
-`pe`
-: When `true`, splits paired-end read files. Items emitted by the source channel must be tuples with the file pairs.
-
-`record`
-: Parse each entry in the FASTQ file into a record. The following fields are available:
-
-  - `readHeader`: Sequence header (without the `@` prefix)
-  - `readString`: The raw sequence data
-  - `qualityHeader`: Base quality header (it may be empty)
-  - `qualityString`: Quality values for the sequence
-
-See also: [countFastq](#countfastq)
-
-(operator-splitjson)=
-
-## splitJson
-
-*Returns: channel*
-
-The `splitJson` operator splits [JSON](https://en.wikipedia.org/wiki/JSON) files or text from a source channel into individual records.
-
-If the source item is a JSON array, each element of the array will be emitted:
-
-```{literalinclude} ../snippets/splitjson-array.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/splitjson-array.out
-:language: console
-```
-
-If the source item is a JSON object, each key-value pair will be emitted as a map with the properties `key`  and `value`:
-
-```{literalinclude} ../snippets/splitjson-object.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/splitjson-object.out
-:language: console
-```
-
-The `path` option can be used to query a section of the JSON document to parse and split:
-
-```{literalinclude} ../snippets/splitjson-with-path.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/splitjson-with-path.out
-:language: console
-```
-
-Available options:
-
-`limit`
-: Limits the number of records to retrieve for each source item (default: no limit).
-
-`path`
-: Defines a query for a section of each source item to parse and split. The expression should be a path similar to [JSONPath](https://goessner.net/articles/JsonPath/). The empty string is the document root (default). An integer in brackets is a zero-based index in a JSON array. A string preceded by a dot `.` is a key in a JSON object.
-
-See also: [countJson](#countjson)
-
-(operator-splittext)=
-
-## splitText
-
-*Returns: channel*
-
-The `splitText` operator splits multi-line text content from a source channel into chunks of *N* lines:
-
-```nextflow
-channel.fromPath('/some/path/*.txt')
-    .splitText()
-    .view()
-```
-
-The above example loads a collection of text files, splits the content of each file into individual lines, and prints each line.
-
-The `by` option can be used to emit chunks of *N* lines:
-
-```nextflow
-channel.fromPath('/some/path/*.txt')
-    .splitText( by: 10 )
-    .subscribe { chunk ->
-        print chunk
-        print "--- end of the chunk ---\n"
-    }
-```
-
-An optional {ref}`closure <script-closure>` can be used to transform each text chunk produced by the operator. The following example shows how to split text files into chunks of 10 lines and transform them to uppercase letters:
-
-```nextflow
-channel.fromPath('/some/path/*.txt')
-    .splitText( by: 10 ) { v -> v.toUpperCase() }
-    .view()
-```
-
-:::{note}
-Text chunks returned by the `splitText` operator are always terminated by a `\n` newline character.
-:::
-
-Available options:
-
-`by`
-: Defines the number of lines in each `chunk` (default: `1`).
-
-`charset`
-: Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
-
-`compress`
-: When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
-
-`decompress`
-: When `true`, decompresses the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
-
-`elem`
-: The index of the element to split when the source items are lists or tuples (default: first file object or first element).
-
-`file`
-: When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
-
-`keepHeader`
-: Parses the first line as header and prepends it to each emitted chunk (default: `false`).
-
-`limit`
-: Limits the number of lines to retrieve for each source item (default: no limit).
-
-See also: [countLines](#countlines)
-
-(operator-subscribe)=
-
-## subscribe
-
-*Returns: nothing*
-
-The `subscribe` operator invokes a custom function for each item from a source channel:
-
-```{literalinclude} ../snippets/subscribe.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/subscribe.out
-:language: console
-```
-
-The `subscribe` operator supports multiple types of event handlers:
-
-```{literalinclude} ../snippets/subscribe-with-on-complete.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/subscribe-with-on-complete.out
-:language: console
-```
-
-:::{note}
-Unlike most operators, `subscribe` is a *terminal operator* and does not emit any values. It should only be used for *side effects*, such as printing to the console, writing to a file, or making HTTP requests.
-:::
-
-Available options:
-
-`onNext`
-: Closure that is invoked when an item is emitted. Equivalent to providing a closure as the first argument.
-
-`onComplete`
-: Closure that is invoked after the last item is emitted by the channel.
-
-`onError`
-: Closure that is invoked when an exception is raised while handling the `onNext` event. It will not make further calls to `onNext` or `onComplete`. The `onError` method takes as its parameter the `Throwable` that caused the error.
-
-(operator-sum)=
-
-## sum
-
-*Returns: dataflow value*
-
-The `sum` operator emits the sum of all items in a source channel:
-
-```{literalinclude} ../snippets/sum.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/sum.out
-:language: console
-```
-
-An optional {ref}`closure <script-closure>` can be used to transform each item before it is added to the sum:
-
-```{literalinclude} ../snippets/sum-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/sum-with-mapper.out
-:language: console
-```
-
-(operator-take)=
-
-## take
-
-*Returns: channel*
-
-The `take` operator takes the first *N* items from a source channel:
-
-```{literalinclude} ../snippets/take.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/take.out
-:language: console
-```
-
-:::{tip}
-Specifying a size of `-1` causes the operator to take all values.
-:::
-
-See also: [until](#until)
-
-## tap
-
-*Returns: channel*
-
-The `tap` operator assigns a source channel to a variable, and emits the source channel. It is a useful way to extract intermediate output channels from a chain of operators. For example:
-
-```{literalinclude} ../snippets/tap.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/tap.out
-:language: console
-```
-
-See also: [set](#set)
-
-## toInteger
-
-*Returns: channel*
-
-The `toInteger` operator converts string values from a source channel to integer values:
-
-```{literalinclude} ../snippets/tointeger.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/tointeger.out
-:language: console
-```
-
-:::{note}
-`toInteger` is equivalent to:
-
-```nextflow
-map { v -> v as Integer }
-```
-:::
-
-:::{note}
-You can also use `toLong`, `toFloat`, and `toDouble` to convert to other numerical types.
-:::
-
-## toList
-
-*Returns: dataflow value*
-
-The `toList` operator collects all the items from a source channel into a list and emits the list as a single item:
-
-```{literalinclude} ../snippets/tolist.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/tolist.out
-:language: console
-```
-
-:::{note}
-There are two main differences between `toList` and `collect`:
-
-- When there is no input, `toList` emits an empty list whereas `collect` emits nothing.
-- By default, `collect` flattens list items by one level.
-
-In other words, `toList` is equivalent to:
-
-```nextflow
-collect(flat: false).ifEmpty([])
-```
-:::
-
-See also: [collect](#collect)
-
-## toSortedList
-
-*Returns: dataflow value*
-
-The `toSortedList` operator collects all the items from a source channel into a sorted list and emits the list as a single item:
-
-```{literalinclude} ../snippets/tosortedlist.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/tosortedlist.out
-:language: console
-```
-
-An optional closure can be used to control how items are compared when sorting. For example, to sort tuples by their second element in descending order:
-
-```{literalinclude} ../snippets/tosortedlist-with-comparator.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/tosortedlist-with-comparator.out
-:language: console
-```
-
-:::{note}
-`toSortedList` is equivalent to:
-
-```nextflow
-collect(flat: false, sort: true).ifEmpty([])
-```
-:::
-
-See also: [collect](#collect)
-
-## transpose
-
-*Returns: channel*
-
-The `transpose` operator "transposes" each tuple from a source channel by flattening any nested list in each tuple, emitting each nested item separately.
-
-To be more precise, the operator transforms a sequence of tuples like *(K, list(V), list(W), ..)* into a sequence of tuples like *(K, V, W, ..)*.
-
-For example:
-
-```{literalinclude} ../snippets/transpose-1.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/transpose-1.out
-:language: console
-```
-
-If each source item has more than two elements, these will be flattened by the first element in the item, and a new item will be emitted only when it is complete:
-
-```{literalinclude} ../snippets/transpose-2.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/transpose-2.out
-:language: console
-```
-
-The `remainder` option can be used to emit any incomplete items:
-
-```{literalinclude} ../snippets/transpose-2-with-remainder.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/transpose-2-with-remainder.out
-:language: console
-```
-
-Available options:
-
-`by`
-: The zero-based index of the element to be transposed. Can also be a list of indices, e.g. `by: [0,2]`. By default, every list element is transposed.
-
-`remainder`
-: When `true`, incomplete tuples are emitted with `null` values for missing elements, otherwise they are discarded (default: `false`). 
-
-See also: [groupTuple](#grouptuple)
-
-(operator-unique)=
-
-## unique
-
-*Returns: channel*
-
-The `unique` operator emits the unique items from a source channel:
-
-```{literalinclude} ../snippets/unique.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/unique.out
-:language: console
-```
-
-An optional {ref}`closure <script-closure>` can be used to transform each item before it is evaluated for uniqueness:
-
-```{literalinclude} ../snippets/unique-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/unique-with-mapper.out
-:language: console
-```
-
-:::{note}
-The difference between `unique` and `distinct` is that `unique` removes *all* duplicate values, whereas `distinct` removes only *consecutive* duplicate values. As a result, `unique` must process the entire source channel before it can emit anything, whereas `distinct` can emit each value immediately.
-:::
-
-See also: [distinct](#distinct)
-
-(operator-until)=
-
-## until
-
-*Returns: channel*
-
-The `until` operator emits each item from a source channel until a stopping condition is satisfied:
-
-```{literalinclude} ../snippets/until.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/until.out
-:language: console
-```
-
-See also: [take](#take)
-
-(operator-view)=
-
-## view
-
-*Returns: channel*
-
-The `view` operator prints each item from a source channel to standard output:
-
-```{literalinclude} ../snippets/view.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/view.out
-:language: console
-```
-
-An optional closure can be used to transform each item before it is printed:
-
-```{literalinclude} ../snippets/view-with-mapper.nf
-:language: nextflow
-```
-
-```{literalinclude} ../snippets/view-with-mapper.out
-:language: console
-```
-
-The `view` operator also emits every item that it receives, allowing it to be chained with other operators.
-
-Available options:
-
-`newLine`
-: Print each item to a separate line (default: `true`).
diff --git a/docs/reference/operator.mdx b/docs/reference/operator.mdx
new file mode 100644
index 0000000000..3f2b36d31f
--- /dev/null
+++ b/docs/reference/operator.mdx
@@ -0,0 +1,1572 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Operators
+
+## branch
+
+*Returns: multiple channels*
+
+The `branch` operator forwards each item from a source channel to one of multiple output channels, based on a selection criteria.
+
+The selection criteria is a [closure][script-closure] that defines, for each output channel, a unique label followed by a boolean expression. When an item is received, it is routed to the first output channel whose expression evaluates to `true`. For example:
+
+```nextflow file=../snippets/branch.nf
+```
+
+```console file=../snippets/branch.out
+```
+
+:::note
+The above output may be printed in any order since the two `view` operations are executed asynchronously.
+:::
+
+A fallback condition can be specified using `true` as the last branch condition:
+
+```nextflow file=../snippets/branch-with-fallback.nf
+```
+
+```console file=../snippets/branch-with-fallback.out
+```
+
+The value emitted to each branch can be customized with an expression statement (or statements) after the branch condition:
+
+```nextflow file=../snippets/branch-with-mapper.nf
+```
+
+```console file=../snippets/branch-with-mapper.out
+```
+
+:::tip
+When the `return` keyword is omitted, the value of the last expression statement is implicitly returned.
+:::
+
+The `branchCriteria()` method can be used to create a branch criteria as a variable that can be passed as an argument to any number of `branch` operations, as shown below:
+
+```nextflow file=../snippets/branch-criteria.nf
+```
+
+```console file=../snippets/branch-criteria.out
+```
+
+## buffer
+
+*Returns: queue channel*
+
+The `buffer` operator collects items from a source channel into subsets and emits each subset separately.
+
+This operator has multiple variants:
+
+##### `buffer( closingCondition )`
+
+Emits each subset when `closingCondition` is satisfied. The closing condition can be a literal value, a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate. For example:
+
+```nextflow file=../snippets/buffer-with-closing.nf
+```
+
+```console file=../snippets/buffer-with-closing.out
+```
+
+##### `buffer( openingCondition, closingCondition )`
+
+Creates a new subset when `openingCondition` is satisfied and emits the subset when is `closingCondition` is satisfied. The opening and closing conditions can each be a literal value, a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate. For example:
+
+```nextflow file=../snippets/buffer-with-opening-closing.nf
+```
+
+```console file=../snippets/buffer-with-opening-closing.out
+```
+
+##### `buffer( size: n, remainder: true | false )`
+
+Emits a new subset for every `n` items. Remaining items are discarded. For example:
+
+```nextflow file=../snippets/buffer-with-size.nf
+```
+
+```console file=../snippets/buffer-with-size.out
+```
+
+The `remainder` option can be used to emit any remaining items as a partial subset:
+
+```nextflow file=../snippets/buffer-with-size-remainder.nf
+```
+
+```console file=../snippets/buffer-with-size-remainder.out
+```
+
+##### `buffer( size: n, skip: m, remainder: true | false )`
+
+Emits a new subset for every `n` items, skipping `m` items before collecting each subset. For example:
+
+```nextflow file=../snippets/buffer-with-size-skip.nf
+```
+
+```console file=../snippets/buffer-with-size-skip.out
+```
+
+The `remainder` option can be used to emit any remaining items as a partial subset.
+
+#
+
+See also: [collate](#collate)
+
+## collate
+
+*Returns: channel*
+
+The `collate` operator collects items from a source channel into groups of *N* items.
+
+This operator has multiple variants:
+
+##### `collate( size, remainder = true )`
+
+Collects items into groups of `size` items:
+
+```nextflow file=../snippets/collate.nf
+```
+
+```console file=../snippets/collate.out
+```
+
+By default, any remaining items are emitted as a partial group. You can specify `false` as the second parameter to discard them instead:
+
+```nextflow file=../snippets/collate-with-no-remainder.nf
+```
+
+```console file=../snippets/collate-with-no-remainder.out
+```
+
+:::note
+This version of `collate` is equivalent to `buffer( size: n, remainder: true | false )`.
+:::
+
+##### `collate( size, step, remainder = true )`
+
+Collects items into groups of `size` items using a *sliding window* that moves by `step` items at a time:
+
+```nextflow file=../snippets/collate-with-step.nf
+```
+
+```console file=../snippets/collate-with-step.out
+```
+
+You can specify `false` as the third parameter to discard any remaining items.
+
+#
+
+See also: [buffer](#buffer)
+
+## collect
+
+*Returns: dataflow value*
+
+The `collect` operator collects all items from a source channel into a list and emits it as a single item:
+
+```nextflow file=../snippets/collect.nf
+```
+
+```console file=../snippets/collect.out
+```
+
+An optional [closure][script-closure] can be used to transform each item before it is collected:
+
+```nextflow file=../snippets/collect-with-mapper.nf
+```
+
+```console file=../snippets/collect-with-mapper.out
+```
+
+Available options:
+
+##### `flat`
+
+When `true`, nested list structures are flattened and their items are collected individually (default: `true`).
+
+##### `sort`
+
+When `true`, the collected items are sorted by their natural ordering (default: `false`). Can also be a [closure][script-closure] or a [Comparator](https://docs.oracle.com/javase/8/docs/api/java/util/Comparator.html) which defines how items are compared during sorting.
+
+#
+
+See also: [toList][operator-tolist], [toSortedList][operator-tosortedlist]
+
+## collectFile
+
+*Returns: channel*
+
+The `collectFile` operator collects the items from a source channel and saves them to one or more files, emitting the collected file(s).
+
+This operator has multiple variants:
+
+##### `collectFile( name: '...', [options] )`
+
+Collects the items and saves them to a single file specified by the `name` option:
+
+```nextflow file=../snippets/collectfile.nf
+```
+
+##### `collectFile( closure, [options] )`
+
+Collects the items into groups and saves each group to a file, using a grouping criteria. The grouping criteria is a [closure][script-closure] that maps each item to a pair, where the first element is the file name for the group and the second element is the content to be appended to that file. For example:
+
+```nextflow file=../snippets/collectfile-closure.nf
+```
+
+```console file=../snippets/collectfile-closure.out
+```
+
+When the items from the source channel are files, the grouping criteria can be omitted. In this case, the items will be grouped by their source filename.
+
+The following example shows how to use a closure to collect and sort all sequences in a FASTA file from shortest to longest:
+
+```nextflow
+channel.fromPath('/data/sequences.fa')
+    .splitFasta( record: [id: true, sequence: true] )
+    .collectFile( name: 'result.fa', sort: { v -> v.size() } ) {
+        v -> v.sequence
+    }
+    .view { fa -> fa.text }
+```
+
+:::warning
+The `collectFile` operator needs to store files in a temporary directory that is automatically deleted on workflow completion. For performance reasons, this directory is located in the machine's local storage, and it should have as much free space as the data that is being collected. The `tempDir` option can be used to specify a different temporary directory.
+:::
+
+Available options:
+
+##### `cache`
+Controls the caching ability of the `collectFile` operator when using the *resume* feature. It follows the same semantic of the [cache][process-cache] directive (default: `true`).
+
+##### `keepHeader`
+Prepend the resulting file with the header fetched in the first collected file. The header size (i.e. lines) can be specified by using the `skip` option (default: `0`), to determine how many lines to remove from all collected files except for the first (where no lines will be removed).
+
+##### `name`
+Name of the file where all received values are stored.
+
+##### `newLine`
+Appends a `newline` character automatically after each entry (default: `false`).
+
+##### `seed`
+A value or a map of values used to initialize the files content.
+
+##### `skip`
+Skip the first `n` lines e.g. `skip: 1` (default: `0`).
+
+##### `sort`
+Defines sorting criteria of content in resulting file(s). Can be one of the following values:
+
+- `false`: Disable content sorting. Entries are appended as they are produced.
+- `true`: Order the content by the entry's natural ordering, i.e. numerical for number, lexicographic for string, etc. See the [Java documentation](http://docs.oracle.com/javase/tutorial/collections/interfaces/order.html) for more information.
+- `'index'`: Order the content by the incremental index number assigned to each entry while they are collected.
+- `'hash'`: (default) Order the content by the hash number associated to each entry
+- `'deep'`: Similar to the previous, but the hash number is created on actual entry content, e.g. when the entry is a file, the hash is created on the actual file content.
+- A custom sorting criteria can be specified with a [closure][script-closure] or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
+
+The file content is sorted in such a way that it does not depend on the order in which entries were added to it, which guarantees that it is consistent (i.e. does not change) across different executions with the same data.
+
+##### `storeDir`
+Folder where the resulting file(s) are stored.
+
+##### `tempDir`
+Folder where temporary files, used by the collecting process, are stored.
+
+## combine
+
+*Returns: channel*
+
+The `combine` operator produces the combinations (i.e. cross product, "Cartesian" product) of two source channels, or a channel and a list (as the right operand), emitting each combination separately.
+
+For example:
+
+```nextflow file=../snippets/combine.nf
+```
+
+```console file=../snippets/combine.out
+```
+
+The `by` option can be used to combine items that share a matching key. The value should be the zero-based index of the tuple, or a list of indices. For example:
+
+```nextflow file=../snippets/combine-by.nf
+```
+
+```console file=../snippets/combine-by.out
+```
+
+:::note
+The `combine` operator is similar to `cross` and `join`, making them easy to confuse. Their differences can be summarized as follows:
+
+- `combine` and `cross` both produce an *outer product* or *cross product*, whereas `join` produces an *inner product*.
+
+- `combine` filters pairs with a matching key only if the `by` option is used, whereas `cross` always filters pairs with a matching key.
+
+- `combine` with the `by` option merges and flattens each pair, whereas `cross` does not. Compare the examples for `combine` and `cross` to see this difference.
+:::
+
+#
+
+See also: [cross](#cross), [join](#join)
+
+## concat
+
+*Returns: channel*
+
+The `concat` operator emits the items from two or more source channels into a single output channel. Each source channel is emitted in the order in which it was specified.
+
+In other words, given *N* channels, the items from the *i+1*-th channel are emitted only after all of the items from the *i*-th channel have been emitted.
+
+For example:
+
+```nextflow file=../snippets/concat.nf
+```
+
+```console file=../snippets/concat.out
+```
+
+#
+
+See also: [mix](#mix)
+
+## count
+
+*Returns: dataflow value*
+
+The `count` operator computes the total number of items in a source channel and emits it:
+
+```nextflow file=../snippets/count.nf
+```
+
+```console file=../snippets/count.out
+```
+
+An optional filter can be provided to select which items to count. The selection criteria can be a literal value, a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate. For example:
+
+```nextflow file=../snippets/count-with-filter-number.nf
+```
+
+```console file=../snippets/count-with-filter-number.out
+```
+
+```nextflow file=../snippets/count-with-filter-regex.nf
+```
+
+```console file=../snippets/count-with-filter-regex.out
+```
+
+```nextflow file=../snippets/count-with-filter-closure.nf
+```
+
+```console file=../snippets/count-with-filter-closure.out
+```
+
+## countFasta
+
+*Returns: dataflow value*
+
+Counts the total number of records in a channel of FASTA files, equivalent to `splitFasta | count`. See [splitFasta](#splitfasta) for the list of available options.
+
+## countFastq
+
+*Returns: dataflow value*
+
+Counts the total number of records in a channel of FASTQ files, equivalent to `splitFastq | count`. See [splitFastq](#splitfastq) for the list of available options.
+
+## countJson
+
+*Returns: dataflow value*
+
+Counts the total number of records in a channel of JSON files, equivalent to `splitJson | count`. See [splitJson](#splitjson) for the list of available options.
+
+## countLines
+
+*Returns: dataflow value*
+
+Counts the total number of lines in a channel of text files, equivalent to `splitText | count`. See [splitLines](#splittext) for the list of available options.
+
+## cross
+
+*Returns: channel*
+
+The `cross` operator emits every pairwise combination of two channels for which the pair has a matching key.
+
+By default, the key is defined as the first entry in a list or map, or the value itself for any other data type. For example:
+
+```nextflow file=../snippets/cross.nf
+```
+
+```console file=../snippets/cross.out
+```
+
+An optional [closure][script-closure] can be used to define the matching key for each item:
+
+```nextflow file=../snippets/cross-with-mapper.nf
+```
+
+```console file=../snippets/cross-with-mapper.out
+```
+
+There are two important caveats when using the `cross` operator:
+
+1. The operator is not *commutative*, i.e. `a.cross(b)` is not the same as `b.cross(a)`
+2. Each source channel should not emit any items with duplicate keys, i.e. each item should have a unique key.
+
+#
+
+See also: [combine](#combine)
+
+## distinct
+
+*Returns: channel*
+
+The `distinct` operator forwards a source channel with *consecutively* repeated items removed, such that each emitted item is different from the preceding one:
+
+```nextflow file=../snippets/distinct.nf
+```
+
+```console file=../snippets/distinct.out
+```
+
+An optional [closure][script-closure] can be used to transform each value before it is evaluated for distinct-ness:
+
+```nextflow file=../snippets/distinct-with-mapper.nf
+```
+
+```console file=../snippets/distinct-with-mapper.out
+```
+
+#
+
+See also: [unique](#unique)
+
+## dump
+
+*Returns: channel*
+
+The `dump` operator prints each item in a source channel when the pipeline is executed with the `-dump-channels` command-line option, otherwise it does nothing. It is a useful way to inspect and debug channels quickly without having to modify the pipeline script.
+
+The `tag` option can be used to select which channels to dump:
+
+```nextflow file=../snippets/dump.nf
+```
+
+Then, you can run your pipeline with `-dump-channels plus1` or `-dump-channels exp2` to dump the content of either channel. Multiple tag names can be specified as a comma-separated list.
+
+Available options:
+
+##### `pretty`
+
+<AddedInVersion version="22.10.0" />
+
+When `true`, format the output as pretty-printed JSON (default: `false`).
+
+##### `tag`
+
+Associate the channel with a tag that can be specified with the `-dump-channels` option to select which channels to dump.
+
+## filter
+
+*Returns: channel*
+
+The `filter` operator emits the items from a source channel that satisfy a condition, discarding all other items. The filter condition can be a literal value, a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate.
+
+The following example filters a channel with a regular expression that only matches strings beginning with `a`:
+
+```nextflow file=../snippets/filter-regex.nf
+```
+
+```console file=../snippets/filter-regex.out
+```
+
+The following example filters a channel with the `Number` type qualifier so that only numbers are emitted:
+
+```nextflow file=../snippets/filter-type.nf
+```
+
+```console file=../snippets/filter-type.out
+```
+
+The following example filters a channel using a boolean predicate, which is a [closure][script-closure] that returns a boolean value. In this case, the predicate is used to select only odd numbers:
+
+```nextflow file=../snippets/filter-closure.nf
+```
+
+```console file=../snippets/filter-closure.out
+```
+
+## first
+
+*Returns: dataflow value*
+
+The `first` operator emits the first item in a source channel, or the first item that matches a condition. The condition can be a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate. For example:
+
+```nextflow file=../snippets/first.nf
+```
+
+## flatMap
+
+*Returns: channel*
+
+The `flatMap` operator applies a *mapping function* to each item from a source channel.
+
+When the mapping function returns a list, each element in the list is emitted separately:
+
+```nextflow file=../snippets/flatmap-list.nf
+```
+
+```console file=../snippets/flatmap-list.out
+```
+
+When the mapping function returns a map, each key-value pair in the map is emitted separately:
+
+```nextflow file=../snippets/flatmap-map.nf
+```
+
+```console file=../snippets/flatmap-map.out
+```
+
+## flatten
+
+*Returns: channel*
+
+The `flatten` operator flattens each item from a source channel that is a list or other collection, such that each element in each collection is emitted separately:
+
+```nextflow file=../snippets/flatten.nf
+```
+
+```console file=../snippets/flatten.out
+```
+
+As shown in the above example, deeply nested collections are also flattened.
+
+#
+
+See also: [flatMap](#flatmap)
+
+## groupTuple
+
+*Returns: queue channel*
+
+The `groupTuple` operator collects lists (i.e. *tuples*) from a source channel into groups based on a grouping key. A new tuple is emitted for each distinct key.
+
+To be more precise, the operator transforms a sequence of tuples like *(K, V, W, ..)* into a sequence of tuples like *(K, list(V), list(W), ..)*.
+
+For example:
+
+```nextflow file=../snippets/grouptuple.nf
+```
+
+```console file=../snippets/grouptuple.out
+```
+
+By default, the first element of each tuple is used as the grouping key. The `by` option can be used to specify a different index, or list of indices. For example, to group by the second element of each tuple:
+
+```nextflow file=../snippets/grouptuple-by.nf
+```
+
+```console file=../snippets/grouptuple-by.out
+```
+
+By default, if you don't specify a size, the `groupTuple` operator will not emit any groups until *all* inputs have been received. If possible, you should always try to specify the number of expected elements in each group using the `size` option, so that each group can be emitted as soon as it's ready. In cases where the size of each group varies based on the grouping key, you can use the built-in `groupKey()` function, which allows you to define a different expected size for each group:
+
+```nextflow file=../snippets/grouptuple-groupkey.nf
+```
+
+```console file=../snippets/grouptuple-groupkey.out
+```
+
+Available options:
+
+##### `by`
+
+The zero-based index of the element to use as the grouping key. Can also be a list of indices, e.g. `by: [0,2]` (default: `[0]`).
+
+##### `remainder`
+
+When `true`, incomplete tuples (i.e. groups with less than `size` items) are emitted as partial groups, otherwise they are discarded (default: `false`). This option can only be used with `size`.
+
+##### `size`
+
+The required number of items for each group. When a group reaches the required size, it is emitted.
+
+##### `sort`
+
+Defines the sorting criteria for the grouped items. Can be one of the following values:
+
+- `false`: No sorting is applied (default).
+- `true`: Order the grouped items by the item's natural ordering, i.e. numerical for number, lexicographic for string, etc. See the [Java documentation](http://docs.oracle.com/javase/tutorial/collections/interfaces/order.html) for more information.
+- `'hash'`: Order the grouped items by the hash number associated to each entry.
+- `'deep'`: Similar to the previous, but the hash number is created on actual entry content, e.g. when the item is a file, the hash is created on the actual file content.
+- A custom sorting criteria used to order the nested list elements of each tuple. It can be a [closure][script-closure] or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
+
+## ifEmpty
+
+*Returns: channel*
+
+The `ifEmpty` operator emits a source channel, or a default value if the source channel is *empty* (doesn't emit any value):
+
+```nextflow file=../snippets/ifempty-1.nf
+```
+
+```console file=../snippets/ifempty-1.out
+```
+
+```nextflow file=../snippets/ifempty-2.nf
+```
+
+```console file=../snippets/ifempty-2.out
+```
+
+The default value can also be a [closure][script-closure], in which case the closure is evaluated and the result is emitted when the source channel is empty.
+
+#
+
+See also: [empty][operator-empty] channel factory
+
+## join
+
+*Returns: channel*
+
+The `join` operator emits the inner product of two source channels using a matching key.
+
+To be more precise, the operator transforms a sequence of tuples like *(K, V1, V2, ..)* and *(K, W1, W1, ..)* into a sequence of tuples like *(K, V1, V2, .., W1, W2, ..)*.
+
+For example:
+
+```nextflow file=../snippets/join.nf
+```
+
+```console file=../snippets/join.out
+```
+
+By default, the first element of each item is used as the key. The `by` option can be used to specify a different index, or list of indices.
+
+By default, unmatched items are discarded. The `remainder` option can be used to emit them at the end:
+
+```nextflow file=../snippets/join-with-remainder.nf
+```
+
+```console file=../snippets/join-with-remainder.out
+```
+
+:::note
+The `join` operator is similar to an SQL *inner join*, or an SQL *outer join* when `remainder` is `true`. The only difference is that `join` does not support duplicate keys, whereas an SQL join produces the cross-product of duplicate keys. The `combine` operator with the `by` option is equivalent to an SQL join.
+:::
+
+Available options:
+
+##### `by`
+
+The zero-based index of each item to use as the matching key. Can also be a list of indices, e.g. `by: [0, 2]` (default: `[0]`).
+
+##### `failOnDuplicate`
+
+When `true`, an error is reported when the operator receives multiple items from the same channel with the same key (default: `false`). Value is set to `true` if [strict mode][config-feature-flags] is enabled.
+
+##### `failOnMismatch`
+
+When `true`, an error is reported when the operator receives an item from one channel for which there no matching item from the other channel (default: `false`). Value is set to `true` if [strict mode][config-feature-flags] is enabled. This option cannot be used with `remainder`.
+
+##### `remainder`
+
+When `true`, unmatched items are emitted at the end, otherwise they are discarded (default: `false`). 
+
+#
+
+See also: [combine](#combine), [cross](#cross)
+
+## last
+
+*Returns: dataflow value*
+
+The `last` operator emits the last item from a source channel:
+
+```nextflow file=../snippets/last.nf
+```
+
+```console file=../snippets/last.out
+```
+
+## map
+
+*Returns: channel*
+
+The `map` operator applies a *mapping function* to each item from a source channel:
+
+```nextflow file=../snippets/map.nf
+```
+
+```console file=../snippets/map.out
+```
+
+:::note
+`null` values are not emitted by `map`.
+:::
+
+## max
+
+*Returns: dataflow value*
+
+The `max` operator emits the item with the greatest value from a source channel:
+
+```nextflow file=../snippets/max.nf
+```
+
+```console file=../snippets/max.out
+```
+
+An optional [closure][script-closure] can be used to control how the items are compared. The closure can be a *mapping function*, which transforms each item before it is compared, or a *comparator function*, which defines how to compare two items more generally.
+
+The following examples show how to find the longest string in a channel:
+
+```nextflow file=../snippets/max-with-mapper.nf
+```
+
+```console file=../snippets/max-with-mapper.out
+```
+
+```nextflow file=../snippets/max-with-comparator.nf
+```
+
+```console file=../snippets/max-with-comparator.out
+```
+
+## merge
+
+*Returns: channel*
+
+The `merge` operator joins the items from two or more channels into a new channel:
+
+```nextflow file=../snippets/merge.nf
+```
+
+```console file=../snippets/merge.out
+```
+
+An optional [closure][script-closure] can be used to control how two items are merged:
+
+```nextflow file=../snippets/merge-with-mapper.nf
+```
+
+```console file=../snippets/merge-with-mapper.out
+```
+
+The `merge` operator may return a channel or value depending on the inputs:
+
+- If the first argument is a channel, the `merge` operator returns a channel merging as many values as are available for all inputs. Dataflow values are re-used for each merged value.
+
+- If the first argument is a dataflow value, the `merge` operator returns a dataflow value, merging the first value from each input, regardless of whether there are channel inputs with additional values.
+
+:::danger
+In general, the use of the `merge` operator is discouraged. Processes and channel operators are not guaranteed to emit items in the order that they were received, as they are executed concurrently. Therefore, if you try to merge output channels from different processes, the resulting channel may be different on each run, which will cause resumed runs to [not work properly][cache-nondeterministic-inputs].
+
+You should always use a matching key (e.g. sample ID) to merge multiple channels, so that they are combined in a deterministic way. For this purpose, you can use the [join](#join) operator.
+:::
+
+## min
+
+*Returns: dataflow value*
+
+The `min` operator emits the item with the lowest value from a source channel:
+
+```nextflow file=../snippets/min.nf
+```
+
+```console file=../snippets/min.out
+```
+
+An optional [closure][script-closure] can be used to control how the items are compared. The closure can be a *mapping function*, which transforms each item before it is compared, or a *comparator function*, which defines how to compare two items more generally.
+
+The following examples show how to find the shortest string in a channel:
+
+```nextflow file=../snippets/min-with-mapper.nf
+```
+
+```console file=../snippets/min-with-mapper.out
+```
+
+```nextflow file=../snippets/min-with-comparator.nf
+```
+
+```console file=../snippets/min-with-comparator.out
+```
+
+## mix
+
+*Returns: channel*
+
+The `mix` operator emits the items from two or more source channels into a single output channel:
+
+```nextflow file=../snippets/mix.nf
+```
+
+```console file=../snippets/mix.out
+```
+
+The items in the mixed output channel may appear in any order, regardless of which source channel they came from. Thus, the previous example could also output the following:
+
+```console
+z
+1
+a
+2
+b
+3
+```
+
+#
+
+See also: [concat](#concat)
+
+## multiMap
+
+*Returns: multiple channels*
+
+The `multiMap` operator applies a set of mapping functions to a source channel, producing a separate output channel for each mapping function.
+
+The multi-map criteria is a [closure][script-closure] that defines, for each output channel, a label followed by a mapping expression.
+
+For example:
+
+```nextflow file=../snippets/multimap.nf
+```
+
+```console file=../snippets/multimap.out
+```
+
+Multiple labels can share the same mapping expression using the following shorthand:
+
+```nextflow file=../snippets/multimap-shared.nf
+```
+
+```console file=../snippets/multimap-shared.out
+```
+
+The above example creates two channels as before, but now they both receive the same items.
+
+You can use the `multiMapCriteria()` method to create a multi-map criteria as a variable that can be passed as an argument to any number of `multiMap` operations, as shown below:
+
+```nextflow file=../snippets/multimap-criteria.nf
+```
+
+:::note
+If you use `multiMap` to split a tuple or map into multiple channels, it is recommended that you retain a matching key (e.g. sample ID) with *each* new channel, so that you can re-combine these channels later on if needed. In general, you should not expect to be able to merge channels correctly without a matching key, due to the concurrent nature of Nextflow pipelines.
+:::
+
+## randomSample
+
+*Returns: channel*
+
+The `randomSample` operator emits a randomly-selected subset of items from a source channel:
+
+```nextflow file=../snippets/random-sample.nf
+```
+
+The above snippet will print 10 randomly-selected numbers between 1 and 100 (without replacement).
+
+An optional second parameter can be used to set the initial *seed* for the random number generator, which ensures that the `randomSample` operator produces the same pseudo-random sequence across runs:
+
+```nextflow file=../snippets/random-sample-with-seed.nf
+```
+
+The above example will print 10 randomly-selected numbers between 1 and 100 (without replacement). Each subsequent script execution will produce the same sequence.
+
+## reduce
+
+*Returns: dataflow value*
+
+The `reduce` operator applies an *accumulator function* sequentially to each item in a source channel, and emits the final accumulated value. The accumulator function takes two parameters -- the accumulated value and the *i*-th emitted item -- and it should return the accumulated result, which is passed to the next invocation with the *i+1*-th item. This process is repeated for each item in the source channel.
+
+For example:
+
+```nextflow file=../snippets/reduce.nf
+```
+
+```console file=../snippets/reduce.out
+```
+
+By default, the first item is used as the initial accumulated value. You can optionally specify a different initial value as shown below:
+
+```nextflow file=../snippets/reduce-with-initial-value.nf
+```
+
+```console file=../snippets/reduce-with-initial-value.out
+```
+
+## set
+
+*Returns: nothing*
+
+The `set` operator assigns a source channel to a variable, whose name is specified as a closure parameter:
+
+```nextflow
+channel.of(10, 20, 30).set { my_channel }
+```
+
+Using `set` is semantically equivalent to assigning a variable:
+
+```nextflow
+my_channel = channel.of(10, 20, 30)
+```
+
+#
+
+See also: [tap](#tap)
+
+## splitCsv
+
+*Returns: channel*
+
+The `splitCsv` operator parses and splits [CSV](http://en.wikipedia.org/wiki/Comma-separated_values) files or text from a source channel into records.
+
+For example:
+
+```nextflow file=../snippets/splitcsv.nf
+```
+
+```console file=../snippets/splitcsv.out
+```
+
+The above example shows hows CSV text is parsed and split into individual rows, where each row is simply a list of columns.
+
+When the CSV begins with a header line defining the column names, and the `header` option is `true`, each row is returned as a map instead:
+
+```nextflow file=../snippets/splitcsv-with-header.nf
+```
+
+```console file=../snippets/splitcsv-with-header.out
+```
+
+The `header` option can also just be a list of columns:
+
+```nextflow file=../snippets/splitcsv-with-columns.nf
+```
+
+```console file=../snippets/splitcsv-with-columns.out
+```
+
+Available options:
+
+##### `by`
+
+When specified, group rows into *chunks* with the given size (default: none).
+
+##### `charset`
+
+Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
+
+##### `decompress`
+
+When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
+
+##### `elem`
+
+The index of the element to split when the source items are lists or tuples (default: first file object or first element).
+
+##### `header`
+
+When `true`, the first line is used as the columns names (default: `false`). Can also be a list of columns names.
+
+##### `limit`
+
+Limits the number of records to retrieve for each source item (default: no limit).
+
+##### `quote`
+
+The character used to quote values (default: `''` or `""`).
+
+##### `sep`
+
+The character used to separate values (default: `,`)
+
+##### `skip`
+
+Number of lines to ignore from the beginning when parsing the CSV text (default: `0`).
+
+##### `strip`
+
+When `true`, remove leading and trailing blanks from values (default: `false`).
+
+## splitFasta
+
+*Returns: channel*
+
+The `splitFasta` operator splits [FASTA](http://en.wikipedia.org/wiki/FASTA_format) files or text from a source channel into individual sequences.
+
+The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTA file and split it into chunks of 10 sequences each:
+
+```nextflow
+channel.fromPath('misc/sample.fa')
+    .splitFasta( by: 10 )
+    .view()
+```
+
+:::warning
+Chunks are stored in memory by default. When splitting large files, specify `file: true` to save the chunks into files in order to avoid running out of memory. See the list of options below for details.
+:::
+
+The `record` option can be used to split FASTA content into *records* instead of text chunks. Each record is a map that allows you to access the FASTA sequence data with ease. For example:
+
+```nextflow
+channel.fromPath('misc/sample.fa')
+    .splitFasta( record: [id: true, seqString: true] )
+    .filter { record -> record.id =~ /^ENST0.*/ }
+    .view { record -> record.seqString }
+```
+
+The above example loads the `misc/sample.fa` file, splits it into records containing the `id` and `seqString` fields (i.e. the sequence id and the sequence data), filters records by their ID, and finally prints the sequence string of each record.
+
+Available options:
+
+##### `by`
+
+Defines the number of sequences in each chunk (default: `1`).
+
+##### `charset`
+
+Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
+
+##### `compress`
+
+When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
+
+##### `decompress`
+
+When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
+
+##### `elem`
+
+The index of the element to split when the source items are lists or tuples (default: first file object or first element).
+
+##### `file`
+When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
+
+##### `limit`
+
+Limits the number of sequences to retrieve for each source item (default: no limit).
+
+##### `record`
+
+Parse each entry in the FASTA file into a record. The following fields are available:
+- `id`: The FASTA sequence identifier, i.e. the word following the `>` symbol up to the first blank or newline character
+- `header`: The first line in a FASTA sequence without the `>` character
+- `desc`: The text in the FASTA header following the ID value
+- `text`: The complete FASTA sequence including the header
+- `seqString`: The sequence as a single-line string, i.e. containing no newline characters
+- `sequence`: The sequence as a multi-line string, i.e. always ending with a newline character
+- `width`: Define the length of a single line when the `sequence` field is used, after which the sequence continues on a new line.
+
+##### `size`
+
+Defines the size of the expected chunks as a memory unit, e.g. `1.MB`.
+
+#
+
+See also: [countFasta](#countfasta)
+
+## splitFastq
+
+*Returns: channel*
+
+The `splitFastq` operator splits [FASTQ](http://en.wikipedia.org/wiki/FASTQ_format) files or text from a source channel into individual sequences.
+
+The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTQ file and split it into chunks of 10 sequences each:
+
+```nextflow
+Channel
+channel.fromPath('misc/sample.fastq')
+    .splitFastq( by: 10 )
+    .view()
+```
+
+:::warning
+Chunks are stored in memory by default. When splitting large files, specify `file: true` to save the chunks into files in order to avoid running out of memory. See the list of options below for details.
+:::
+
+The `record` option can be used to split FASTQ content into *records* instead of text chunks. Each record is a map that allows you to access the FASTQ sequence data with ease. For example:
+
+```nextflow
+channel.fromPath('misc/sample.fastq')
+    .splitFastq( record: true )
+    .view { record -> record.readHeader }
+```
+
+The `pe` option can be used to split paired-end FASTQ files. The source channel must emit tuples containing the file pairs. For example:
+
+```nextflow
+channel.fromFilePairs('/my/data/SRR*_{1,2}.fastq', flat: true)
+    .splitFastq(by: 100_000, pe: true, file: true)
+    .view()
+```
+
+:::note
+`channel.fromFilePairs()` requires the `flat: true` option in order to emit the file pairs as separate elements in the produced tuples.
+:::
+
+:::note
+This operator assumes that the order of the paired-end reads correspond with each other and that both files contain the same number of reads.
+:::
+
+Available options:
+
+##### `by`
+
+Defines the number of sequences in each chunk (default: `1`).
+
+##### `charset`
+
+Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
+
+##### `compress`
+
+When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
+
+##### `decompress`
+
+When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
+
+##### `elem`
+
+The index of the element to split when the source items are lists or tuples (default: first file object or first element).
+
+##### `file`
+
+When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
+
+##### `limit`
+
+Limits the number of sequences to retrieve for each source item (default: no limit).
+
+##### `pe`
+
+When `true`, splits paired-end read files. Items emitted by the source channel must be tuples with the file pairs.
+
+##### `record`
+
+Parse each entry in the FASTQ file into a record. The following fields are available:
+- `readHeader`: Sequence header (without the `@` prefix)
+- `readString`: The raw sequence content
+- `qualityHeader`: Base quality header (it may be empty)
+- `qualityString`: Quality values for the sequence
+
+#
+
+See also: [countFastq](#countfastq)
+
+## splitJson
+
+*Returns: channel*
+
+The `splitJson` operator splits [JSON](https://en.wikipedia.org/wiki/JSON) files or text from a source channel into individual records.
+
+If the source item is a JSON array, each element of the array will be emitted:
+
+```nextflow file=../snippets/splitjson-array.nf
+```
+
+```console file=../snippets/splitjson-array.out
+```
+
+If the source item is a JSON object, each key-value pair will be emitted as a map with the properties `key`  and `value`:
+
+```nextflow file=../snippets/splitjson-object.nf
+```
+
+```console file=../snippets/splitjson-object.out
+```
+
+The `path` option can be used to query a section of the JSON document to parse and split:
+
+```nextflow file=../snippets/splitjson-with-path.nf
+```
+
+```console file=../snippets/splitjson-with-path.out
+```
+
+Available options:
+
+##### `limit`
+
+Limits the number of records to retrieve for each source item (default: no limit).
+
+##### `path`
+
+Defines a query for a section of each source item to parse and split. The expression should be a path similar to [JSONPath](https://goessner.net/articles/JsonPath/). The empty string is the document root (default). An integer in brackets is a zero-based index in a JSON array. A string preceded by a dot `.` is a key in a JSON object.
+
+#
+
+See also: [countJson](#countjson)
+
+## splitText
+
+*Returns: channel*
+
+The `splitText` operator splits multi-line text content from a source channel into chunks of *N* lines:
+
+```nextflow
+Channel
+    .fromPath('/some/path/*.txt')
+    .splitText()
+    .view()
+```
+
+The above example loads a collection of text files, splits the content of each file into individual lines, and prints each line.
+
+The `by` option can be used to emit chunks of *N* lines:
+
+```nextflow
+channel.fromPath('/some/path/*.txt')
+    .splitText( by: 10 )
+    .subscribe { chunk ->
+        print chunk
+        print "--- end of the chunk ---\n"
+    }
+```
+
+An optional [closure][script-closure] can be used to transform each text chunk produced by the operator. The following example shows how to split text files into chunks of 10 lines and transform them to uppercase letters:
+
+```nextflow
+channel.fromPath('/some/path/*.txt')
+    .splitText( by: 10 ) { v -> v.toUpperCase() }
+    .view()
+```
+
+:::note
+Text chunks returned by the `splitText` operator are always terminated by a `\n` newline character.
+:::
+
+Available options:
+
+##### `by`
+
+Defines the number of lines in each `chunk` (default: `1`).
+
+##### `charset`
+
+Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
+
+##### `compress`
+
+When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
+
+##### `decompress`
+
+When `true`, decompresses the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
+
+##### `elem`
+
+The index of the element to split when the source items are lists or tuples (default: first file object or first element).
+
+##### `file`
+
+When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
+
+##### `keepHeader`
+
+Parses the first line as header and prepends it to each emitted chunk (default: `false`).
+
+##### `limit`
+
+Limits the number of lines to retrieve for each source item (default: no limit).
+
+#
+
+See also: [countLines](#countlines)
+
+## subscribe
+
+*Returns: nothing*
+
+The `subscribe` operator invokes a custom function for each item from a source channel:
+
+```nextflow file=../snippets/subscribe.nf
+```
+
+```console file=../snippets/subscribe.out
+```
+
+The `subscribe` operator supports multiple types of event handlers:
+
+```nextflow file=../snippets/subscribe-with-on-complete.nf
+```
+
+```console file=../snippets/subscribe-with-on-complete.out
+```
+
+:::note
+Unlike most operators, `subscribe` is a *terminal operator* and does not emit any values. It should only be used for *side effects*, such as printing to the console, writing to a file, or making HTTP requests.
+:::
+
+Available options:
+
+##### `onNext`
+
+Closure that is invoked when an item is emitted. Equivalent to providing a closure as the first argument.
+
+##### `onComplete`
+
+Closure that is invoked after the last item is emitted by the channel.
+
+##### `onError`
+
+Closure that is invoked when an exception is raised while handling the `onNext` event. It will not make further calls to `onNext` or `onComplete`. The `onError` method takes as its parameter the `Throwable` that caused the error.
+
+## sum
+
+*Returns: dataflow value*
+
+The `sum` operator emits the sum of all items in a source channel:
+
+```nextflow file=../snippets/sum.nf
+```
+
+```console file=../snippets/sum.out
+```
+
+An optional [closure][script-closure] can be used to transform each item before it is added to the sum:
+
+```nextflow file=../snippets/sum-with-mapper.nf
+```
+
+```console file=../snippets/sum-with-mapper.out
+```
+
+## take
+
+*Returns: channel*
+
+The `take` operator takes the first *N* items from a source channel:
+
+```nextflow file=../snippets/take.nf
+```
+
+```console file=../snippets/take.out
+```
+
+:::tip
+Specifying a size of `-1` causes the operator to take all values.
+:::
+
+#
+
+See also: [until](#until)
+
+## tap
+
+*Returns: channel*
+
+The `tap` operator assigns a source channel to a variable, and emits the source channel. It is a useful way to extract intermediate output channels from a chain of operators. For example:
+
+```nextflow file=../snippets/tap.nf
+```
+
+```console file=../snippets/tap.out
+```
+
+#
+
+See also: [set](#set)
+
+## toInteger
+
+*Returns: channel*
+
+The `toInteger` operator converts string values from a source channel to integer values:
+
+```nextflow file=../snippets/tointeger.nf
+```
+
+```console file=../snippets/tointeger.out
+```
+
+:::note
+`toInteger` is equivalent to:
+
+```nextflow
+map { v -> v as Integer }
+```
+:::
+
+:::note
+You can also use `toLong`, `toFloat`, and `toDouble` to convert to other numerical types.
+:::
+
+## toList
+
+*Returns: dataflow value*
+
+The `toList` operator collects all the items from a source channel into a list and emits the list as a single item:
+
+```nextflow file=../snippets/tolist.nf
+```
+
+```console file=../snippets/tolist.out
+```
+
+:::note
+There are two main differences between `toList` and `collect`:
+
+- When there is no input, `toList` emits an empty list whereas `collect` emits nothing.
+- By default, `collect` flattens list items by one level.
+
+In other words, `toList` is equivalent to:
+
+```nextflow
+collect(flat: false).ifEmpty([])
+```
+:::
+
+#
+
+See also: [collect](#collect)
+
+## toSortedList
+
+*Returns: dataflow value*
+
+The `toSortedList` operator collects all the items from a source channel into a sorted list and emits the list as a single item:
+
+```nextflow file=../snippets/tosortedlist.nf
+```
+
+```console file=../snippets/tosortedlist.out
+```
+
+An optional [closure][script-closure] can be used to control how items are compared when sorting. For example, to sort tuples by their second element in descending order:
+
+```nextflow file=../snippets/tosortedlist-with-comparator.nf
+```
+
+```console file=../snippets/tosortedlist-with-comparator.out
+```
+
+:::note
+`toSortedList` is equivalent to:
+
+```nextflow
+collect(flat: false, sort: true).ifEmpty([])
+```
+:::
+
+#
+
+See also: [collect](#collect)
+
+## transpose
+
+*Returns: channel*
+
+The `transpose` operator "transposes" each tuple from a source channel by flattening any nested list in each tuple, emitting each nested item separately.
+
+To be more precise, the operator transforms a sequence of tuples like *(K, list(V), list(W), ..)* into a sequence of tuples like *(K, V, W, ..)*.
+
+For example:
+
+```nextflow file=../snippets/transpose-1.nf
+```
+
+```console file=../snippets/transpose-1.out
+```
+
+If each source item has more than two elements, these will be flattened by the first element in the item, and a new item will be emitted only when it is complete:
+
+```nextflow file=../snippets/transpose-2.nf
+```
+
+```console file=../snippets/transpose-2.out
+```
+
+The `remainder` option can be used to emit any incomplete items:
+
+```nextflow file=../snippets/transpose-2-with-remainder.nf
+```
+
+```console file=../snippets/transpose-2-with-remainder.out
+```
+
+Available options:
+
+##### `by`
+
+The zero-based index of the element to be transposed. Can also be a list of indices, e.g. `by: [0,2]`. By default, every list element is transposed.
+
+##### `remainder`
+
+When `true`, incomplete tuples are emitted with `null` values for missing elements, otherwise they are discarded (default: `false`). 
+
+#
+
+See also: [groupTuple](#grouptuple)
+
+## unique
+
+*Returns: channel*
+
+The `unique` operator emits the unique items from a source channel:
+
+```nextflow file=../snippets/unique.nf
+```
+
+```console file=../snippets/unique.out
+```
+
+An optional [closure][script-closure] can be used to transform each item before it is evaluated for uniqueness:
+
+```nextflow file=../snippets/unique-with-mapper.nf
+```
+
+```console file=../snippets/unique-with-mapper.out
+```
+
+:::note
+The difference between `unique` and `distinct` is that `unique` removes *all* duplicate values, whereas `distinct` removes only *consecutive* duplicate values. As a result, `unique` must process the entire source channel before it can emit anything, whereas `distinct` can emit each value immediately.
+:::
+
+#
+
+See also: [distinct](#distinct)
+
+## until
+
+*Returns: channel*
+
+The `until` operator emits each item from a source channel until a stopping condition is satisfied:
+
+```nextflow file=../snippets/until.nf
+```
+
+```console file=../snippets/until.out
+```
+
+#
+
+See also: [take](#take)
+
+## view
+
+*Returns: channel*
+
+The `view` operator prints each item from a source channel to standard output:
+
+```nextflow file=../snippets/view.nf
+```
+
+```console file=../snippets/view.out
+```
+
+An optional [closure][script-closure] can be used to transform each item before it is printed:
+
+```nextflow file=../snippets/view-with-mapper.nf
+```
+
+```console file=../snippets/view-with-mapper.out
+```
+
+The `view` operator also emits every item that it receives, allowing it to be chained with other operators.
+
+Available options:
+
+##### `newLine`
+Print each item to a separate line (default: `true`).
+
+[cache-nondeterministic-inputs]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#non-deterministic-process-inputs
+[config-feature-flags]: /nextflow_docs/nextflow_repo/docs/reference/feature-flags.mdx
+[process-cache]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cache
diff --git a/docs/reference/process.md b/docs/reference/process.md
deleted file mode 100644
index a1fe0ff747..0000000000
--- a/docs/reference/process.md
+++ /dev/null
@@ -1,1774 +0,0 @@
-(process-reference)=
-
-# Process reference
-
-This page lists the task properties, input/output methods, and directives available in {ref}`process <process-page>` definitions.
-
-## Task properties
-
-The following task properties are defined in the process body:
-
-`task.attempt`
-: The current task attempt.
-
-`task.exitStatus`
-: *Available only in `script:` and `shell:` blocks*
-: The exit code returned by the task script.
-: The exit code is only available after the task has been executed (e.g., the [errorStrategy](#errorstrategy) directive).
-
-`task.hash`
-: *Available only in `exec:` blocks*
-: The task hash.
-
-`task.index`
-: The process-level task index.
-
-`task.name`
-: *Available only in `exec:` blocks*
-: The task name.
-
-`task.previousException`
-: :::{versionadded} 24.10.0
-  :::
-: The exception reported by the previous task attempt.
-: Since the exception is available after a failed task attempt, it can only be accessed when retrying a failed task execution, i.e., when `task.attempt` is greater than 1.
-
-`task.previousTrace`
-: :::{versionadded} 24.10.0
-  :::
-: The trace record associated with the previous task attempt.
-: Since the trace record is available after a failed task attempt, it can only be accessed when retrying a failed task execution, i.e., when `task.attempt` is greater than 1.
-
-`task.process`
-: The name of the process that spawned the task.
-
-`task.workDir`
-: *Available only in `exec:` blocks*
-: The unique directory path for the task.
-
-:::{note}
-[Directive values](#directives) for a task can be accessed via `task.<directive>`. See {ref}`task-directive-values` for more information.
-:::
-
-(process-reference-typed)=
-
-## Inputs and outputs (typed)
-
-:::{versionadded} 25.10.0
-:::
-
-:::{note}
-Typed processes require the `nextflow.preview.types` feature flag to be enabled in every script that uses them.
-:::
-
-### Stage directives
-
-The following directives can be used in the `stage:` section of a typed process:
-
-`env( name: String, String value )`
-: Declares an environment variable with the specified name and value in the task environment.
-
-`stageAs( filePattern: String, value: Path )`
-: Stages a file into the task directory under the given alias.
-
-`stageAs( filePattern: String, value: Iterable<Path> )`
-: Stages a collection of files into the task directory under the given alias.
-
-`stdin( value: String )`
-: Stages the given value as the standard input (i.e., `stdin`) to the task script.
-
-### Outputs
-
-The following functions are available in the `output:` and `topic:` sections of a typed process:
-
-`env( name: String ) -> String`
-: Returns the value of an environment variable from the task environment.
-
-`eval( command: String ) -> String`
-: Returns the standard output of the specified command, which is executed in the task environment after the task script completes.
-
-`file( pattern: String, [options] ) -> Path`
-: Returns a file from the task environment that matches the specified pattern.
-
-: Available options:
-
-  `followLinks: Boolean`
-  : When `true`, target files are returned in place of any matching symlink (default: `true`).
-
-  `glob: Boolean`
-  : When `true`, the file name is interpreted as a glob pattern (default: `true`).
-
-  `hidden: Boolean`
-  : When `true`, hidden files are included in the matching output files (default: `false`).
-
-  `includeInputs: Boolean`
-  : When `true` and the file name is a glob pattern, any input files matching the pattern are also included in the output (default: `false`).
-
-  `maxDepth: Integer`
-  : Maximum number of directory levels to visit (default: no limit).
-
-  `optional: Boolean`
-  : When `true`, the task will not fail if the given file is missing (default: `false`).
-
-  `type: String`
-  : Type of paths returned, either `file`, `dir` or `any` (default: `any`, or `file` if the given file name contains a double star (`**`)).
-
-`files( pattern: String, [options] ) -> Set<Path>`
-: Returns files from the task environment that match the given pattern.
-
-: Supports the same options as `file()` (except for `optional`).
-
-`stdout() -> String`
-: Returns the standard output of the task script.
-
-(process-reference-legacy)=
-
-## Inputs and outputs (legacy)
-
-(process-reference-inputs)=
-
-### Inputs
-
-`val( identifier )`
-
-: Declare a variable input. The received value can be any type, and it will be made available to the process body (i.e. `script`, `shell`, `exec`) as a variable given by `identifier`.
-
-`file( identifier | stageName )`
-
-: :::{deprecated} 19.10.0
-  Use `path` instead.
-  :::
-
-: Declare a file input. The received value can be any type, and it will be staged into the task directory. If the received value is not a file or collection of files, it is implicitly converted to a string and written to a file.
-
-: The argument can be an identifier or string. If an identifier, the received value will be made available to the process body as a variable. If a string, the received value will be staged into the task directory under the given alias.
-
-`path( identifier | stageName )`
-
-: Declare a file input. The received value should be a file or collection of files and will be staged into the task directory.
-
-: The argument can be an identifier or string. If an identifier, the received value will be made available to the process body as a variable. If a string, the received value will be staged into the task directory under the given alias.
-
-: Available options:
-
-  `arity`
-  : :::{versionadded} 23.09.0-edge
-    :::
-  : Specify the number of expected files. Can be a number, e.g. `'1'`, or a range, e.g. `'1..*'`. If a task receives an invalid number of files for this `path` input, it will fail.
-
-  `name`
-  : Specify how the file should be named in the task work directory. Can be a name or a pattern.
-
-  `stageAs`
-  : Alias of `name`.
-
-`env( name )`
-
-: Declare an environment variable input. The received value should be a string, and it will be exported to the task environment as an environment variable given by `name`.
-
-`stdin`
-
-: Declare a `stdin` input. The received value should be a string, and it will be provided as the standard input (i.e. `stdin`) to the task script. It should be declared only once for a process.
-
-`tuple( arg1, arg2, ... )`
-
-: Declare a tuple input. Each argument should be an input declaration such as `val`, `path`, `env`, or `stdin`.
-
-: The received value should be a tuple with the same number of elements as the `tuple` declaration, and each received element should be compatible with the corresponding `tuple` argument. Each tuple element is treated the same way as if it were a standalone input.
-
-(process-reference-outputs)=
-
-### Outputs
-
-`val( value )`
-
-: Declare a variable output. The argument can be any value, and it can reference any output variables defined in the process body (i.e. variables declared without the `def` keyword).
-
-`file( pattern )`
-
-: :::{deprecated} 19.10.0
-  Use `path` instead.
-  :::
-
-: Declare a file output. It receives the output files from the task environment that match the given pattern.
-
-: Multiple patterns can be specified using the colon separator (`:`). The union of all files matched by each pattern will be collected.
-
-`path( pattern, [options] )`
-
-: Declare a file output. It receives the output files from the task environment that match the given pattern.
-
-: Available options:
-
-  `arity`
-  : :::{versionadded} 23.09.0-edge
-    :::
-  : Specify the number of expected files. Can be a number or a range. If a task produces an invalid number of files for this `path` output, it will fail.
-
-  : If the arity is `1`, a single file will be emitted. Otherwise, a list will always be emitted, even if only one file is produced.
-  
-  : :::{warning}
-    If the arity is not specified, a single file or list will be emitted based on whether a single file or multiple files are produced at runtime, resulting potentially in an output channel with a mixture of files and file collections.
-    :::
-
-  `followLinks`
-  : When `true`, target files are returned in place of any matching symlink (default: `true`).
-
-  `glob`
-  : When `true`, the specified name is interpreted as a glob pattern (default: `true`).
-
-  `hidden`
-  : When `true`, hidden files are included in the matching output files (default: `false`).
-
-  `includeInputs`
-  : When `true` and the output path is a glob pattern, any input files matching the pattern are also included in the output (default: `false`).
-
-  `maxDepth`
-  : Maximum number of directory levels to visit (default: no limit).
-
-  `type`
-  : Type of paths returned, either `file`, `dir` or `any` (default: `any`, or `file` if the specified file name pattern contains a double star (`**`)).
-
-`env( name )`
-
-: Declare an environment variable output. It receives the value of the environment variable (given by `name`) from the task environment.
-
-: :::{versionchanged} 23.12.0-edge
-  Prior to this version, if the environment variable contained multiple lines of output, the output would be compressed to a single line by converting newlines to spaces.
-  :::
-
-`stdout`
-
-: Declare a `stdout` output. It receives the standard output of the task script.
-
-`eval( command )`
-
-: :::{versionadded} 24.02.0-edge
-  :::
-
-: Declare an `eval` output. It receives the standard output of the given command, which is executed in the task environment after the task script.
-
-: If the command fails, the task will also fail.
-
-`tuple( arg1, arg2, ... )`
-
-: Declare a tuple output. Each argument should be an output declaration such as `val`, `path`, `env`, `stdin`, or `eval`. Each tuple element is treated the same way as if it were a standalone output.
-
-(process-additional-options)=
-
-### Generic options
-
-The following options are available for all process outputs:
-
-`emit: <name>`
-
-: Defines the name of the output channel.
-
-`optional: true | false`
-
-: When `true`, the task will not fail if the specified output is missing (default: `false`).
-
-`topic: <name>`
-
-: :::{versionadded} 23.11.0-edge
-  :::
-
-: *Experimental: may change in a future release.*
-
-: Defines the {ref}`channel topic <channel-topic>` to which the output will be sent.
-
-(process-reference-directives)=
-
-## Directives
-
-(process-accelerator)=
-
-### accelerator
-
-:::{versionadded} 19.09.0-edge
-:::
-
-The `accelerator` directive allows you to request hardware accelerators (e.g. GPUs) for the task execution. For example:
-
-```nextflow
-process hello {
-    accelerator 4, type: 'nvidia-tesla-k80'
-
-    script:
-    """
-    your_gpu_enabled --command --line
-    """
-}
-```
-
-The above examples will request 4 GPUs of type `nvidia-tesla-k80`.
-
-:::{note}
-This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-:::{note}
-Additional options may be required to fully enable the use of accelerators. When using containers with GPUs, you must pass the GPU drivers through to the container. For Docker, this requires the option `--gpus all` in the docker run command. For Apptainer/Singularity, this requires the option `--nv`. The specific implementation details depend on the accelerator and container type being used.
-:::
-
-:::{note}
-The accelerator `type` option depends on the target execution platform. Refer to the platform-specific documentation for details on the available accelerators:
-
-- [Google Cloud](https://cloud.google.com/compute/docs/gpus/)
-- [Kubernetes](https://kubernetes.io/docs/tasks/manage-gpus/scheduling-gpus/#clusters-containing-different-types-of-gpus)
-
-The accelerator `type` option is not supported for AWS Batch. You can control the accelerator type indirectly through the allowed instance types in your Compute Environment. See the [AWS Batch FAQs](https://aws.amazon.com/batch/faqs/?#GPU_Scheduling_) for more information.
-:::
-
-(process-afterscript)=
-
-### afterScript
-
-The `afterScript` directive allows you to execute a custom (Bash) snippet immediately *after* the main process has run. This may be useful to clean up your staging area.
-
-:::{note}
-When combined with the {ref}`container directive <process-container>`, the `afterScript` will be executed outside the specified container. In other words, the `afterScript` is always executed in the host environment.
-:::
-
-(process-arch)=
-
-### arch
-
-The `arch` directive allows you to define the CPU architecture to build the software in use by the process' task. For example:
-
-```nextflow
-process blast {
-    spack 'blast-plus@2.13.0'
-    arch 'linux/x86_64', target: 'cascadelake'
-
-    script:
-    """
-    blastp -query input_sequence -num_threads ${task.cpus}
-    """
-}
-```
-
-The example above declares that the CPU generic architecture is `linux/x86_64` (X86 64 bit), and more specifically that the microarchitecture is `cascadelake` (a specific generation of Intel CPUs).
-
-This directive is currently used by the following Nextflow functionalities:
-
-- by the [spack](#spack) directive, to build microarchitecture-optimised applications;
-- by the {ref}`wave-page` service, to build containers for one of the generic families of CPU architectures (see below);
-- by the `spack` strategy within {ref}`wave-page`, to optimise the container builds for specific CPU microarchitectures.
-
-Allowed values for the `arch` directive are as follows, grouped by equivalent family (choices available for the sake of compatibility):
-- X86 64 bit: `linux/x86_64`, `x86_64`, `linux/amd64`, `amd64`
-- ARM 64 bit: `linux/aarch64`, `aarch64`, `linux/arm64`, `arm64`, `linux/arm64/v8`
-- ARM 64 bit, older generation: `linux/arm64/v7`
-
-Examples of values for the architecture `target` option are `cascadelake`, `icelake`, `zen2` and `zen3`. See the [Spack documentation](https://spack.readthedocs.io/en/latest/basic_usage.html#support-for-specific-microarchitectures) for the full and up-to-date list of meaningful targets.
-
-(process-array)=
-
-### array
-
-:::{versionadded} 24.04.0
-:::
-
-:::{warning} *Experimental: may change in a future release.*
-:::
-
-The `array` directive allows you to submit tasks as *job arrays* for executors that support it.
-
-A job array is a collection of jobs with the same resource requirements and the same script (parameterized by an index). Job arrays incur significantly less scheduling overhead compared to individual jobs, and as a result they are preferred by HPC schedulers where possible.
-
-The directive should be specified with a given array size, along with an executor that supports job arrays. For example:
-
-```nextflow
-process hello {
-    executor 'slurm'
-    array 100
-
-    script:
-    """
-    your_command --here
-    """
-}
-```
-
-Nextflow currently supports job arrays for the following executors:
-
-- {ref}`awsbatch-executor`
-- {ref}`google-batch-executor`
-- {ref}`lsf-executor`
-- {ref}`pbs-executor`
-- {ref}`pbspro-executor`
-- {ref}`sge-executor`
-- {ref}`slurm-executor`
-
-A process using job arrays will collect tasks and submit each batch as a job array when it is ready. Any "leftover" tasks will be submitted as a partial job array.
-
-Once a job array is submitted, each "child" task is executed as an independent job. Any tasks that fail (and can be retried) will be retried without interfering with the tasks that succeeded. Retried tasks are submitted individually rather than through a job array, in order to allow for the use of {ref}`dynamic resources <dynamic-task-resources>`.
-
-The following directives must be uniform across all tasks in a process that uses job arrays, because these directives are specified once for the entire job array:
-
-- {ref}`process-accelerator`
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-disk`
-- {ref}`process-machineType`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-resourcelabels`
-- {ref}`process-resourcelimits`
-- {ref}`process-time`
-
-For cloud-based executors like AWS Batch, or when using Fusion with any executor, the following additional directives must be uniform:
-
-- {ref}`process-container`
-- {ref}`process-containerOptions`
-
-When using Wave, the following additional directives must be uniform:
-
-- {ref}`process-conda`
-
-(process-beforescript)=
-
-### beforeScript
-
-The `beforeScript` directive allows you to execute a custom (Bash) snippet *before* the main process script is run. This may be useful to initialise the underlying cluster environment or for other custom initialisation.
-
-For example:
-
-```nextflow
-process hello {
-  beforeScript 'source /cluster/bin/setup'
-
-  script:
-  """
-  echo 'hello'
-  """
-}
-```
-
-When the process is containerized (using the {ref}`process-container` directive), the `beforeScript` will be executed in the container only if the executor is *container-native* (e.g. cloud batch executors, Kubernetes). Otherwise, the `beforeScript` will be executed outside the container.
-
-(process-cache)=
-
-### cache
-
-The `cache` directive allows you to store the process results to a local cache. When the cache is enabled *and* the pipeline is launched with the {ref}`resume <getstarted-resume>` option, any task executions that are already cached will be re-used. See the {ref}`cache-resume-page` page for more information about how the cache works.
-
-The cache is enabled by default, but you can disable it for a specific process by setting the `cache` directive to `false`. For example:
-
-```nextflow
-process hello {
-  cache false
-  // ...
-}
-```
-
-The following options are available:
-
-`false`
-: Disable caching.
-
-`true` (default)
-: Enable caching. Input file metadata (name, size, last updated timestamp) are included in the cache keys.
-
-`'deep'`
-: Enable caching. Input file content is included in the cache keys.
-
-`'lenient'`
-: Enable caching. Minimal input file metadata (name and size only) are included in the cache keys.
-: This strategy provides a workaround for incorrect caching invalidation observed on shared file systems due to inconsistent file timestamps.
-
-(process-clusteroptions)=
-
-### clusterOptions
-
-The `clusterOptions` directive allows the usage of any native configuration option accepted by your cluster submit command. You can use it to request non-standard resources or use settings that are specific to your cluster and not supported out of the box by Nextflow.
-
-The cluster options can be a string:
-
-```nextflow
-process hello {
-  clusterOptions '-x 1 -y 2'
-  // ...
-}
-```
-
-:::{versionchanged} 24.04.0
-Prior to this version, grid executors that require each option to be on a separate line in the job script would attempt to split multiple options using a variety of different conventions. Multiple options can now be specified more clearly using a string list as shown below.
-:::
-
-The cluster options can also be a string list:
-
-```nextflow
-process hello {
-  clusterOptions '-x 1', '-y 2', '--flag'
-  // ...
-}
-```
-
-Grid executors that require one option per line will write each option to a separate line, while grid executors that allow multiple options per line will write all options to a single line, the same as with a string. This form is useful to control how the options are split across lines when it is required by the scheduler.
-
-:::{note}
-This directive is only used by grid executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-:::{warning}
-While you can use the `clusterOptions` directive to specify options that are supported as process directives (`queue`, `memory`, `time`, etc), you should not use both at the same time, as it will cause undefined behavior. Most HPC schedulers will either fail or simply ignore one or the other.
-:::
-
-(process-conda)=
-
-### conda
-
-The `conda` directive allows for the definition of the process dependencies using the [Conda](https://conda.io) package manager.
-
-Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. For example:
-
-```nextflow
-process hello {
-  conda 'bwa=0.7.15'
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-Multiple packages can be specified separating them with a blank space e.g. `bwa=0.7.15 fastqc=0.11.5`. The name of the channel from where a specific package needs to be downloaded can be specified using the usual Conda notation i.e. prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
-
-The `conda` directive also allows the specification of a Conda environment file path or the path of an existing environment directory. See the {ref}`conda-page` page for further details.
-
-(process-container)=
-
-### container
-
-The `container` directive allows you to execute the process script in a [Docker](http://docker.io) container.
-
-It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the *local* executor or the cluster nodes when the pipeline is deployed through a *grid* executor.
-
-For example:
-
-```nextflow
-process hello_docker {
-  container 'dockerbox:tag'
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-Simply replace in the above script `dockerbox:tag` with the name of the Docker image you want to use.
-
-:::{tip}
-Containers are a very useful way to execute your scripts in a reproducible self-contained environment or to run your pipeline in the cloud.
-:::
-
-:::{note}
-This directive is ignored for processes that are {ref}`executed natively <process-native>`.
-:::
-
-(process-containeroptions)=
-
-### containerOptions
-
-The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path:
-
-```nextflow
-process hello_docker {
-    container 'busybox:latest'
-    containerOptions '--volume /data/db:/db'
-
-    output:
-    path 'output.txt'
-
-    script:
-    """
-    your_command --data /db > output.txt
-    """
-}
-```
-
-:::{warning}
-This feature is not supported by the {ref}`k8s-executor` executor.
-:::
-
-(process-cpus)=
-
-### cpus
-
-The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. For example:
-
-```nextflow
-process blast {
-  cpus 8
-
-  script:
-  """
-  blastp -query input_sequence -num_threads ${task.cpus}
-  """
-}
-```
-
-This directive is required for tasks that execute multi-process or multi-threaded commands/tools and it is meant to reserve enough CPUs when a pipeline task is executed through a cluster resource manager.
-
-See also: [penv](#penv), [memory](#memory), [time](#time), [queue](#queue), [maxForks](#maxforks)
-
-(process-debug)=
-
-### debug
-
-By default the `stdout` produced by the commands executed in all processes is ignored. By setting the `debug` directive to `true`, you can forward the process `stdout` to the current top running process `stdout` file, showing it in the shell terminal.
-
-For example:
-
-```nextflow
-process hello {
-  debug true
-
-  script:
-  """
-  echo Hello
-  """
-}
-```
-
-```
-Hello
-```
-
-Without specifying `debug true`, you won't see the `Hello` string printed out when executing the above example.
-
-(process-disk)=
-
-### disk
-
-The `disk` directive allows you to define how much local disk storage the process is allowed to use. For example:
-
-```nextflow
-process hello {
-    disk 2.GB
-
-    script:
-    """
-    your_command --here
-    """
-}
-```
-
-The following memory unit suffix can be used when specifying the disk value:
-
-| Unit | Description |
-| ---- | ----------- |
-| B    | Bytes       |
-| KB   | Kilobytes   |
-| MB   | Megabytes   |
-| GB   | Gigabytes   |
-| TB   | Terabytes   |
-
-See {ref}`stdlib-types-memoryunit` for more information.
-
-:::{note}
-This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-See also: [cpus](#cpus), [memory](#memory) [time](#time), [queue](#queue) and {ref}`dynamic-task-resources`.
-
-(process-echo)=
-
-### echo
-
-:::{deprecated} 22.04.0
-Use `debug` instead
-:::
-
-(process-error-strategy)=
-
-### errorStrategy
-
-The `errorStrategy` directive allows you to define how the process manages an error condition. By default, when an error status is returned by the executed script (i.e. when it ends with a non-zero exit status), the process stops immediately, forcing the entire pipeline to terminate.
-
-The following error strategies are available:
-
-`'terminate'` (default)
-: When a task fails, terminate the pipeline immediately and report an error. Pending and running jobs are killed.
-
-`'finish'`
-: When a task fails, wait for submitted and running tasks to finish and then terminate the pipeline, reporting an error.
-
-`'ignore'`
-: When a task fails, ignore it and continue the pipeline execution. If the `workflow.failOnIgnore` config option is set to `true`, the pipeline will report an error (i.e. return a non-zero exit code) upon completion. Otherwise, the pipeline will complete successfully.
-: See the {ref}`stdlib-namespaces-workflow` namespace for more information.
-
-`'retry'`
-: When a task fails, retry it.
-
-When setting the `errorStrategy` directive to `ignore` the process doesn't stop on an error condition, it just reports a message notifying you of the error event.
-
-For example:
-
-```nextflow
-process hello {
-  errorStrategy 'ignore'
-
-  // ...
-}
-```
-
-In this case, the workflow will complete successfully and return an exit status of 0. However, if you set `workflow.failOnIgnore = true` in your Nextflow configuration, the workflow will return a non-zero exit status and report the failed tasks as an error.
-
-The `retry` error strategy allows you to re-submit for execution a process returning an error condition. For example:
-
-```nextflow
-process hello {
-  errorStrategy 'retry'
-
-  // ...
-}
-```
-
-The number of times a failing process is re-executed is defined by the [maxRetries](#maxretries) and [maxErrors](#maxerrors) directives.
-
-:::{tip}
-More complex strategies depending on the task exit status or other parametric values can be defined using a dynamic `errorStrategy`. See {ref}`dynamic-directives` for details.
-:::
-
-See also: [maxErrors](#maxerrors), [maxRetries](#maxretries) and {ref}`dynamic-task-resources`.
-
-(process-executor)=
-
-### executor
-
-The `executor` defines the underlying system where processes are executed. By default a process uses the executor defined globally in the `nextflow.config` file.
-
-The `executor` directive allows you to configure what executor has to be used by the process, overriding the default configuration.
-
-The following executors are available:
-
-| Name                  | Executor                                                                                    |
-| --------------------- | ------------------------------------------------------------------------------------------- |
-| `awsbatch`            | [AWS Batch](https://aws.amazon.com/batch/) service                                          |
-| `azurebatch`          | [Azure Batch](https://azure.microsoft.com/en-us/services/batch/) service                    |
-| `condor`              | [HTCondor](https://research.cs.wisc.edu/htcondor/) job scheduler                            |
-| `k8s`                 | [Kubernetes](https://kubernetes.io/) cluster                                                |
-| `local`               | The computer where `Nextflow` is launched                                                   |
-| `lsf`                 | [Platform LSF](http://en.wikipedia.org/wiki/Platform_LSF) job scheduler                     |
-| `moab`                | [Moab](http://www.adaptivecomputing.com/moab-hpc-basic-edition/) job scheduler              |
-| `nqsii`               | [NQSII](https://www.rz.uni-kiel.de/en/our-portfolio/hiperf/nec-linux-cluster) job scheduler |
-| `oge`                 | Alias for the `sge` executor                                                                |
-| `pbs`                 | [PBS/Torque](http://en.wikipedia.org/wiki/Portable_Batch_System) job scheduler              |
-| `pbspro`              | [PBS Pro](https://www.pbsworks.com/) job scheduler                                          |
-| `sge`                 | Sun Grid Engine / [Open Grid Engine](http://gridscheduler.sourceforge.net/)                 |
-| `slurm`               | [SLURM](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) workload manager              |
-| `uge`                 | Alias for the `sge` executor                                                                |
-
-The following example shows how to set the process's executor:
-
-```nextflow
-process hello {
-  executor 'sge'
-
-  // ...
-}
-```
-
-:::{note}
-Each executor supports additional directives and `executor` configuration options. See {ref}`executor-page` for more information.
-:::
-
-(process-ext)=
-
-### ext
-
-The `ext` is a special directive used as *namespace* for user custom process directives. This can be useful for advanced configuration options. For example:
-
-```nextflow
-process star {
-  container "biocontainers/star:${task.ext.version}"
-
-  input:
-  path genome
-  tuple val(sampleId), path(reads)
-
-  script:
-  """
-  STAR --genomeDir $genome --readFilesIn $reads ${task.ext.args ?: ''}
-  """
-}
-```
-
-In the above example, the process container version is controlled by `ext.version`, and the script supports additional command line arguments through `ext.args`.
-
-The `ext` directive can be set in the process definition:
-
-```nextflow
-process hello {
-  ext version: '2.5.3', args: '--alpha --beta'
-
-  // ...
-}
-```
-
-Or in the Nextflow configuration:
-
-```groovy
-process.ext.version = '2.5.3'
-process.ext.args = '--alpha --beta'
-```
-
-(process-fair)=
-
-### fair
-
-:::{versionadded} 22.12.0-edge
-:::
-
-The `fair` directive, when enabled, guarantees that process outputs will be emitted in the order in which they were received. For example:
-
-```nextflow
-process hello {
-    fair true
-
-    input:
-    val x
-
-    output:
-    tuple val(task.index), val(x)
-
-    script:
-    """
-    sleep \$((RANDOM % 3))
-    """
-}
-
-workflow {
-    channel.of('A','B','C','D') | hello | view
-}
-```
-
-The above example produces:
-
-```
-[1, A]
-[2, B]
-[3, C]
-[4, D]
-```
-
-(process-label)=
-
-### label
-
-The `label` directive allows the annotation of processes with mnemonic identifier of your choice. For example:
-
-```nextflow
-process hello {
-  label 'big_mem'
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-The same label can be applied to more than a process and multiple labels can be applied to the same process using the `label` directive more than one time.
-
-:::{note}
-A label must consist of alphanumeric characters or `_`, must start with an alphabetic character and must end with an alphanumeric character.
-:::
-
-Labels are useful to organize workflow processes in separate groups which can be referenced in the configuration file to select and configure a subset of processes having similar computing requirements. See {ref}`config-process-selectors` for more information.
-
-See also: [resourceLabels](#resourcelabels)
-
-(process-machinetype)=
-
-### machineType
-
-:::{versionadded} 19.07.0
-:::
-
-The `machineType` can be used to specify a predefined Google Compute Platform [machine type](https://cloud.google.com/compute/docs/machine-types) when running using the {ref}`Google Batch <google-batch-executor>`, or when using the autopools feature of the {ref}`Azure Batch executor<azurebatch-executor>`.
-
-This directive is optional and if specified overrides the cpus and memory directives:
-
-```nextflow
-process hello {
-  machineType 'n1-highmem-8'
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-See also: [cpus](#cpus) and [memory](#memory).
-
-(process-maxerrors)=
-
-### maxErrors
-
-The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled, you can set it as shown in the example below:
-
-```nextflow
-process hello {
-  errorStrategy 'retry'
-  maxErrors 5
-
-  script:
-  """
-  echo 'do this as that .. '
-  """
-}
-```
-
-:::{note}
-This setting considers the **total** errors accumulated for a given process, across all instances. If you want to control the number of times a process **instance** (aka task) can fail, use `maxRetries`.
-:::
-
-See also: [errorStrategy](#errorstrategy) and [maxRetries](#maxretries).
-
-(process-maxforks)=
-
-### maxForks
-
-The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1.
-
-If you want to execute a process in a sequential manner, set this directive to one. For example:
-
-```nextflow
-process hello {
-  maxForks 1
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-(process-maxretries)=
-
-### maxRetries
-
-The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the `retry` error strategy. By default only one retry is allowed, you can increase this value as shown below:
-
-```nextflow
-process hello {
-    errorStrategy 'retry'
-    maxRetries 3
-
-    script:
-    """
-    echo 'do this as that .. '
-    """
-}
-```
-
-:::{note}
-There is a subtle but important difference between `maxRetries` and the `maxErrors` directive. The latter defines the total number of errors that are allowed during the process execution (the same process can launch different execution instances), while the `maxRetries` defines the maximum number of times the same process execution can be retried in case of an error.
-:::
-
-See also: [errorStrategy](#errorstrategy) and [maxErrors](#maxerrors).
-
-(process-maxsubmitawait)=
-
-### maxSubmitAwait
-
-The `maxSubmitAwait` directive allows you to specify how long a task can remain in submission queue without being executed.
-Elapsed this time the task execution will fail.
-
-When used along with `retry` error strategy, it can be useful to re-schedule the task to a difference queue or
-resource requirement. For example:
-
-```nextflow
-process hello {
-  errorStrategy 'retry'
-  maxSubmitAwait 10.m
-  maxRetries 3
-  queue "${task.submitAttempt==1 ? 'spot-compute' : 'on-demand-compute'}"
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-In the above example the task is submitted to the `spot-compute` on the first attempt (`task.submitAttempt==1`). If the
-task execution does not start in the 10 minutes, a failure is reported and a new submission is attempted using the
-queue named `on-demand-compute`.
-
-(process-memory)=
-
-### memory
-
-The `memory` directive allows you to define how much memory the process is allowed to use. For example:
-
-```nextflow
-process hello {
-    memory 2.GB
-
-    script:
-    """
-    your_command --here
-    """
-}
-```
-
-The following memory unit suffix can be used when specifying the memory value:
-
-| Unit | Description |
-| ---- | ----------- |
-| B    | Bytes       |
-| KB   | Kilobytes   |
-| MB   | Megabytes   |
-| GB   | Gigabytes   |
-| TB   | Terabytes   |
-
-See {ref}`stdlib-types-memoryunit` for more information.
-
-See also: [cpus](#cpus), [time](#time), [queue](#queue) and {ref}`dynamic-task-resources`.
-
-(process-module)=
-
-### module
-
-[Environment Modules](http://modules.sourceforge.net/) is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool.
-
-If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline.
-
-In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. For example:
-
-```nextflow
-process blast {
-  module 'ncbi-blast/2.2.27'
-
-  script:
-  """
-  blastp -query <etc..>
-  """
-}
-```
-
-You can repeat the `module` directive for each module you need to load. Alternatively multiple modules can be specified in a single `module` directive by separating all the module names by using a `:` (colon) character as shown below:
-
-```nextflow
-process blast {
-  module 'ncbi-blast/2.2.27:t_coffee/10.0:clustalw/2.1'
-
-  script:
-  """
-  blastp -query <etc..>
-  """
-}
-```
-
-(process-penv)=
-
-### penv
-
-The `penv` directive allows you to define the parallel environment to be used when submitting a parallel task to the {ref}`SGE <sge-executor>` resource manager. For example:
-
-```nextflow
-process blast {
-  cpus 4
-  penv 'smp'
-  executor 'sge'
-
-  script:
-  """
-  blastp -query input_sequence -num_threads ${task.cpus}
-  """
-}
-```
-
-This configuration depends on the parallel environment provided by your grid engine installation. Refer to your cluster documentation or contact your admin to learn more about this.
-
-See also: [cpus](#cpus), [memory](#memory), [time](#time)
-
-(process-pod)=
-
-### pod
-
-The `pod` directive allows the definition of pod specific settings, such as environment variables, secrets, and config maps, when using the {ref}`k8s-executor` executor.
-
-For example:
-
-```nextflow
-process echo {
-  pod env: 'MESSAGE', value: 'hello world'
-
-  script:
-  """
-  echo $MESSAGE
-  """
-}
-```
-
-The above snippet defines an environment variable named `MESSAGE` whose value is `'hello world'`.
-
-When defined in the Nextflow configuration file, a pod setting can be defined as a map:
-
-```groovy
-process {
-  pod = [env: 'MESSAGE', value: 'hello world']
-}
-```
-
-Or as a list of maps:
-
-```groovy
-process {
-  pod = [
-    [env: 'MESSAGE', value: 'hello world'],
-    [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
-  ]
-}
-```
-
-The following options are available:
-
-`affinity: <config>`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specifies the pod [affinity](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#affinity-and-anti-affinity) with the given configuration.
-
-`annotation: '<name>', value: '<value>'`
-: *Can be specified multiple times*
-: Defines a pod [annotation](https://kubernetes.io/docs/concepts/overview/working-with-objects/annotations/) with the given name and value.
-
-`automountServiceAccountToken: true | false`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specifies whether to [automount service account token](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/#opt-out-of-api-credential-automounting) into the pod (default: `true`).
-
-`config: '<configMap>/<key>', mountPath: '</absolute/path>'`
-: *Can be specified multiple times*
-: Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `ConfigMap` are exposed in that path.
-
-`csi: '<config>', mountPath: '</absolute/path>'`
-: :::{versionadded} 22.11.0-edge
-  :::
-: *Can be specified multiple times*
-: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) with the given configuration to the given path.
-
-`emptyDir: <config>, mountPath: '</absolute/path>'`
-: :::{versionadded} 22.11.0-edge
-  :::
-: *Can be specified multiple times*
-: Mounts an [emptyDir](https://kubernetes.io/docs/concepts/storage/volumes/#emptydir) with the given configuration to the given path.
-
-`env: '<name>', config: '<configMap>/<key>'`
-: *Can be specified multiple times*
-: Defines an environment variable whose value is defined by the given [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) and key.
-
-`env: '<name>', fieldPath: '<fieldPath>'`
-: :::{versionadded} 21.09.1-edge
-  :::
-: *Can be specified multiple times*
-: Defines an environment variable whose value is defined by the given [field path](https://kubernetes.io/docs/tasks/inject-data-application/environment-variable-expose-pod-information/#use-pod-fields-as-values-for-environment-variables) value.
-
-: For example, the following pod option:
-
-  ```groovy
-  pod = [env: 'MY_NODE_NAME', fieldPath: 'spec.nodeName']
-  ```
-
-  Maps to the following pod spec:
-
-  ```yaml
-  env:
-    - name: MY_NODE_NAME
-      valueFrom:
-        fieldRef:
-          fieldPath: spec.nodeName
-  ```
-
-`env: '<name>', secret: '<secret>/<key>'`
-: *Can be specified multiple times*
-: Defines an environment variable whose value is defined by the given [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) and key.
-
-`env: '<name>', value: '<value>'`
-: *Can be specified multiple times*
-: Defines an environment variable with the given name and value.
-
-`hostPath: '/host/absolute/path', mountPath: '</pod/absolute/path>'`
-: :::{versionadded} 23.10.0
-  :::
-: *Can be specified multiple times*
-: Allows creating [hostPath](https://kubernetes.io/docs/concepts/storage/volumes/#hostpath) volume and access it with the specified `mountPath` in the pod.
-
-`imagePullPolicy: 'IfNotPresent' | 'Always' | 'Never'`
-: Specifies the [image pull policy](https://kubernetes.io/docs/concepts/containers/images/#image-pull-policy) used by the pod to pull the container image.
-
-`imagePullSecret: '<name>'`
-: Specifies the [image pull secret](https://kubernetes.io/docs/concepts/containers/images/#specifying-imagepullsecrets-on-a-pod) used to access a private container image registry.
-
-`label: '<name>', value: '<value>'`
-: *Can be specified multiple times*
-: Defines a pod [label](https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/) with the given name and value.
-
-`nodeSelector: <config>`
-: Specifies the [node selector](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#nodeselector) with the given configuration.
-
-: The configuration can be a map or a string:
-
-  ```groovy
-  // map
-  pod = [nodeSelector: [disktype: 'ssd', cpu: 'intel']]
-
-  // string
-  pod = [nodeSelector: 'disktype=ssd,cpu=intel']
-  ```
-
-`priorityClassName: '<name>'`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specifies the [priority class name](https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/) for pods.
-
-`privileged: true | false`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Specifies whether the pod should run as a *privileged* container (default: `false`).
-
-`runAsUser: '<uid>'`
-: Specifies the user ID with which to run the container. Shortcut for the `securityContext` option.
-
-`schedulerName: '<name>'`
-: Specifies which [scheduler](https://kubernetes.io/docs/tasks/extend-kubernetes/configure-multiple-schedulers/#specify-schedulers-for-pods) is used to schedule the container.
-
-`secret: '<secret>/<key>', mountPath: '</absolute/path>'`
-: *Can be specified multiple times*
-: Mounts a [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `Secret` are exposed in that path.
-
-`securityContext: <config>`
-: Specifies the pod [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) with the given configuration.
-
-`toleration: <config>`
-: :::{versionadded} 22.04.0
-  :::
-: *Can be specified multiple times*
-: Specifies the pod [toleration](https://kubernetes.io/docs/concepts/scheduling-eviction/taint-and-toleration/) with the given configuration.
-
-: The configuration should be a map corresponding to a single toleration rule. For example, the following pod options:
-
-  ```groovy
-  pod = [
-      [toleration: [key: 'key1', operator: 'Equal', value: 'value1', effect: 'NoSchedule']],
-      [toleration: [key: 'key1', operator: 'Exists', effect: 'NoSchedule']],
-  ]
-  ```
-
-  Maps to the following pod spec:
-
-  ```yaml
-  tolerations:
-    - key: "key1"
-      operator: "Equal"
-      value: "value1"
-      effect: "NoSchedule"
-    - key: "key1"
-      operator: "Exists"
-      effect: "NoSchedule"
-  ```
-
-`ttlSecondsAfterFinished`
-: :::{versionadded} 24.02.0-edge
-  :::
-: Specifies the [TTL mechanism](https://kubernetes.io/docs/concepts/workloads/controllers/job/#ttl-mechanism-for-finished-jobs) for finished jobs in seconds. Applies to both successful and failed jobs.
-
-`volumeClaim: '<name>', mountPath: '</absolute/path>' [, subPath: '<path>', readOnly: true | false]`
-: *Can be specified multiple times*
-: Mounts a [Persistent volume claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/) with the given name to the given path.
-: The `subPath` option can be used to mount a sub-directory of the volume instead of its root.
-: The `readOnly` option can be used to mount the volume as read-only (default: `false`)
-
-(process-publishdir)=
-
-### publishDir
-
-The `publishDir` directive allows you to publish the process output files to a specified folder. For example:
-
-```nextflow
-process hello {
-    publishDir '/data/chunks'
-
-    output:
-    path 'chunk_*'
-
-    script:
-    """
-    printf 'Hola' | split -b 1 - chunk_
-    """
-}
-```
-
-The above example splits the string `Hola` into file chunks of a single byte. When complete the `chunk_*` output files are published into the `/data/chunks` folder.
-
-:::{note}
-Only files that match the declaration in the `output` block are published, not all the outputs of the process.
-:::
-
-:::{tip}
-The `publishDir` directive can be specified more than once in order to publish output files to different target directories based on different rules.
-:::
-
-By default files are published to the target folder creating a *symbolic link* for each process output that links the file produced into the process working directory. This behavior can be modified using the `mode` option, for example:
-
-```nextflow
-process hello {
-    publishDir '/data/chunks', mode: 'copy', overwrite: false
-
-    output:
-    path 'chunk_*'
-
-    script:
-    """
-    printf 'Hola' | split -b 1 - chunk_
-    """
-}
-```
-
-:::{warning}
-Files are copied into the specified directory in an *asynchronous* manner, so they may not be immediately available in the publish directory at the end of the process execution. For this reason, downstream processes should not try to access output files through the publish directory, but through the outputs of the originating process.
-:::
-
-Available options:
-
-`contentType`
-: :::{versionadded} 22.10.0
-  :::
-: *Experimental: currently only supported for S3.*
-: Allow specifying the media content type of the published file a.k.a. [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_Types). If set to `true`, the content type is inferred from the file extension (default: `false`).
-
-`enabled`
-: Enable or disable the publish rule depending on the boolean value specified (default: `true`).
-
-`failOnError`
-: :::{versionchanged} 24.03.0-edge
-  The default value was changed from `false` to `true`
-  :::
-: When `true` abort the execution if some file can't be published to the specified target directory or bucket for any cause (default: `true`)
-
-`mode`
-: The file publishing method. Can be one of the following values:
-
-  - `'copy'`: Copies the output files into the publish directory.
-  - `'copyNoFollow'`: Copies the output files into the publish directory without following symlinks ie. copies the links themselves.
-  - `'link'`: Creates a hard link in the publish directory for each output file.
-  - `'move'`: Moves the output files into the publish directory. **Note**: this is only supposed to be used for a *terminal* process i.e. a process whose output is not consumed by any other downstream process.
-  - `'rellink'`: Creates a relative symbolic link in the publish directory for each output file.
-  - `'symlink'`: Creates an absolute symbolic link in the publish directory for each output file (default).
-
-`overwrite`
-: When `true` any existing file in the specified folder will be overridden (default: `true` during normal pipeline execution and `false` when pipeline execution is `resumed`).
-
-`path`
-: Specifies the directory where files need to be published. **Note**: the syntax `publishDir '/some/dir'` is a shortcut for `publishDir path: '/some/dir'`.
-
-`pattern`
-: Specifies a [glob][glob] file pattern that selects which files to publish from the overall set of output files.
-
-`saveAs`
-: A closure which, given the name of the file being published, returns the actual file name or a full path where the file is required to be stored. This can be used to rename or change the destination directory of the published files dynamically by using a custom strategy. Return the value `null` from the closure to *not* publish a file. This is useful when the process has multiple output files, but you want to publish only some of them.
-
-`storageClass`
-: :::{versionadded} 22.12.0-edge
-  :::
-: *Experimental: currently only supported for S3.*
-: Allow specifying the storage class to be used for the published file.
-
-`tags`
-: :::{versionadded} 21.12.0-edge
-  :::
-: *Experimental: currently only supported for S3.*
-: Allow the association of arbitrary tags with the published file e.g. `tags: [MESSAGE: 'Hello world']`.
-
-(process-queue)=
-
-### queue
-
-The `queue` directive allows you to set the `queue` where jobs are scheduled when using a grid based executor in your pipeline. For example:
-
-```nextflow
-process hello {
-    queue 'long'
-    executor 'sge'
-
-    script:
-    """
-    your_command --here
-    """
-}
-```
-
-:::{tip}
-Some grid executors support multiple queue names as a comma-separated list:
-
-```nextflow
-queue 'short,long,cn-el6'
-```
-
-However, this does not generally apply to other executors such as AWS Batch, Azure Batch, Google Batch.
-:::
-
-:::{note}
-This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-(process-resourcelabels)=
-
-### resourceLabels
-
-:::{versionadded} 22.09.1-edge
-:::
-
-The `resourceLabels` directive allows you to specify custom name-value pairs that Nextflow applies to the computing resource used to carry out the process execution. Resource labels can be specified using the syntax shown below:
-
-```nextflow
-process hello {
-    resourceLabels region: 'some-region', user: 'some-username'
-
-    script:
-    """
-    your_command --here
-    """
-}
-```
-
-The limits and the syntax of the corresponding cloud provider should be taken into consideration when using resource labels.
-
-Resource labels are currently supported by the following executors:
-
-- {ref}`awsbatch-executor`
-- {ref}`azurebatch-executor`
-- {ref}`google-batch-executor`
-- {ref}`k8s-executor`
-
-:::{versionadded} 23.09.0-edge
-Resource labels are supported for Azure Batch when using automatic pool creation.
-
-Resource labels in Azure are added to pools, rather than jobs, in order to facilitate cost analysis. A new pool will be created for each new set of resource labels, therefore it is recommended to also set `azure.batch.deletePoolsOnCompletion = true` when using process-specific resource labels.
-:::
-
-See also: [label](#label)
-
-(process-resourcelimits)=
-
-### resourceLimits
-
-:::{versionadded} 24.04.0
-:::
-
-The `resourceLimits` directive allows you to specify environment-specific limits for task resource requests. Resource limits can be specified in a process as follows:
-
-```nextflow
-process hello {
-  resourceLimits cpus: 24, memory: 768.GB, time: 72.h
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-Or in the Nextflow configuration:
-
-```nextflow
-process {
-    resourceLimits = [ cpus: 24, memory: 768.GB, time: 72.h ]
-}
-```
-
-Resource limits can be defined for the following directives:
-
-- [cpus](#cpus)
-- [disk](#disk)
-- [memory](#memory)
-- [time](#time)
-
-Resource limits are a useful way to specify environment-specific limits alongside tasks with {ref}`dynamic resources <dynamic-task-resources>`. Normally, if a task requests more resources than can be provisioned (e.g. a task requests 32 cores but the largest node in the cluster has 24), the task will either fail or cause the pipeline to hang forever as it will never be scheduled. If the `resourceLimits` directive is defined with these limits, the task resources will be automatically reduced to comply with these limits before the job is submitted.
-
-(process-scratch)=
-
-### scratch
-
-The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node.
-
-This is useful when your pipeline is launched by using a grid executor, because it allows you to decrease the NFS overhead by running the pipeline processes in a temporary directory in the local disk of the actual execution node. Only the files declared as output in the process definition will be copied in the pipeline working area.
-
-In its basic form simply specify `true` at the directive value, as shown below:
-
-```nextflow
-process hello {
-  scratch true
-
-  output:
-  path 'data_out'
-
-  script:
-  """
-  your_command --here
-  """
-}
-```
-
-By doing this, it tries to execute the script in the directory defined by the variable `$TMPDIR` in the execution node. If this variable does not exist, it will create a new temporary directory by using the Linux command `mktemp`.
-
-Nextflow creates a subdirectory within the scratch directory for each task and automatically deletes it once the task completes.
-
-:::{note}
-Cloud-based executors use `scratch = true` by default, since the work directory resides in object storage.
-:::
-
-The following values are supported:
-
-`false`
-: Do not use a scratch directory.
-
-`true`
-: Create a scratch directory in the directory defined by the `$TMPDIR` environment variable, or `$(mktemp /tmp)` if `$TMPDIR` is not set.
-
-`'$YOUR_VAR'`
-: Create a scratch directory in the directory defined by the given environment variable, or `$(mktemp /tmp)` if that variable is not set. The value must use single quotes, otherwise the environment variable will be evaluated in the pipeline script context.
-
-`'/my/tmp/path'`
-: Create a scratch directory in the specified directory.
-
-`'ram-disk'`
-: Create a scratch directory in the RAM disk `/dev/shm/`.
-
-(process-secret)=
-
-### secret
-
-The `secret` directive allows a process to access secrets.
-
-Secrets can be added to a process as follows:
-
-```nextflow
-process hello_secret {
-    secret 'MY_ACCESS_KEY'
-    secret 'MY_SECRET_KEY'
-
-    script:
-    """
-    your_command --access \$MY_ACCESS_KEY --secret \$MY_SECRET_KEY
-    """
-}
-```
-
-See {ref}`secrets-page` for more information. 
-
-:::{warning}
-Secrets are made available as environment variables in the process script. To prevent evaluation in the Nextflow script context, escape variable names with a backslash (e.g., `\$MY_ACCESS_KEY`) as shown above.
-:::
-
-:::{note}
-Secrets can only be used with the local or grid executors (e.g., Slurm or Grid Engine). Secrets can be used with the AWS Batch executor when launched from Seqera Platform.
-:::
-
-(process-directive-shell)=
-
-### shell
-
-The `shell` directive allows you to define a custom shell command for process scripts. By default, script blocks are executed with `/bin/bash -ue`.
-
-```nextflow
-process hello {
-    shell '/bin/bash', '-euo', 'pipefail'
-
-    script:
-    """
-    your_command --here
-    """
-}
-```
-
-The same directive could be specified in your Nextflow configuration as follows:
-
-```groovy
-process.shell = ['/bin/bash', '-euo', 'pipefail']
-```
-
-(process-spack)=
-
-### spack
-
-The `spack` directive allows for the definition of the process dependencies using the [Spack](https://spack.io) package manager.
-
-Nextflow automatically sets up an environment for the given package names listed by in the `spack` directive. For example:
-
-```nextflow
-process hello {
-    spack 'bwa@0.7.15'
-
-    script:
-    """
-    your_command --here
-    """
-}
-```
-
-Multiple packages can be specified separating them with a blank space, e.g. `bwa@0.7.15 fastqc@0.11.5`.
-
-The `spack` directive also allows the specification of a Spack environment file path or the path of an existing environment directory. See the {ref}`spack-page` page for further details.
-
-(process-stageinmode)=
-
-### stageInMode
-
-The `stageInMode` directive defines how input files are staged into the process work directory. The following values are allowed:
-
-`'copy'`
-: Input files are staged in the process work directory by creating a copy.
-
-`'link'`
-: Input files are staged in the process work directory by creating a hard link for each of them.
-
-`'rellink'`
-: Input files are staged in the process work directory by creating a symbolic link with a relative path for each of them.
-
-`'symlink'`
-: Input files are staged in the process work directory by creating a symbolic link with an absolute path for each of them (default).
-
-(process-stageoutmode)=
-
-### stageOutMode
-
-The `stageOutMode` directive defines how output files are staged out from the scratch directory to the process work directory. The following values are allowed:
-
-`'copy'`
-: Output files are copied from the scratch directory to the work directory.
-
-`'fcp'`
-: :::{versionadded} 23.02.0-edge
-  :::
-: Output files are copied from the scratch directory to the work directory by using the [fcp](https://github.com/Svetlitski/fcp) utility (note: it must be available in your cluster computing nodes).
-
-`'move'`
-: Output files are moved from the scratch directory to the work directory.
-
-`'rclone'`
-: :::{versionadded} 23.01.0-edge
-  :::
-: Output files are copied from the scratch directory to the work directory by using the [rclone](https://rclone.org) utility (note: it must be available in your cluster computing nodes).
-
-`'rsync'`
-: Output files are copied from the scratch directory to the work directory by using the `rsync` utility.
-
-See also: [scratch](#scratch).
-
-(process-storedir)=
-
-### storeDir
-
-The `storeDir` directive allows you to define a directory that is used as a *permanent* cache for your process results.
-
-In more detail, it affects the process execution in two main ways:
-
-1. The process is executed only if the files declared in the `output` block do not exist in the directory specified by the `storeDir` directive. When the files exist the process execution is skipped and these files are used as the actual process result.
-2. Whenever a process is successfully completed the files listed in the `output` block are moved into the directory specified by the `storeDir` directive.
-
-The following example shows how to use the `storeDir` directive to create a directory containing a BLAST database for each species specified by an input parameter:
-
-```nextflow
-process make_blast_db {
-  storeDir '/db/genomes'
-
-  input:
-  path species
-
-  output:
-  path "${dbName}.*"
-
-  script:
-  dbName = species.baseName
-  """
-  makeblastdb -dbtype nucl -in ${species} -out ${dbName}
-  """
-}
-```
-
-:::{warning}
-If a process uses `storeDir` and all of its outputs are optional, the process will always be skipped, even if the store directory is empty. This issue can be avoided by specifying at least one required file output.
-:::
-
-:::{warning}
-The `storeDir` directive should not be used to publish workflow outputs. Use the [publishDir](#publishdir) directive or the {ref}`workflow output definition <workflow-output-def>` instead.
-:::
-
-(process-tag)=
-
-### tag
-
-The `tag` directive allows you to associate each process execution with a custom label, so that it will be easier to identify them in the log file or in the trace execution report. For example:
-
-```nextflow
-process hello {
-  tag "$code"
-
-  input:
-  val code
-
-  script:
-  """
-  echo $code
-  """
-}
-
-workflow {
-  channel.of('alpha', 'gamma', 'omega') | hello
-}
-```
-
-The above snippet will print a log similar to the following one, where process names contain the tag value:
-
-```
-[6e/28919b] Submitted process > hello (alpha)
-[d2/1c6175] Submitted process > hello (gamma)
-[1c/3ef220] Submitted process > hello (omega)
-```
-
-See also {ref}`Trace execution report <trace-report>`
-
-(process-time)=
-
-### time
-
-The `time` directive allows you to define how long a process is allowed to run. For example:
-
-```nextflow
-process hello {
-    time 1.h
-
-    script:
-    """
-    your_command --here
-    """
-}
-```
-
-The following time unit suffixes can be used when specifying the duration value:
-
-| Unit | Description  |
-| ---- | ------------ |
-| `ms` | Milliseconds |
-| `s`  | Seconds      |
-| `m`  | Minutes      |
-| `h`  | Hours        |
-| `d`  | Days         |
-
-See {ref}`stdlib-types-duration` for more information.
-
-:::{note}
-This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-See also: [cpus](#cpus), [memory](#memory), [queue](#queue) and {ref}`dynamic-task-resources`.
diff --git a/docs/reference/process.mdx b/docs/reference/process.mdx
new file mode 100644
index 0000000000..cc2bd59702
--- /dev/null
+++ b/docs/reference/process.mdx
@@ -0,0 +1,1802 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Process reference
+
+This page lists the task properties, input/output methods, and directives available in [process][process-page] definitions.
+
+## Task properties
+
+The following task properties are defined in the process body:
+
+##### `task.attempt`
+
+The current task attempt.
+
+##### `task.exitStatus`
+
+The exit code of the task script. Only applicable for processes with a `script:` or `shell:` block.
+
+Since the exit code is only available after the task has been executed, it can only be used by certain process directives such as [errorStrategy](#errorstrategy).
+
+##### `task.previousException`
+
+<AddedInVersion version="24.10.0"/>
+
+The exception reported by the previous task attempt.
+
+Since the exception is available after a failed task attempt, it can only be accessed when retrying a failed task execution, i.e., when `task.attempt` is greater than 1.
+
+##### `task.previousTrace`
+
+<AddedInVersion version="24.10.0"/>
+
+The trace record associated with the previous task attempt.
+
+Since the trace record is available after a failed task attempt, it can only be accessed when retrying a failed task execution, i.e., when `task.attempt` is greater than 1.
+
+##### `task.process`
+
+The name of the process that spawned the task.
+
+##### `task.workDir`
+
+*Available only in `exec:` blocks*
+
+The unique directory path for the task.
+
+:::note
+[Directive values](#directives) for a task can be accessed via `task.<directive>`.
+:::
+
+## Inputs and outputs (typed)
+
+<AddedInVersion version="25.10.0"/>
+
+:::note
+Typed processes require the `nextflow.preview.types` feature flag to be enabled in every script that uses them.
+:::
+
+### Stage directives
+
+The following directives can be used in the `stage:` section of a typed process:
+
+##### `env( name: String, String value )`
+
+Declares an environment variable with the specified name and value in the task environment.
+
+##### `stageAs( filePattern: String, value: Path )`
+
+Stages a file into the task directory under the given alias.
+
+###### `stageAs( filePattern: String, value: Iterable<Path> )`
+
+Stages a collection of files into the task directory under the given alias.
+
+##### `stdin( value: String )`
+
+Stages the given value as the standard input (i.e., `stdin`) to the task script.
+
+### Outputs
+
+The following functions are available in the `output:` and `topic:` sections of a typed process:
+
+##### `env( name: String ) -> String`
+
+Returns the value of an environment variable from the task environment.
+
+##### `eval( command: String ) -> String`
+
+Returns the standard output of the specified command, which is executed in the task environment after the task script completes.
+
+##### `file( pattern: String, [options] ) -> Path`
+
+Returns a file from the task environment that matches the specified pattern.
+
+Available options:
+
+###### `followLinks: Boolean`
+
+When `true`, target files are returned in place of any matching symlink (default: `true`).
+
+###### `glob: Boolean`
+
+When `true`, the file name is interpreted as a glob pattern (default: `true`).
+
+###### `hidden: Boolean`
+
+When `true`, hidden files are included in the matching output files (default: `false`).
+
+###### `includeInputs: Boolean`
+
+When `true` and the file name is a glob pattern, any input files matching the pattern are also included in the output (default: `false`).
+
+###### `maxDepth: Integer`
+
+Maximum number of directory levels to visit (default: no limit).
+
+###### `optional: Boolean`
+
+When `true`, the task will not fail if the given file is missing (default: `false`).
+
+###### `type: String`
+
+Type of paths returned, either `file`, `dir` or `any` (default: `any`, or `file` if the given file name contains a double star (`**`)).
+
+##### `files( pattern: String, [options] ) -> Set<Path>`
+
+Returns files from the task environment that match the given pattern.
+
+Supports the same options as `file()` (except for `optional`).
+
+##### `stdout() -> String`
+
+Returns the standard output of the task script.
+
+
+## Inputs and outputs (legacy)
+
+### Inputs
+
+##### `val( identifier )`
+
+Declare a variable input. The received value can be any type, and it will be made available to the process body (i.e. `script`, `shell`, `exec`) as a variable given by `identifier`.
+
+##### `file( identifier | stageName )`
+
+<DeprecatedInVersion version="19.10.0">
+Use `path` instead.
+</DeprecatedInVersion>
+
+Declare a file input. The received value can be any type, and it will be staged into the task directory. If the received value is not a file or collection of files, it is implicitly converted to a string and written to a file.
+
+The argument can be an identifier or string. If an identifier, the received value will be made available to the process body as a variable. If a string, the received value will be staged into the task directory under the given alias.
+
+##### `path( identifier | stageName )`
+
+Declare a file input. The received value should be a file or collection of files and will be staged into the task directory.
+
+The argument can be an identifier or string. If an identifier, the received value will be made available to the process body as a variable. If a string, the received value will be staged into the task directory under the given alias.
+
+Available options:
+
+##### `arity`
+
+<AddedInVersion version="23.09.0-edge" />
+
+Specify the number of expected files. Can be a number, e.g. `'1'`, or a range, e.g. `'1..*'`. If a task receives an invalid number of files for this `path` input, it will fail.
+
+##### `name`
+
+Specify how the file should be named in the task work directory. Can be a name or a pattern.
+
+##### `stageAs`
+
+Alias of `name`.
+
+##### `env( name )`
+
+Declare an environment variable input. The received value should be a string, and it will be exported to the task environment as an environment variable given by `name`.
+
+##### `stdin`
+
+Declare a `stdin` input. The received value should be a string, and it will be provided as the standard input (i.e. `stdin`) to the task script. It should be declared only once for a process.
+
+##### `tuple( arg1, arg2, ... )`
+
+Declare a tuple input. Each argument should be an input declaration such as `val`, `path`, `env`, or `stdin`.
+
+The received value should be a tuple with the same number of elements as the `tuple` declaration, and each received element should be compatible with the corresponding `tuple` argument. Each tuple element is treated the same way as if it were a standalone input.
+
+### Outputs
+
+##### `val( value )`
+
+Declare a variable output. The argument can be any value, and it can reference any output variables defined in the process body (i.e. variables declared without the `def` keyword).
+
+##### `file( pattern )`
+
+<DeprecatedInVersion version="19.10.0">
+Use `path` instead.
+</DeprecatedInVersion>
+
+Declare a file output. It receives the output files from the task environment that match the given pattern.
+
+Multiple patterns can be specified using the colon separator (`:`). The union of all files matched by each pattern will be collected.
+
+##### `path( pattern, [options] )`
+
+Declare a file output. It receives the output files from the task environment that match the given pattern.
+
+Available options:
+
+##### `arity`
+
+<AddedInVersion version="23.09.0-edge" />
+
+Specify the number of expected files. Can be a number or a range. If a task produces an invalid number of files for this `path` output, it will fail.
+
+If the arity is `1`, a single file will be emitted. Otherwise, a list will always be emitted, even if only one file is produced.
+
+:::warning
+If the arity is not specified, a single file or list will be emitted based on whether a single file or multiple files are produced at runtime, resulting potentially in an output channel with a mixture of files and file collections.
+:::
+
+##### `followLinks`
+
+When `true`, target files are returned in place of any matching symlink (default: `true`).
+
+##### `glob`
+
+When `true`, the specified name is interpreted as a glob pattern (default: `true`).
+
+##### `hidden`
+
+When `true`, hidden files are included in the matching output files (default: `false`).
+
+##### `includeInputs`
+
+When `true` and the output path is a glob pattern, any input files matching the pattern are also included in the output (default: `false`).
+
+##### `maxDepth`
+
+Maximum number of directory levels to visit (default: no limit).
+
+##### `type`
+
+Type of paths returned, either `file`, `dir` or `any` (default: `any`, or `file` if the specified file name pattern contains a double star (`**`)).
+
+##### `env( name )`
+
+Declare an environment variable output. It receives the value of the environment variable (given by `name`) from the task environment.
+
+<AddedInVersion version="23.12.0-edge">
+Prior to this version, if the environment variable contained multiple lines of output, the output would be compressed to a single line by converting newlines to spaces.
+</AddedInVersion>
+
+##### `stdout`
+
+Declare a `stdout` output. It receives the standard output of the task script.
+
+##### `eval( command )`
+
+<AddedInVersion version="24.02.0-edge" />
+
+Declare an `eval` output. It receives the standard output of the given command, which is executed in the task environment after the task script.
+
+If the command fails, the task will also fail.
+
+##### `tuple( arg1, arg2, ... )`
+
+Declare a tuple output. Each argument should be an output declaration such as `val`, `path`, `env`, `stdin`, or `eval`. Each tuple element is treated the same way as if it were a standalone output.
+
+### Options
+
+The following options are available for all process outputs:
+
+##### `emit: <name>`
+
+Defines the name of the output channel.
+
+##### `optional: true | false`
+
+When `true`, the task will not fail if the specified output is missing (default: `false`).
+
+##### `topic: <name>`
+
+<AddedInVersion version="23.11.0-edge" />
+
+*Experimental: may change in a future release.*
+
+Defines the [channel topic][channel-topic>] to which the output will be sent.
+
+## Directives
+
+### accelerator
+
+<AddedInVersion version="19.09.0-edge" />
+
+The `accelerator` directive allows you to request hardware accelerators (e.g. GPUs) for the task execution. For example:
+
+```nextflow
+process hello {
+    accelerator 4, type: 'nvidia-tesla-k80'
+
+    script:
+    """
+    your_gpu_enabled --command --line
+    """
+}
+```
+
+The above examples will request 4 GPUs of type `nvidia-tesla-k80`.
+
+:::note
+This directive is only used by certain executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+:::note
+Additional options may be required to fully enable the use of accelerators. When using containers with GPUs, you must pass the GPU drivers through to the container. For Docker, this requires the option `--gpus all` in the docker run command. For Apptainer/Singularity, this requires the option `--nv`. The specific implementation details depend on the accelerator and container type being used.
+:::
+
+:::note
+The accelerator `type` option depends on the target execution platform. Refer to the platform-specific documentation for details on the available accelerators:
+
+- [Google Cloud](https://cloud.google.com/compute/docs/gpus/)
+- [Kubernetes](https://kubernetes.io/docs/tasks/manage-gpus/scheduling-gpus/#clusters-containing-different-types-of-gpus)
+
+The accelerator `type` option is not supported for AWS Batch. You can control the accelerator type indirectly through the allowed instance types in your Compute Environment. See the [AWS Batch FAQs](https://aws.amazon.com/batch/faqs/?#GPU_Scheduling_) for more information.
+:::
+
+### afterScript
+
+The `afterScript` directive allows you to execute a custom (Bash) snippet immediately *after* the main process has run. This may be useful to clean up your staging area.
+
+:::note
+When combined with the [container](#container) directive, the `afterScript` will be executed outside the specified container. In other words, the `afterScript` is always executed in the host environment.
+:::
+
+### arch
+
+The `arch` directive allows you to define the CPU architecture to build the software in use by the process' task. For example:
+
+```nextflow
+process blast {
+    spack 'blast-plus@2.13.0'
+    arch 'linux/x86_64', target: 'cascadelake'
+
+    script:
+    """
+    blastp -query input_sequence -num_threads ${task.cpus}
+    """
+}
+```
+
+The example above declares that the CPU generic architecture is `linux/x86_64` (X86 64 bit), and more specifically that the microarchitecture is `cascadelake` (a specific generation of Intel CPUs).
+
+This directive is currently used by the following Nextflow functionalities:
+
+- by the [spack](#spack) directive, to build microarchitecture-optimised applications;
+- by the [Wave][wave-page] service, to build containers for one of the generic families of CPU architectures (see below);
+- by the `spack` strategy within [Wave][wave-page], to optimize the container builds for specific CPU microarchitectures.
+
+Allowed values for the `arch` directive are as follows, grouped by equivalent family (choices available for the sake of compatibility):
+- X86 64 bit: `linux/x86_64`, `x86_64`, `linux/amd64`, `amd64`
+- ARM 64 bit: `linux/aarch64`, `aarch64`, `linux/arm64`, `arm64`, `linux/arm64/v8`
+- ARM 64 bit, older generation: `linux/arm64/v7`
+
+Examples of values for the architecture `target` option are `cascadelake`, `icelake`, `zen2` and `zen3`. See the [Spack documentation](https://spack.readthedocs.io/en/latest/basic_usage.html#support-for-specific-microarchitectures) for the full and up-to-date list of meaningful targets.
+
+### array
+
+<AddedInVersion version="24.04.0" />
+
+:::warning *Experimental: may change in a future release.*
+:::
+
+The `array` directive allows you to submit tasks as *job arrays* for executors that support it.
+
+A job array is a collection of jobs with the same resource requirements and the same script (parameterized by an index). Job arrays incur significantly less scheduling overhead compared to individual jobs, and as a result they are preferred by HPC schedulers where possible.
+
+The directive should be specified with a given array size, along with an executor that supports job arrays. For example:
+
+```nextflow
+process hello {
+    executor 'slurm'
+    array 100
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Nextflow currently supports job arrays for the following executors:
+
+- [AWS Batch][awsbatch-executor]
+- [Google Cloud Batch][google-batch-executor]
+- [LSF][lsf-executor]
+- [PBS][pbs-executor]
+- [PBS Pro][pbspro-executor]
+- [SGE][sge-executor]
+- [SLURM][slurm-executor]
+
+A process using job arrays will collect tasks and submit each batch as a job array when it is ready. Any "leftover" tasks will be submitted as a partial job array.
+
+Once a job array is submitted, each "child" task is executed as an independent job. Any tasks that fail (and can be retried) will be retried without interfering with the tasks that succeeded. Retried tasks are submitted individually rather than through a job array, in order to allow for the use of [dynamic task resources][dynamic-task-resources].
+
+The following directives must be uniform across all tasks in a process that uses job arrays, because these directives are specified once for the entire job array:
+
+- [accelerator](#accelerator)
+- [clusterOptions](#clusteroptions)
+- [cpus](#cpus)
+- [disk](#disk)
+- [machineType](#machinetype)
+- [memory](#memory)
+- [queue](#queue)
+- [resourceLabels](#resourcelabels)
+- [resourceLimits](#resourcelimits)
+- [time](#time)
+
+For cloud-based executors like AWS Batch, or when using Fusion with any executor, the following additional directives must be uniform:
+
+- [container](#container)
+- [containerOptions](#containeroptions)
+
+When using Wave, the following additional directives must be uniform:
+
+- [conda](#conda)
+
+### beforeScript
+
+The `beforeScript` directive allows you to execute a custom (Bash) snippet *before* the main process script is run. This may be useful to initialize the underlying cluster environment or for other custom initialization.
+
+For example:
+
+```nextflow
+process hello {
+    beforeScript 'source /cluster/bin/setup'
+
+    script:
+    """
+    echo 'hello'
+    """
+}
+```
+
+When the process is containerized (using the [container](#container) directive), the `beforeScript` will be executed in the container only if the executor is *container-native* (e.g. cloud batch executors, Kubernetes). Otherwise, the `beforeScript` will be executed outside the container.
+
+### cache
+
+The `cache` directive allows you to store the process results to a local cache. When the cache is enabled *and* the pipeline is launched with the [resume][getstarted-resume] option, any task executions that are already cached will be re-used. See [Cache and resume][cache-resume-page] for more information about how the cache works.
+
+The cache is enabled by default, but you can disable it for a specific process by setting the `cache` directive to `false`. For example:
+
+```nextflow
+process hello {
+    cache false
+    // ...
+}
+```
+
+The following options are available:
+
+######  `true`
+
+Enable caching. Input file metadata (name, size, last updated timestamp) are included in the cache keys (default).
+
+###### `false`
+
+Disable caching.
+
+######  `'deep'`
+
+Enable caching. Input file content is included in the cache keys.
+
+###### `'lenient'`
+
+Enable caching. Minimal input file metadata (name and size only) are included in the cache keys.
+
+This strategy provides a workaround for incorrect caching invalidation observed on shared file systems due to inconsistent file timestamps.
+
+### clusterOptions
+
+The `clusterOptions` directive allows the usage of any native configuration option accepted by your cluster submit command. You can use it to request non-standard resources or use settings that are specific to your cluster and not supported out of the box by Nextflow.
+
+The cluster options can be a string:
+
+```nextflow
+process hello {
+    clusterOptions '-x 1 -y 2'
+    // ...
+}
+```
+
+<ChangedInVersion version="24.04.0">
+Prior to this version, grid executors that require each option to be on a separate line in the job script would attempt to split multiple options using a variety of different conventions. Multiple options can now be specified more clearly using a string list as shown below.
+</ChangedInVersion>
+
+The cluster options can also be a string list:
+
+```nextflow
+process hello {
+    clusterOptions '-x 1', '-y 2', '--flag'
+    // ...
+}
+```
+
+Grid executors that require one option per line will write each option to a separate line, while grid executors that allow multiple options per line will write all options to a single line, the same as with a string. This form is useful to control how the options are split across lines when it is required by the scheduler.
+
+:::note
+This directive is only used by grid executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+:::warning
+While you can use the `clusterOptions` directive to specify options that are supported as process directives (`queue`, `memory`, `time`, etc), you should not use both at the same time, as it will cause undefined behavior. Most HPC schedulers will either fail or simply ignore one or the other.
+:::
+
+### conda
+
+The `conda` directive allows for the definition of the process dependencies using the [Conda](https://conda.io) package manager.
+
+Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. For example:
+
+```nextflow
+process hello {
+    conda 'bwa=0.7.15'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Multiple packages can be specified separating them with a blank space e.g. `bwa=0.7.15 fastqc=0.11.5`. The name of the channel from where a specific package needs to be downloaded can be specified using the usual Conda notation i.e. prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
+
+The `conda` directive also allows the specification of a Conda environment file path or the path of an existing environment directory. See [Conda][conda-page] for further details.
+
+### container
+
+The `container` directive allows you to execute the process script in a [Docker](http://docker.io) container.
+
+It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the *local* executor or the cluster nodes when the pipeline is deployed through a *grid* executor.
+
+For example:
+
+```nextflow
+process hello_docker {
+    container 'dockerbox:tag'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Simply replace in the above script `dockerbox:tag` with the name of the Docker image you want to use.
+
+:::tip
+Containers are a very useful way to execute your scripts in a reproducible self-contained environment or to run your pipeline in the cloud.
+:::
+
+:::note
+This directive is ignored for processes that are [executed natively][process-native].
+:::
+
+### containerOptions
+
+The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path:
+
+```nextflow
+process hello_docker {
+    container 'busybox:latest'
+    containerOptions '--volume /data/db:/db'
+
+    output:
+    path 'output.txt'
+
+    script:
+    """
+    your_command --data /db > output.txt
+    """
+}
+```
+
+:::warning
+This feature is not supported by the [Kubernetes][k8s-executor] executor.
+:::
+
+### cpus
+
+The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. For example:
+
+```nextflow
+process blast {
+    cpus 8
+
+    script:
+    """
+    blastp -query input_sequence -num_threads ${task.cpus}
+    """
+}
+```
+
+This directive is required for tasks that execute multi-process or multi-threaded commands/tools and it is meant to reserve enough CPUs when a pipeline task is executed through a cluster resource manager.
+
+See also: [penv](#penv), [memory](#memory), [time](#time), [queue](#queue), [maxForks](#maxforks)
+
+### debug
+
+By default the `stdout` produced by the commands executed in all processes is ignored. By setting the `debug` directive to `true`, you can forward the process `stdout` to the current top running process `stdout` file, showing it in the shell terminal.
+
+For example:
+
+```nextflow
+process hello {
+    debug true
+
+    script:
+    """
+    echo Hello
+    """
+}
+```
+
+```
+Hello
+```
+
+Without specifying `debug true`, you won't see the `Hello` string printed out when executing the above example.
+
+### disk
+
+The `disk` directive allows you to define how much local disk storage the process is allowed to use. For example:
+
+```nextflow
+process hello {
+    disk 2.GB
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following memory unit suffix can be used when specifying the disk value:
+
+| Unit | Description |
+| ---- | ----------- |
+| B    | Bytes       |
+| KB   | Kilobytes   |
+| MB   | Megabytes   |
+| GB   | Gigabytes   |
+| TB   | Terabytes   |
+
+See [memoryUnit][stdlib-types-memoryunit] for more information.
+
+:::note
+This directive is only used by certain executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+See also: [cpus](#cpus), [memory](#memory) [time](#time), [queue](#queue). and [dynamic task resources][dynamic-task-resources].
+
+### echo
+
+<DeprecatedInVersion version="22.04.0">
+Use `debug` instead
+</DeprecatedInVersion>
+
+### errorStrategy
+
+The `errorStrategy` directive allows you to define how the process manages an error condition. By default, when an error status is returned by the executed script (i.e. when it ends with a non-zero exit status), the process stops immediately, forcing the entire pipeline to terminate.
+
+The following error strategies are available:
+
+##### `terminate` (default)
+
+When a task fails, terminate the pipeline immediately and report an error. Pending and running jobs are killed.
+
+##### `finish`
+
+When a task fails, wait for submitted and running tasks to finish and then terminate the pipeline, reporting an error.
+
+##### `ignore`
+
+When a task fails, ignore it and continue the pipeline execution. If the `workflow.failOnIgnore` config option is set to `true`, the pipeline will report an error (i.e. return a non-zero exit code) upon completion. Otherwise, the pipeline will complete successfully.
+
+See the [Workflow][stdlib-namespaces-workflow] namespace for more information.
+
+##### `retry`
+
+When a task fails, retry it.
+
+#
+
+When setting the `errorStrategy` directive to `ignore` the process doesn't stop on an error condition, it just reports a message notifying you of the error event.
+
+For example:
+
+```nextflow
+process hello {
+    errorStrategy 'ignore'
+
+    // ...
+}
+```
+
+In this case, the workflow will complete successfully and return an exit status of 0. However, if you set `workflow.failOnIgnore = true` in your Nextflow configuration, the workflow will return a non-zero exit status and report the failed tasks as an error.
+
+The `retry` error strategy allows you to re-submit for execution a process returning an error condition. For example:
+
+```nextflow
+process hello {
+    errorStrategy 'retry'
+
+    // ...
+}
+```
+
+The number of times a failing process is re-executed is defined by the [maxRetries](#maxretries) and [maxErrors](#maxerrors) directives.
+
+:::tip
+More complex strategies depending on the task exit status or other parametric values can be defined using a dynamic `errorStrategy`. See [Dynamic directives][dynamic-directives] for details.
+:::
+
+See also: [maxErrors](#maxerrors), [maxRetries](#maxretries) and [dynamic task resources][dynamic-task-resources].
+
+### executor
+
+The `executor` defines the underlying system where processes are executed. By default a process uses the executor defined globally in the `nextflow.config` file.
+
+The `executor` directive allows you to configure what executor has to be used by the process, overriding the default configuration.
+
+The following executors are available:
+
+| Name                  | Executor                                                                                    |
+| --------------------- | ------------------------------------------------------------------------------------------- |
+| `awsbatch`            | [AWS Batch](https://aws.amazon.com/batch/) service                                          |
+| `azurebatch`          | [Azure Batch](https://azure.microsoft.com/en-us/services/batch/) service                    |
+| `condor`              | [HTCondor](https://research.cs.wisc.edu/htcondor/) job scheduler                            |
+| `k8s`                 | [Kubernetes](https://kubernetes.io/) cluster                                                |
+| `local`               | The computer where `Nextflow` is launched                                                   |
+| `lsf`                 | [Platform LSF](http://en.wikipedia.org/wiki/Platform_LSF) job scheduler                     |
+| `moab`                | [Moab](http://www.adaptivecomputing.com/moab-hpc-basic-edition/) job scheduler              |
+| `nqsii`               | [NQSII](https://www.rz.uni-kiel.de/en/our-portfolio/hiperf/nec-linux-cluster) job scheduler |
+| `oge`                 | Alias for the `sge` executor                                                                |
+| `pbs`                 | [PBS/Torque](http://en.wikipedia.org/wiki/Portable_Batch_System) job scheduler              |
+| `pbspro`              | [PBS Pro](https://www.pbsworks.com/) job scheduler                                          |
+| `sge`                 | Sun Grid Engine / [Open Grid Engine](http://gridscheduler.sourceforge.net/)                 |
+| `slurm`               | [SLURM](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) workload manager              |
+| `uge`                 | Alias for the `sge` executor                                                                |
+
+The following example shows how to set the process's executor:
+
+```nextflow
+process hello {
+  executor 'sge'
+
+  // ...
+}
+```
+
+:::note
+Each executor supports additional directives and `executor` configuration options. See [Executors][executor-page] for more information.
+:::
+
+### ext
+
+The `ext` is a special directive used as *namespace* for user custom process directives. This can be useful for advanced configuration options. For example:
+
+```nextflow
+process star {
+    container "biocontainers/star:${task.ext.version}"
+
+    input:
+    path genome
+    tuple val(sampleId), path(reads)
+
+    script:
+    """
+    STAR --genomeDir $genome --readFilesIn $reads ${task.ext.args ?: ''}
+    """
+}
+```
+
+In the above example, the process container version is controlled by `ext.version`, and the script supports additional command line arguments through `ext.args`.
+
+The `ext` directive can be set in the process definition:
+
+```nextflow
+process hello {
+    ext version: '2.5.3', args: '--alpha --beta'
+
+    // ...
+}
+```
+
+Or in the Nextflow configuration:
+
+```groovy
+process.ext.version = '2.5.3'
+process.ext.args = '--alpha --beta'
+```
+
+### fair
+
+<AddedInVersion version="22.12.0-edge" />
+
+The `fair` directive, when enabled, guarantees that process outputs will be emitted in the order in which they were received. For example:
+
+```nextflow
+process hello {
+    fair true
+
+    input:
+    val x
+
+    output:
+    tuple val(task.index), val(x)
+
+    script:
+    """
+    sleep \$((RANDOM % 3))
+    """
+}
+
+workflow {
+    channel.of('A','B','C','D') | hello | view
+}
+```
+
+The above example produces:
+
+```
+[1, A]
+[2, B]
+[3, C]
+[4, D]
+```
+
+### label
+
+The `label` directive allows the annotation of processes with mnemonic identifier of your choice. For example:
+
+```nextflow
+process hello {
+    label 'big_mem'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The same label can be applied to more than a process and multiple labels can be applied to the same process using the `label` directive more than one time.
+
+:::note
+A label must consist of alphanumeric characters or `_`, must start with an alphabetic character and must end with an alphanumeric character.
+:::
+
+Labels are useful to organize workflow processes in separate groups which can be referenced in the configuration file to select and configure a subset of processes having similar computing requirements. See [Process selectors][config-process-selectors] for more information.
+
+See also: [resourceLabels](#resourcelabels)
+
+### machineType
+
+<AddedInVersion version="19.07.0" />
+
+The `machineType` can be used to specify a predefined Google Compute Platform [machine type](https://cloud.google.com/compute/docs/machine-types) when running using the [Google Batch][google-batch-executor], or when using the autopools feature of the [Azure Batch executor][azurebatch-executor].
+
+This directive is optional and if specified overrides the cpus and memory directives:
+
+```nextflow
+process hello {
+    machineType 'n1-highmem-8'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+See also: [cpus](#cpus) and [memory](#memory).
+
+### maxErrors
+
+The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled, you can set it as shown in the example below:
+
+```nextflow
+process hello {
+    errorStrategy 'retry'
+    maxErrors 5
+
+    script:
+    """
+    echo 'do this as that .. '
+    """
+}
+```
+:::note
+This setting considers the **total** errors accumulated for a given process, across all instances. If you want to control the number of times a process **instance** (aka task) can fail, use `maxRetries`.
+:::
+
+See also: [errorStrategy](#errorstrategy) and [maxRetries](#maxretries).
+
+### maxForks
+
+The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1.
+
+If you want to execute a process in a sequential manner, set this directive to one. For example:
+
+```nextflow
+process hello {
+    maxForks 1
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+### maxRetries
+
+The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the `retry` error strategy. By default only one retry is allowed, you can increase this value as shown below:
+
+```nextflow
+process hello {
+    errorStrategy 'retry'
+    maxRetries 3
+
+    script:
+    """
+    echo 'do this as that .. '
+    """
+}
+```
+
+:::note
+There is a subtle but important difference between `maxRetries` and the `maxErrors` directive. The latter defines the total number of errors that are allowed during the process execution (the same process can launch different execution instances), while the `maxRetries` defines the maximum number of times the same process execution can be retried in case of an error.
+:::
+
+See also: [errorStrategy](#errorstrategy) and [maxErrors](#maxerrors).
+
+### maxSubmitAwait
+
+The `maxSubmitAwait` directive allows you to specify how long a task can remain in submission queue without being executed.
+Elapsed this time the task execution will fail.
+
+When used along with `retry` error strategy, it can be useful to re-schedule the task to a difference queue or
+resource requirement. For example:
+
+```nextflow
+process hello {
+  errorStrategy 'retry'
+  maxSubmitAwait 10.m
+  maxRetries 3
+  queue "${task.submitAttempt==1 ? 'spot-compute' : 'on-demand-compute'}"
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+In the above example the task is submitted to the `spot-compute` on the first attempt (`task.submitAttempt==1`). If the
+task execution does not start in the 10 minutes, a failure is reported and a new submission is attempted using the
+queue named `on-demand-compute`.
+
+### memory
+
+The `memory` directive allows you to define how much memory the process is allowed to use. For example:
+
+```nextflow
+process hello {
+    memory 2.GB
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following memory unit suffix can be used when specifying the memory value:
+
+| Unit | Description |
+| ---- | ----------- |
+| B    | Bytes       |
+| KB   | Kilobytes   |
+| MB   | Megabytes   |
+| GB   | Gigabytes   |
+| TB   | Terabytes   |
+
+See [memoryUnit][stdlib-types-memoryunit] for more information.
+
+See also: [cpus](#cpus), [time](#time), [queue](#queue) and [dynamic task resources][dynamic-task-resources].
+
+### module
+
+[Environment Modules](http://modules.sourceforge.net/) is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool.
+
+If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline.
+
+In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. For example:
+
+```nextflow
+process blast {
+    module 'ncbi-blast/2.2.27'
+
+    script:
+    """
+    blastp -query <etc..>
+    """
+}
+```
+
+You can repeat the `module` directive for each module you need to load. Alternatively multiple modules can be specified in a single `module` directive by separating all the module names by using a `:` (colon) character as shown below:
+
+```nextflow
+process blast {
+    module 'ncbi-blast/2.2.27:t_coffee/10.0:clustalw/2.1'
+
+    script:
+    """
+    blastp -query <etc..>
+    """
+}
+```
+
+### penv
+
+The `penv` directive allows you to define the parallel environment to be used when submitting a parallel task to the [SGE][sge-executor] resource manager. For example:
+
+```nextflow
+process blast {
+    cpus 4
+    penv 'smp'
+    executor 'sge'
+
+    script:
+    """
+    blastp -query input_sequence -num_threads ${task.cpus}
+    """
+}
+```
+
+This configuration depends on the parallel environment provided by your grid engine installation. Refer to your cluster documentation or contact your admin to learn more about this.
+
+See also: [cpus](#cpus), [memory](#memory), [time](#time)
+
+### pod
+
+The `pod` directive allows the definition of pod specific settings, such as environment variables, secrets, and config maps, when using the [Kubernetes][k8s-executor] executor.
+
+For example:
+
+```nextflow
+process echo {
+    pod env: 'MESSAGE', value: 'hello world'
+
+    script:
+    """
+    echo $MESSAGE
+    """
+}
+```
+
+The above snippet defines an environment variable named `MESSAGE` whose value is `'hello world'`.
+
+When defined in the Nextflow configuration file, a pod setting can be defined as a map:
+
+```groovy
+process {
+    pod = [env: 'MESSAGE', value: 'hello world']
+}
+```
+
+Or as a list of maps:
+
+```groovy
+process {
+    pod = [
+        [env: 'MESSAGE', value: 'hello world'],
+        [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
+    ]
+}
+```
+
+The following options are available:
+
+##### `affinity: <config>`
+
+<AddedInVersion version="22.01.0-edge" />
+
+Specifies the pod [affinity](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#affinity-and-anti-affinity) with the given configuration.
+
+#####  `annotation: '<name>', value: '<value>'`
+
+*Can be specified multiple times*
+
+Defines a pod [annotation](https://kubernetes.io/docs/concepts/overview/working-with-objects/annotations/) with the given name and value.
+
+#####  `automountServiceAccountToken: true | false`
+
+<AddedInVersion version="22.01.0-edge" />
+
+Specifies whether to [automount service account token](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/#opt-out-of-api-credential-automounting) into the pod (default: `true`).
+
+#####  `config: '<configMap>/<key>', mountPath: '</absolute/path>'`
+
+*Can be specified multiple times*
+
+Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `ConfigMap` are exposed in that path.
+
+##### `csi: '<config>', mountPath: '</absolute/path>'`
+
+<AddedInVersion version="22.11.0-edge" />
+
+*Can be specified multiple times*
+
+Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) with the given configuration to the given path.
+
+##### `emptyDir: <config>, mountPath: '</absolute/path>'`
+
+<AddedInVersion version="22.11.0-edge" />
+
+*Can be specified multiple times*
+
+Mounts an [emptyDir](https://kubernetes.io/docs/concepts/storage/volumes/#emptydir) with the given configuration to the given path.
+
+##### `env: '<name>', config: '<configMap>/<key>'`
+
+*Can be specified multiple times*
+
+Defines an environment variable whose value is defined by the given [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) and key.
+
+##### `env: '<name>', fieldPath: '<fieldPath>'`
+
+<AddedInVersion version="21.09.1-edge" />
+
+*Can be specified multiple times*
+
+Defines an environment variable whose value is defined by the given [field path](https://kubernetes.io/docs/tasks/inject-data-application/environment-variable-expose-pod-information/#use-pod-fields-as-values-for-environment-variables) value.
+
+For example, the following pod option:
+
+```groovy
+pod = [env: 'MY_NODE_NAME', fieldPath: 'spec.nodeName']
+```
+
+Maps to the following pod spec:
+
+```yaml
+env:
+  - name: MY_NODE_NAME
+    valueFrom:
+      fieldRef:
+        fieldPath: spec.nodeName
+```
+
+##### `env: '<name>', secret: '<secret>/<key>'`
+
+*Can be specified multiple times*
+
+Defines an environment variable whose value is defined by the given [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) and key.
+
+##### `env: '<name>', value: '<value>'`
+
+*Can be specified multiple times*
+
+Defines an environment variable with the given name and value.
+
+##### `hostPath: '/host/absolute/path', mountPath: '</pod/absolute/path>'`
+
+<AddedInVersion version="23.10.0" />
+
+*Can be specified multiple times*
+
+Allows creating [hostPath](https://kubernetes.io/docs/concepts/storage/volumes/#hostpath) volume and access it with the specified `mountPath` in the pod.
+
+##### `imagePullPolicy: 'IfNotPresent' | 'Always' | 'Never'`
+
+Specifies the [image pull policy](https://kubernetes.io/docs/concepts/containers/images/#image-pull-policy) used by the pod to pull the container image.
+
+##### `imagePullSecret: '<name>'`
+
+Specifies the [image pull secret](https://kubernetes.io/docs/concepts/containers/images/#specifying-imagepullsecrets-on-a-pod) used to access a private container image registry.
+
+##### `label: '<name>', value: '<value>'`
+
+*Can be specified multiple times*
+
+Defines a pod [label](https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/) with the given name and value.
+
+##### `nodeSelector: <config>`
+
+Specifies the [node selector](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#nodeselector) with the given configuration.
+
+The configuration can be a map or a string:
+
+```groovy
+// map
+pod = [nodeSelector: [disktype: 'ssd', cpu: 'intel']]
+
+// string
+pod = [nodeSelector: 'disktype=ssd,cpu=intel']
+```
+
+##### `priorityClassName: '<name>'`
+
+<AddedInVersion version="22.01.0-edge" />
+
+Specifies the [priority class name](https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/) for pods.
+
+##### `privileged: true | false`
+
+<AddedInVersion version="22.05.0-edge" />
+
+Specifies whether the pod should run as a *privileged* container (default: `false`).
+
+##### `runAsUser: '<uid>'`
+
+Specifies the user ID with which to run the container. Shortcut for the `securityContext` option.
+
+##### `schedulerName: '<name>'`
+
+Specifies which [scheduler](https://kubernetes.io/docs/tasks/extend-kubernetes/configure-multiple-schedulers/#specify-schedulers-for-pods) is used to schedule the container.
+
+##### `secret: '<secret>/<key>', mountPath: '</absolute/path>'`
+
+*Can be specified multiple times*
+
+Mounts a [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `Secret` are exposed in that path.
+
+##### `securityContext: <config>`
+
+Specifies the pod [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) with the given configuration.
+
+##### `toleration: <config>`
+
+<AddedInVersion version="22.04.0" />
+
+*Can be specified multiple times*
+
+Specifies the pod [toleration](https://kubernetes.io/docs/concepts/scheduling-eviction/taint-and-toleration/) with the given configuration.
+
+The configuration should be a map corresponding to a single toleration rule. For example, the following pod options:
+
+```groovy
+pod = [
+  [toleration: [key: 'key1', operator: 'Equal', value: 'value1', effect: 'NoSchedule']],
+  [toleration: [key: 'key1', operator: 'Exists', effect: 'NoSchedule']],
+]
+```
+
+Maps to the following pod spec:
+
+```yaml
+tolerations:
+  - key: "key1"
+    operator: "Equal"
+    value: "value1"
+    effect: "NoSchedule"
+  - key: "key1"
+    operator: "Exists"
+    effect: "NoSchedule"
+```
+
+##### `ttlSecondsAfterFinished`
+
+<AddedInVersion version="24.02.0-edge" />
+
+Specifies the [TTL mechanism](https://kubernetes.io/docs/concepts/workloads/controllers/job/#ttl-mechanism-for-finished-jobs) for finished jobs in seconds. Applies to both successful and failed jobs.
+
+##### `volumeClaim: '<name>', mountPath: '</absolute/path>' [, subPath: '<path>', readOnly: true | false]`
+
+*Can be specified multiple times*
+
+Mounts a [Persistent volume claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/) with the given name to the given path.
+
+The `subPath` option can be used to mount a sub-directory of the volume instead of its root.
+
+The `readOnly` option can be used to mount the volume as read-only (default: `false`)
+
+### publishDir
+
+The `publishDir` directive allows you to publish the process output files to a specified folder. For example:
+
+```nextflow
+process hello {
+    publishDir '/data/chunks'
+
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf 'Hola' | split -b 1 - chunk_
+    """
+}
+```
+
+The above example splits the string `Hola` into file chunks of a single byte. When complete the `chunk_*` output files are published into the `/data/chunks` folder.
+
+:::note
+Only files that match the declaration in the `output` block are published, not all the outputs of the process.
+:::
+
+:::tip
+The `publishDir` directive can be specified more than once in order to publish output files to different target directories based on different rules.
+:::
+
+By default files are published to the target folder creating a *symbolic link* for each process output that links the file produced into the process working directory. This behavior can be modified using the `mode` option, for example:
+
+```nextflow
+process hello {
+    publishDir '/data/chunks', mode: 'copy', overwrite: false
+
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf 'Hola' | split -b 1 - chunk_
+    """
+}
+```
+
+:::warning
+Files are copied into the specified directory in an *asynchronous* manner, so they may not be immediately available in the publish directory at the end of the process execution. For this reason, downstream processes should not try to access output files through the publish directory, but through the outputs of the originating process.
+:::
+
+Available options:
+
+##### `contentType`
+
+<AddedInVersion version="22.10.0" />
+
+*Experimental: currently only supported for S3.*
+
+Allow specifying the media content type of the published file a.k.a. [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_Types). If set to `true`, the content type is inferred from the file extension (default: `false`).
+
+##### `enabled`
+
+Enable or disable the publish rule depending on the boolean value specified (default: `true`).
+
+##### `failOnError`
+
+<AddedInVersion version="24.03.0-edge">
+The default value was changed from `false` to `true`
+</AddedInVersion>
+
+When `true` abort the execution if some file can't be published to the specified target directory or bucket for any cause (default: `true`)
+
+##### `mode`
+
+The file publishing method. Can be one of the following values:
+
+- `'copy'`: Copies the output files into the publish directory.
+- `'copyNoFollow'`: Copies the output files into the publish directory without following symlinks ie. copies the links themselves.
+- `'link'`: Creates a hard link in the publish directory for each output file.
+- `'move'`: Moves the output files into the publish directory. **Note**: this is only supposed to be used for a *terminal* process i.e. a process whose output is not consumed by any other downstream process.
+- `'rellink'`: Creates a relative symbolic link in the publish directory for each output file.
+- `'symlink'`: Creates an absolute symbolic link in the publish directory for each output file (default).
+
+##### `overwrite`
+
+When `true` any existing file in the specified folder will be overridden (default: `true` during normal pipeline execution and `false` when pipeline execution is `resumed`).
+
+##### `path`
+
+Specifies the directory where files need to be published. **Note**: the syntax `publishDir '/some/dir'` is a shortcut for `publishDir path: '/some/dir'`.
+
+##### `pattern`
+
+Specifies a [glob][glob] file pattern that selects which files to publish from the overall set of output files.
+
+##### `saveAs`
+
+A closure which, given the name of the file being published, returns the actual file name or a full path where the file is required to be stored. This can be used to rename or change the destination directory of the published files dynamically by using a custom strategy. Return the value `null` from the closure to *not* publish a file. This is useful when the process has multiple output files, but you want to publish only some of them.
+
+##### `storageClass`
+
+<AddedInVersion version="22.12.0-edge" />
+
+*Experimental: currently only supported for S3.*
+
+Allow specifying the storage class to be used for the published file.
+
+##### `tags`
+
+<AddedInVersion version="21.12.0-edge" />
+
+*Experimental: currently only supported for S3.*
+
+Allow the association of arbitrary tags with the published file e.g. `tags: [MESSAGE: 'Hello world']`.
+
+### queue
+
+The `queue` directive allows you to set the `queue` where jobs are scheduled when using a grid based executor in your pipeline. For example:
+
+```nextflow
+process hello {
+    queue 'long'
+    executor 'sge'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+:::tip
+Some grid executors support multiple queue names as a comma-separated list:
+
+```nextflow
+queue 'short,long,cn-el6'
+```
+
+However, this does not generally apply to other executors such as AWS Batch, Azure Batch, Google Batch.
+:::
+
+:::note
+This directive is only used by certain executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+### resourceLabels
+
+<AddedInVersion version="22.09.1-edge" />
+
+The `resourceLabels` directive allows you to specify custom name-value pairs that Nextflow applies to the computing resource used to carry out the process execution. Resource labels can be specified using the syntax shown below:
+
+```nextflow
+process hello {
+    resourceLabels region: 'some-region', user: 'some-username'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The limits and the syntax of the corresponding cloud provider should be taken into consideration when using resource labels.
+
+Resource labels are currently supported by the following executors:
+
+- [AWS Batch][awsbatch-executor]
+- [Azure Batch][azurebatch-executor]
+- [Google Cloud Batch][google-batch-executor]
+- [Kubernetes][k8s-executor]
+
+<AddedInVersion version="23.09.0-edge">
+Resource labels are supported for Azure Batch when using automatic pool creation.
+
+Resource labels in Azure are added to pools, rather than jobs, in order to facilitate cost analysis. A new pool will be created for each new set of resource labels, therefore it is recommended to also set `azure.batch.deletePoolsOnCompletion = true` when using process-specific resource labels.
+</AddedInVersion>
+
+See also: [label](#label)
+
+### resourcelimits
+
+<AddedInVersion version="24.04.0" />
+
+The `resourceLimits` directive allows you to specify environment-specific limits for task resource requests. Resource limits can be specified in a process:
+
+```nextflow
+process hello {
+    resourceLimits cpus: 24, memory: 768.GB, time: 72.h
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Or in the Nextflow configuration:
+
+```nextflow
+process {
+    resourceLimits = [ cpus: 24, memory: 768.GB, time: 72.h ]
+}
+```
+
+Resource limits can be defined for the following directives:
+
+- [cpus](#cpus)
+- [disk](#disk)
+- [memory](#memory)
+- [time](#time)
+
+Resource limits are a useful way to specify environment-specific limits alongside tasks with [dynamic task resources][dynamic-task-resources]. Normally, if a task requests more resources than can be provisioned (e.g. a task requests 32 cores but the largest node in the cluster has 24), the task will either fail or cause the pipeline to hang forever as it will never be scheduled. If the `resourceLimits` directive is defined with these limits, the task resources will be automatically reduced to comply with these limits before the job is submitted.
+
+### scratch
+
+The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node.
+
+This is useful when your pipeline is launched by using a grid executor, because it allows you to decrease the NFS overhead by running the pipeline processes in a temporary directory in the local disk of the actual execution node. Only the files declared as output in the process definition will be copied in the pipeline working area.
+
+In its basic form simply specify `true` at the directive value, as shown below:
+
+```nextflow
+process hello {
+    scratch true
+
+    output:
+    path 'data_out'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+By doing this, it tries to execute the script in the directory defined by the variable `$TMPDIR` in the execution node. If this variable does not exist, it will create a new temporary directory by using the Linux command `mktemp`.
+
+Nextflow creates a subdirectory within the scratch directory for each task and automatically deletes it once the task completes.
+
+:::note
+Cloud-based executors use `scratch = true` by default, since the work directory resides in object storage.
+:::
+
+The following values are supported:
+
+##### `false`
+
+Do not use a scratch directory.
+
+##### `true`
+
+Create a scratch directory in the directory defined by the `$TMPDIR` environment variable, or `$(mktemp /tmp)` if `$TMPDIR` is not set.
+
+##### `'$YOUR_VAR'`
+
+Create a scratch directory in the directory defined by the given environment variable, or `$(mktemp /tmp)` if that variable is not set. The value must use single quotes, otherwise the environment variable will be evaluated in the pipeline script context.
+
+##### `'/my/tmp/path'`
+
+Create a scratch directory in the specified directory.
+
+##### `'ram-disk'`
+
+Create a scratch directory in the RAM disk `/dev/shm/`.
+
+### secret
+
+The `secret` directive allows a process to access secrets.
+
+Secrets can be added to a process as follows:
+
+```nextflow
+process hello_secret {
+    secret 'MY_ACCESS_KEY'
+    secret 'MY_SECRET_KEY'
+
+    script:
+    """
+    your_command --access \$MY_ACCESS_KEY --secret \$MY_SECRET_KEY
+    """
+}
+```
+
+See [Secrets][secrets-page] for more information.
+
+:::warning
+Secrets are made available as environment variables in the process script. To prevent evaluation in the Nextflow script context, escape variable names with a backslash (e.g., `\$MY_ACCESS_KEY`) as shown above.
+:::
+
+:::note
+Secrets can only be used with the local or grid executors (e.g., Slurm or Grid Engine). Secrets can be used with the AWS Batch executor when launched from Seqera Platform.
+:::
+
+### shell
+
+The `shell` directive allows you to define a custom shell command for process scripts. By default, script blocks are executed with `/bin/bash -ue`.
+
+```nextflow
+process hello {
+    shell '/bin/bash', '-euo', 'pipefail'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The same directive could be specified in your Nextflow configuration as follows:
+
+```groovy
+process.shell = ['/bin/bash', '-euo', 'pipefail']
+```
+
+### spack
+
+The `spack` directive allows for the definition of the process dependencies using the [Spack](https://spack.io) package manager.
+
+Nextflow automatically sets up an environment for the given package names listed by in the `spack` directive. For example:
+
+```nextflow
+process hello {
+    spack 'bwa@0.7.15'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Multiple packages can be specified separating them with a blank space, e.g. `bwa@0.7.15 fastqc@0.11.5`.
+
+The `spack` directive also allows the specification of a Spack environment file path or the path of an existing environment directory. See [Spack][spack-page] for further details.
+
+### stageInMode
+
+The `stageInMode` directive defines how input files are staged into the process work directory. The following values are allowed:
+
+##### `'copy'`
+
+Input files are staged in the process work directory by creating a copy.
+
+##### `'link'`
+
+Input files are staged in the process work directory by creating a hard link for each of them.
+
+##### `'rellink'`
+
+Input files are staged in the process work directory by creating a symbolic link with a relative path for each of them.
+
+##### `'symlink'`
+
+Input files are staged in the process work directory by creating a symbolic link with an absolute path for each of them (default).
+
+### stageOutMode
+
+The `stageOutMode` directive defines how output files are staged out from the scratch directory to the process work directory. The following values are allowed:
+
+##### `'copy'`
+
+Output files are copied from the scratch directory to the work directory.
+
+##### `'fcp'`
+
+<AddedInVersion version="23.02.0-edge" />
+
+Output files are copied from the scratch directory to the work directory by using the [fcp](https://github.com/Svetlitski/fcp) utility (note: it must be available in your cluster computing nodes).
+
+##### `'move'`
+
+Output files are moved from the scratch directory to the work directory.
+
+##### `'rclone'`
+
+<AddedInVersion version="23.01.0-edge" />
+
+Output files are copied from the scratch directory to the work directory by using the [rclone](https://rclone.org) utility (note: it must be available in your cluster computing nodes).
+
+##### `'rsync'`
+
+Output files are copied from the scratch directory to the work directory by using the `rsync` utility.
+
+See also: [scratch](#scratch).
+
+### storeDir
+
+The `storeDir` directive allows you to define a directory that is used as a *permanent* cache for your process results.
+
+In more detail, it affects the process execution in two main ways:
+
+1. The process is executed only if the files declared in the `output` block do not exist in the directory specified by the `storeDir` directive. When the files exist the process execution is skipped and these files are used as the actual process result.
+2. Whenever a process is successfully completed the files listed in the `output` block are moved into the directory specified by the `storeDir` directive.
+
+The following example shows how to use the `storeDir` directive to create a directory containing a BLAST database for each species specified by an input parameter:
+
+```nextflow
+process make_blast_db {
+    storeDir '/db/genomes'
+
+    input:
+    path species
+
+    output:
+    path "${dbName}.*"
+
+    script:
+    dbName = species.baseName
+    """
+    makeblastdb -dbtype nucl -in ${species} -out ${dbName}
+    """
+}
+```
+
+:::warning
+If a process uses `storeDir` and all of its outputs are optional, the process will always be skipped, even if the store directory is empty. This issue can be avoided by specifying at least one required file output.
+:::
+
+:::warning
+The `storeDir` directive should not be used to publish workflow outputs. Use the [publishDir](#publishdir) directive or the [workflow output definition][workflow-output-def] instead.
+:::
+
+### tag
+
+The `tag` directive allows you to associate each process execution with a custom label, so that it will be easier to identify them in the log file or in the trace execution report. For example:
+
+```nextflow
+process hello {
+    tag "$code"
+
+    input:
+    val code
+
+    script:
+    """
+    echo $code
+    """
+}
+
+workflow {
+    channel.of('alpha', 'gamma', 'omega') | hello
+}
+```
+
+The above snippet will print a log similar to the following one, where process names contain the tag value:
+
+```
+[6e/28919b] Submitted process > hello (alpha)
+[d2/1c6175] Submitted process > hello (gamma)
+[1c/3ef220] Submitted process > hello (omega)
+```
+
+See also: [Trace file][trace-report]
+
+### time
+
+The `time` directive allows you to define how long a process is allowed to run. For example:
+
+```nextflow
+process hello {
+    time 1.h
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following time unit suffixes can be used when specifying the duration value:
+
+| Unit | Description  |
+| ---- | ------------ |
+| `ms` | Milliseconds |
+| `s`  | Seconds      |
+| `m`  | Minutes      |
+| `h`  | Hours        |
+| `d`  | Days         |
+
+See [Duration][stdlib-types-duration] for more information.
+
+:::note
+This directive is only used by certain executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+See also: [cpus](#cpus), [memory](#memory), [queue](#queue) and [dynamic task resources][dynamic-task-resources].
+
+[awsbatch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#aws-batch
+[azurebatch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#azure-batch
+[cache-resume-page]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx
+[channel-topic]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#topic
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[conda-page]: /nextflow_docs/nextflow_repo/docs/conda.mdx
+[dynamic-directives]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-directives
+[dynamic-task-resources]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-task-resources
+[executor-page]: /nextflow_docs/nextflow_repo/docs/executor.mdx
+[google-batch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#google-cloud-batch
+[k8s-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#kubernetes
+[lsf-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#lsf
+[pbs-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#pbstorque
+[pbspro-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#pbs-pro
+[process-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[process-native]: /nextflow_docs/nextflow_repo/docs/process.mdx#native-execution
+[getstarted-resume]: /nextflow_docs/nextflow_repo/docs/your-first-script.mdx#modify-and-resume
+[secrets-page]: /nextflow_docs/nextflow_repo/docs/secrets.mdx
+[sge-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#sge
+[slurm-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#slurm
+[spack-page]: /nextflow_docs/nextflow_repo/docs/spack.mdx
+[stdlib-namespaces-workflow]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-namespaces.mdx#workflow
+[stdlib-types-duration]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#duration
+[stdlib-types-memoryunit]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#memoryunit
+[trace-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
diff --git a/docs/reference/stdlib-groovy.md b/docs/reference/stdlib-groovy.mdx
similarity index 72%
rename from docs/reference/stdlib-groovy.md
rename to docs/reference/stdlib-groovy.mdx
index add202a445..c41a0ef48e 100644
--- a/docs/reference/stdlib-groovy.md
+++ b/docs/reference/stdlib-groovy.mdx
@@ -1,4 +1,7 @@
-(stdlib-groovy)=
+---
+title: Groovy and Java classes
+description: Groovy and Java classes available to Nextflow at runtime
+---
 
 # Groovy and Java classes
 
@@ -20,6 +23,8 @@ def vals = [1, 2, 3]
 println groovy.json.JsonOutput.toJson(vals)
 ```
 
-:::{note}
-The set of classes in Nextflow's runtime classpath can change between different Nextflow versions. As a best practice, any code that uses classes outside the Nextflow standard library should either be refactored to only use the Nextflow standard library or be refactored as a {ref}`plugin <dev-plugins-page>` with explicit dependencies.
+:::note
+The set of classes in Nextflow's runtime classpath can change between different Nextflow versions. As a best practice, any code that uses classes outside the Nextflow standard library should either be refactored to only use the Nextflow standard library or be refactored as a [plugin][plugins-dev-page] with explicit dependencies.
 :::
+
+[plugins-dev-page]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx
\ No newline at end of file
diff --git a/docs/reference/stdlib-namespaces.md b/docs/reference/stdlib-namespaces.md
deleted file mode 100644
index 691549285c..0000000000
--- a/docs/reference/stdlib-namespaces.md
+++ /dev/null
@@ -1,286 +0,0 @@
-(stdlib-namespaces)=
-
-# Namespaces
-
-This page lists all of the available namespaces in the Nextflow standard library.
-
-(stdlib-namespaces-global)=
-
-## Global namespace
-
-The global namespace contains globally available constants and functions.
-
-**Constants**
-
-`baseDir: Path`
-: :::{deprecated} 20.04.0
-  :::
-: Alias of `workflow.projectDir`.
-
-`launchDir: Path`
-: Alias of `workflow.launchDir`.
-
-`moduleDir: Path`
-: Directory where a module script is located (equivalent to `projectDir` if used in the main script).
-
-`params`
-: Map of workflow parameters specified in the config file or as command line options.
-
-`projectDir: Path`
-: Alias of `workflow.projectDir`.
-
-`secrets: Map<String,String>`
-: :::{versionadded} 24.02.0-edge
-  :::
-: Map of pipeline secrets. See {ref}`secrets-page` for more information.
-
-`workDir: Path`
-: Alias of `workflow.workDir`.
-
-**Functions**
-
-`branchCriteria( criteria: Closure ) -> Closure`
-: Create a branch criteria to use with the {ref}`operator-branch` operator.
-
-`env( name: String ) -> String`
-: :::{versionadded} 24.11.0-edge
-  :::
-: Get the value of the environment variable with the specified name in the Nextflow launch environment.
-
-`error( message: String = null )`
-: Throw a script runtime error with an optional error message.
-
-`exit( exitCode: int = 0, message: String = null )`
-: :::{deprecated} 22.06.0-edge
-  Use `error()` instead
-  :::
-: Stop the pipeline execution and return an exit code and optional error message.
-
-`file( filePattern: String, [options] ) -> Path`
-: Get a file from a file name or glob pattern.
-
-: The following options are available:
-
-  `checkIfExists: boolean`
-  : When `true`, throws an exception if the specified path does not exist in the file system (default: `false`)
-
-  `followLinks: boolean`
-  : When `true`, follows symbolic links when traversing a directory tree, otherwise treats them as files (default: `true`)
-
-  `glob: boolean`
-  : When `true`, interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
-
-  `hidden: boolean`
-  : When `true`, includes hidden files in the resulting paths (default: `false`)
-
-  `maxDepth: int`
-  : Maximum number of directory levels to visit (default: *no limit*)
-
-  `type: String`
-  : Type of paths returned, can be `'file'`, `'dir'` or `'any'` (default: `'file'`)
-
-: :::{note}
-  This function returns a collection if the glob pattern yields zero or multiple files. Use `files()` to get a collection of files.
-  :::
-
-`files( filePattern: String, [options] ) -> List<Path>`
-: Get a collection of files from a file name or glob pattern. Supports the same options as `file()`.
-: See also: {ref}`channel.fromPath <channel-path>`.
-
-`groupKey( key, size: int ) -> GroupKey`
-: Create a grouping key to use with the {ref}`operator-grouptuple` operator.
-
-`multiMapCriteria( criteria: Closure ) -> Closure`
-: Create a multi-map criteria to use with the {ref}`operator-multiMap` operator.
-
-`print( value )`
-: Print a value to standard output.
-
-`printf( format: String, values... )`
-: Print a formatted string with the given values to standard output.
-
-`println( value )`
-: Print a value to standard output with a newline.
-
-`sendMail( [options] )`
-: Send an email. See {ref}`mail-page` for more information.
-
-`sleep( milliseconds: long )`
-: Sleep for the given number of milliseconds.
-
-`tuple( args... ) -> Tuple`
-: Create a tuple object from the given arguments.
-
-(stdlib-namespaces-channel)=
-
-## `channel`
-
-The `channel` namespace contains the built-in channel factories. See {ref}`channel-factory` for details.
-
-(stdlib-namespaces-nextflow)=
-
-## `log`
-
-The `log` namepsace contains functions for logging messages to the console.
-
-`error( message: String )`
-: Log an error message to the console.
-: This function does not terminate the pipeline -- use the global `error()` function instead.
-
-`info( message: String )`
-: Log an info message to the console.
-
-`warn( message: String )`
-: Log a warning message to the console.
-
-## `nextflow`
-
-The `nextflow` namespace contains information about the current Nextflow runtime.
-
-`build: int`
-: Nextflow runtime build number.
-
-`timestamp: String`
-: Nextflow runtime compile timestamp.
-
-`version: VersionNumber`
-: Nextflow runtime version number. See {ref}`VersionNumber <stdlib-types-versionnumber>` for more information.
-
-(stdlib-namespaces-workflow)=
-
-## `workflow`
-
-The `workflow` namespace contains information about the current workflow run.
-
-**Properties**
-
-`commandLine: String`
-: Command line as entered by the user to launch the workflow execution.
-
-`commitId: String`
-: Git commit ID of the executed workflow repository.
-: When providing a Git tag, branch name, or commit hash using the `-r` CLI option, the associated `workflow.commitId` is also populated.
-
-`complete: OffsetDateTime`
-: *Available only in the `workflow.onComplete` handler*
-: Timestamp of workflow when execution is completed.
-
-`configFiles: List<Path>`
-: Configuration files used for the workflow execution.
-
-`container: String | Map<String,String>`
-: Docker image used to run workflow tasks, or a map of process names to process containers when multiple images are used.
-
-`containerEngine: String`
-: Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.
-
-`duration: Duration`
-: *Available only in the `workflow.onComplete` handler*
-: Time elapsed to complete workflow execution.
-
-`errorMessage: String`
-: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
-: Error message of the task that caused the workflow execution to fail.
-
-`errorReport: String`
-: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
-: Detailed error of the task that caused the workflow execution to fail.
-
-`exitStatus: int`
-: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
-: Exit status of the task that caused the workflow execution to fail.
-
-`failOnIgnore: boolean`
-: :::{versionadded} 24.05.0-edge
-  :::
-: Whether the `workflow.failOnIgnore` config option was enabled.
-: See also: {ref}`process-error-strategy`
-
-`fusion`
-: Namespace containing information about the current Fusion runtime. The following properties are available:
-
-: `enabled: boolean`
-  : Whether Fusion is enabled.
-
-: `version: String`
-  : The Fusion version being used.
-
-`homeDir: Path`
-: User system home directory.
-
-`launchDir: Path`
-: Directory where the workflow was launched.
-
-`manifest`
-: Namespace corresponding to the {ref}`config-manifest` config scope.
-
-`outputDir: Path`
-: :::{versionadded} 24.10.0
-  :::
-: Workflow output directory.
-
-`preview: boolean`
-: :::{versionadded} 24.04.0
-  :::
-: Whether the current workflow run is a preview run.
-
-`profile: String`
-: Comma-separated list of active configuration profiles.
-
-`projectDir: Path`
-: Directory where the workflow project is located.
-
-`repository: String`
-: Project repository Git remote URL.
-
-`resume: boolean`
-: Returns `true` whenever the current instance is resumed from a previous execution.
-
-`revision: String`
-: Git branch/tag of the executed workflow repository.
-: When providing a Git tag or branch name using the `-r` CLI option, the `workflow.revision` is also populated.
-
-`runName: String`
-: Mnemonic name assigned to this execution instance.
-
-`scriptFile: Path`
-: Project main script file path.
-
-`scriptId: String`
-: Project main script unique hash ID.
-
-`scriptName: String`
-: Project main script file name.
-
-`sessionId: UUID`
-: Unique identifier (UUID) associated to current execution.
-
-`start: OffsetDateTime`
-: Timestamp of workflow at execution start.
-
-`stubRun: boolean`
-: Returns `true` whenever the current instance is a stub-run execution .
-
-`success: boolean`
-: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
-: Reports if the execution completed successfully.
-
-`userName: String`
-: User system account name.
-
-`wave`
-: Namespace containing Wave runtime information. The following properties are available:
-
-: `enabled: boolean`
-  : Whether Wave is enabled.
-
-`workDir: Path`
-: The directory where task temporary files are stored.
-
-**Functions**
-
-`onComplete( action: Closure )`
-: Define an action to take when the workflow completes (whether successful or not).
-
-`onError( action: Closure )`
-: Define an action to take if the workflow is terminated due to a runtime error or task failure.
diff --git a/docs/reference/stdlib-namespaces.mdx b/docs/reference/stdlib-namespaces.mdx
new file mode 100644
index 0000000000..931a31d0fb
--- /dev/null
+++ b/docs/reference/stdlib-namespaces.mdx
@@ -0,0 +1,379 @@
+---
+title: Namespaces
+description: Namespaces in the Nextflow standard library
+---
+
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Namespaces
+
+This page lists all of the available namespaces in the Nextflow standard library.
+
+## Global namespace
+
+The global namespace contains globally available constants and functions.
+
+### Constants
+
+##### `baseDir: Path`
+
+<DeprecatedInVersion version="20.04.0" />
+
+Alias of `workflow.projectDir`.
+
+##### `launchDir: Path`
+
+Alias of `workflow.launchDir`.
+
+##### `moduleDir: Path`
+
+Directory where a module script is located (equivalent to `projectDir` if used in the main script).
+
+
+##### `params`
+
+Map of workflow parameters specified in the config file or as command line options.
+
+
+##### `projectDir: Path`
+
+Alias of `workflow.projectDir`.
+
+##### `secrets: Map<String,String>`
+
+<AddedInVersion version="24.02.0-edge" />
+
+Map of pipeline secrets. See [Secrets][secrets-page] for more information.
+
+##### `workDir: Path`
+
+Alias of `workflow.workDir`.
+
+### Functions
+
+##### `branchCriteria( criteria: Closure ) -> Closure`
+
+Create a branch criteria to use with the [branch][operator-branch] operator.
+
+##### `env( name: String ) -> String`
+
+<AddedInVersion version="24.11.0-edge" />
+
+Get the value of the environment variable with the specified name in the Nextflow launch environment.
+
+##### `error( message: String = null )`
+
+Throw a script runtime error with an optional error message.
+
+##### `exit( exitCode: int = 0, message: String = null )`
+
+<DeprecatedInVersion version="22.06.0-edge">
+Use `error()` instead
+</DeprecatedInVersion>
+
+Stop the pipeline execution and return an exit code and optional error message.
+
+##### `file( filePattern: String, [options] ) -> Path | List<Path>`
+
+Get a file from a file name or glob pattern. Returns a collection of files if the glob pattern yields zero or multiple files.
+
+The following options are available:
+
+###### `checkIfExists: boolean`
+
+When `true`, throws an exception if the specified path does not exist in the file system (default: `false`).
+
+###### `followLinks: boolean`
+
+When `true`, follows symbolic links when traversing a directory tree, otherwise treats them as files (default: `true`).
+
+###### `glob: boolean`
+
+When `true`, interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`).
+
+###### `hidden: boolean`
+
+When `true`, includes hidden files in the resulting paths (default: `false`).
+
+
+###### `maxDepth: int`
+
+Maximum number of directory levels to visit (default: *no limit*).
+
+###### `type: String`
+
+Type of paths returned, can be `'file'`, `'dir'` or `'any'` (default: `'file'`).
+
+See also: [channel.fromPath][channel-path].
+
+##### `files( filePattern: String, [options] ) -> List<Path>`
+
+Get a collection of files from a file name or glob pattern. Supports the same options as `file()`.
+
+##### `groupKey( key, size: int ) -> GroupKey`
+
+Create a grouping key to use with the [groupTuple][operator-grouptuple] operator.
+
+##### `multiMapCriteria( criteria: Closure ) -> Closure`
+
+Create a multi-map criteria to use with the [multiMap][operator-multimap] operator.
+
+##### `print( value )`
+
+Print a value to standard output.
+
+##### `printf( format: String, values... )`
+
+Print a formatted string with the given values to standard output.
+
+##### `println( value )`
+
+Print a value to standard output with a newline.
+
+##### `sendMail( [options] )`
+
+Send an email. See [Notifications][mail-page] for more information.
+
+##### `sleep( milliseconds: long )`
+
+Sleep for the given number of milliseconds.
+
+##### `tuple( collection: List ) -> ArrayTuple`
+
+Create a tuple object from the given arguments.
+
+## `channel`
+
+The `channel` namespace contains the built-in channel factories. See [Channel factories][channel-factory] for details.
+
+## `log`
+
+The `log` namepsace contains functions for logging messages to the console.
+
+##### `error( message: String )`
+
+Log an error message to the console.
+
+This function does not terminate the pipeline -- use the global `error()` function instead.
+
+##### `info( message: String )`
+
+Log an info message to the console.
+
+##### `warn( message: String )`
+
+Log a warning message to the console.
+
+## `nextflow`
+
+The `nextflow` namespace contains information about the current Nextflow runtime.
+
+##### `build: int`
+
+Nextflow runtime build number.
+
+##### `timestamp: String`
+
+Nextflow runtime compile timestamp.
+
+##### `version: VersionNumber`
+
+Nextflow runtime version number. See [VersionNumber][stdlib-types-versionnumber] for more information.
+
+## `workflow`
+
+The `workflow` namespace contains information about the current workflow run.
+
+### Properties
+
+##### `commandLine: String`
+
+Command line as entered by the user to launch the workflow execution.
+
+##### `commitId: String`
+
+Git commit ID of the executed workflow repository.
+
+When providing a Git tag, branch name, or commit hash using the `-r` CLI option, the associated `workflow.commitId` is also populated.
+
+##### `complete: OffsetDateTime`
+
+*Available only in the `workflow.onComplete` handler*
+
+Timestamp of workflow when execution is completed.
+
+##### `configFiles: List<Path>`
+
+Configuration files used for the workflow execution.
+
+##### `container: String | Map<String,String>`
+
+Docker image used to run workflow tasks, or a map of process names to process containers when multiple images are used.
+
+##### `containerEngine: String`
+
+Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.
+
+##### `duration: Duration`
+
+*Available only in the `workflow.onComplete` handler*
+
+Time elapsed to complete workflow execution.
+
+##### `errorMessage: String`
+
+*Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+
+Error message of the task that caused the workflow execution to fail.
+
+##### `errorReport: String`
+
+*Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+
+Detailed error of the task that caused the workflow execution to fail.
+
+##### `exitStatus: int`
+
+*Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+
+Exit status of the task that caused the workflow execution to fail.
+
+##### `failOnIgnore: boolean`
+
+<AddedInVersion version="24.05.0-edge" />
+Whether the `workflow.failOnIgnore` config option was enabled.
+
+See also: [errorStrategy][process-error-strategy]
+
+##### `fusion`
+
+Namespace containing information about the current Fusion runtime.
+
+The following properties are available:
+
+###### `enabled: boolean`
+
+Whether Fusion is enabled.
+
+###### `version: String`
+
+The Fusion version being used.
+
+##### `homeDir: Path`
+
+User system home directory.
+
+##### `launchDir: Path`
+
+Directory where the workflow was launched.
+
+##### `manifest`
+
+Namespace corresponding to the [`manifest`][config-manifest] config scope.
+
+##### `outputDir: Path`
+
+<AddedInVersion version="24.10.0" />
+
+Workflow output directory.
+
+##### `preview: boolean`
+
+<AddedInVersion version="24.04.0" />
+
+Whether the current workflow run is a preview run.
+
+##### `profile: String`
+
+Comma-separated list of active configuration profiles.
+
+##### `projectDir: Path`
+
+Directory where the workflow project is located.
+
+##### `repository: String`
+
+Project repository Git remote URL.
+
+##### `resume: boolean`
+
+Returns `true` whenever the current instance is resumed from a previous execution.
+
+##### `revision: String`
+
+Git branch/tag of the executed workflow repository.
+
+When providing a Git tag or branch name using the `-r` CLI option, the `workflow.revision` is also populated.
+
+##### `runName: String`
+
+Mnemonic name assigned to this execution instance.
+
+##### `scriptFile: Path`
+
+Project main script file path.
+
+##### `scriptId: String`
+
+Project main script unique hash ID.
+
+##### `scriptName: String`
+
+Project main script file name.
+
+##### `sessionId: UUID`
+
+Unique identifier (UUID) associated to current execution.
+
+##### `start: OffsetDateTime`
+
+Timestamp of workflow at execution start.
+
+##### `stubRun: boolean`
+
+Returns `true` whenever the current instance is a stub-run execution .
+
+##### `success: boolean`
+
+*Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+
+Reports if the execution completed successfully.
+
+##### `userName: String`
+
+User system account name.
+
+##### `wave`
+
+Namespace containing Wave runtime information.
+
+The following properties are available:
+
+###### `enabled: boolean`
+
+Whether Wave is enabled.
+
+##### `workDir: Path`
+
+The directory where task temporary files are stored.
+
+### Functions
+
+##### `onComplete( action: Closure )`
+
+Define an action to take when the workflow completes (whether successful or not).
+
+##### `onError( action: Closure )`
+
+Define an action to take if the workflow is terminated due to a runtime error or task failure.
+
+[channel-factory]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx
+[channel-path]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#frompath
+[config-manifest]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#manifest
+[mail-page]: /nextflow_docs/nextflow_repo/docs/notifications.mdx
+[operator-branch]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#branch
+[operator-grouptuple]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#grouptuple
+[operator-multimap]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#multimap
+[process-error-strategy]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#errorstrategy
+[secrets-page]: /nextflow_docs/nextflow_repo/docs/secrets.mdx
+[stdlib-types-versionnumber]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#versionnumber
diff --git a/docs/reference/stdlib-types.md b/docs/reference/stdlib-types.md
deleted file mode 100644
index 2005b32c4e..0000000000
--- a/docs/reference/stdlib-types.md
+++ /dev/null
@@ -1,1055 +0,0 @@
-(stdlib-types)=
-
-# Types
-
-This page describes the standard types in the Nextflow standard library.
-
-(stdlib-types-bag)=
-
-## Bag\<E\>
-
-*Implements the {ref}`stdlib-types-iterable` trait.*
-
-A bag is an unordered collection of values of type `E`.
-
-The following operations are supported for bags:
-
-`+ : (Bag<E>, Bag<E>) -> Bag<E>`
-: Concatenates two bags.
-
-`in, !in : (E, Bag<E>) -> Boolean`
-: Given a value and a bag, returns `true` if the bag contains the value (or not).
-
-:::{note}
-Lists in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Collection.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Collection.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
-:::
-
-(stdlib-types-boolean)=
-
-## Boolean
-
-A boolean can be `true` or `false`.
-
-The following operations are supported for booleans:
-
-- `&&`: logical AND
-- `||`: logical OR
-- `!`: logical NOT
-
-:::{note}
-Booleans in Nextflow can be backed by any of the following Java types: `boolean`, `Boolean`.
-:::
-
-(stdlib-types-channel)=
-
-## Channel\<E\>
-
-A channel (also known as a *dataflow channel* or *queue channel*) is an asynchronous sequence of values of type `E`. It is used to facilitate dataflow logic in a workflow.
-
-See {ref}`dataflow-page` for an overview of dataflow types. See {ref}`operator-page` for the available methods for channels.
-
-(stdlib-types-duration)=
-
-## Duration
-
-A Duration represents a duration of time with millisecond precision.
-
-A Duration can be created by adding a unit suffix to an integer (e.g. `1.h`), or by explicitly casting to `Duration`:
-
-```nextflow
-// integer with suffix
-oneDay = 24.h
-
-// integer value (milliseconds)
-oneSecond = 1000 as Duration
-
-// simple string value
-oneHour = '1h' as Duration
-
-// complex string value
-complexDuration = '1day 6hours 3minutes 30seconds' as Duration
-```
-
-The following suffixes are available:
-
-| Unit                            | Description  |
-| ------------------------------- | ------------ |
-| `ms`, `milli`, `millis`         | Milliseconds |
-| `s`, `sec`, `second`, `seconds` | Seconds      |
-| `m`, `min`, `minute`, `minutes` | Minutes      |
-| `h`, `hour`, `hours`            | Hours        |
-| `d`, `day`, `days`              | Days         |
-
-Durations can be compared like numbers, and they support basic arithmetic operations:
-
-```nextflow
-a = 1.h
-b = 2.h
-
-assert a < b
-assert a + a == b
-assert b - a == a
-assert a * 2 == b
-assert b / 2 == a
-```
-
-The following methods are available for a Duration:
-
-`toDays() -> Integer`
-: Get the duration value in days (rounded down).
-
-`toHours() -> Integer`
-: Get the duration value in hours (rounded down).
-
-`toMillis() -> Integer`
-: Get the duration value in milliseconds.
-
-`toMinutes() -> Integer`
-: Get the duration value in minutes (rounded down).
-
-`toSeconds() -> Integer`
-: Get the duration value in seconds (rounded down).
-
-:::{note}
-These methods are also available as `getDays()`, `getHours()`, `getMillis()`, `getMinutes()`, and `getSeconds()`.
-:::
-
-(stdlib-types-float)=
-
-## Float
-
-A float is a floating-point number (i.e. real number) that can be positive or negative.
-
-The following operations are supported for floats:
-
-- `+, -, *, /`: addition, subtraction, multiplication, division
-- `**`: exponentation
-
-:::{note}
-Floats in Nextflow can be backed by any of the following Java types: `float`, `double`, `Float`, `Double`.
-:::
-
-(stdlib-types-integer)=
-
-## Integer
-
-An integer is a whole number that can be positive or negative.
-
-The following operations are supported for integers:
-
-- `+, -, *, /`: addition, subtraction, multiplication, integer division
-- `%`: remainder of integer division (i.e. modulus)
-- `**`: exponentation
-- `&`, `|`, `^`, `~`: bitwise AND, OR, XOR, NOT
-- `<<`, `>>`: left and right bit-shift
-
-:::{note}
-Integers in Nextflow can be backed by any of the following Java types: `int`, `long`, `Integer`, `Long`.
-:::
-
-(stdlib-types-iterable)=
-
-## Iterable\<E\>
-
-*Implemented by the following types: {ref}`stdlib-types-bag`, {ref}`stdlib-types-list`, {ref}`stdlib-types-set`*
-
-`Iterable` is a trait implemented by collection types that support iteration.
-
-Types that implement `Iterable` can be passed as an `Iterable` parameter of a method, and they can use all of the methods described below.
-
-The following methods are available for iterables:
-
-`any( condition: (E) -> Boolean ) -> Boolean`
-: Returns `true` if any element in the iterable satisfies the given condition.
-
-`collect( transform: (E) -> R ) -> Iterable<R>`
-: Returns a new iterable with each element transformed by the given closure.
-
-`collectMany( transform: (E) -> Iterable<R> ) -> Iterable<R>`
-: Transforms each element in the iterable into a collection with the given closure and concatenates the resulting collections into a list.
-
-`contains( value: E ) -> Boolean`
-: Returns `true` if the iterable contains the given value.
-
-`each( action: (E) -> () )`
-: Invokes the given closure for each element in the iterable.
-
-`every( condition: (E) -> Boolean ) -> Boolean`
-: Returns `true` if every element in the iterable satisfies the given condition.
-
-`findAll( condition: (E) -> Boolean ) -> Iterable<E>`
-: Returns the elements in the iterable that satisfy the given condition.
-
-`groupBy( transform: (E) -> K ) -> Map<K,Iterable<E>>`
-: Collect the elements of an iterable into groups based on a matching key. The closure should return the key for a given element.
-
-`inject( accumulator: (E,E) -> E ) -> E`
-: Apply the given accumulator to each element in the iterable and return the final accumulated value. The closure should accept two parameters, corresponding to the current accumulated value and the current iterable element, and return the next accumulated value.
-: The first element from the iterable is used as the initial accumulated value.
-
-`inject( initialValue: R, accumulator: (R,E) -> R ) -> R`
-: Apply the given accumulator to each element in the iterable and return the final accumulated value. The closure should accept two parameters, corresponding to the current accumulated value and the current iterable element, and return the next accumulated value.
-
-`isEmpty() -> Boolean`
-: Returns `true` if the iterable is empty.
-
-`join( separator: String = '' ) -> String`
-: Concatenates the string representation of each element in the iterable, with the given string as the separator between each element.
-
-`max() -> E`
-: Returns the maximum element in the iterable.
-
-`max( comparator: (E) -> R ) -> E`
-: Returns the maximum element in the iterable according to the given closure.
-: The closure should follow the same semantics as the closure parameter of `toSorted()`.
-
-`max( comparator: (E,E) -> Integer ) -> E`
-: Returns the maximum element in the iterable according to the given closure.
-: The closure should follow the same semantics as the closure parameter of `toSorted()`.
-
-`min() -> E`
-: Returns the minimum element in the iterable.
-
-`min( comparator: (E) -> R ) -> E`
-: Returns the minimum element in the iterable according to the given closure.
-: The closure should follow the same semantics as the closure parameter of `toSorted()`.
-
-`min( comparator: (E,E) -> Integer ) -> E`
-: Returns the minimum element in the iterable according to the given closure.
-: The closure should follow the same semantics as the closure parameter of `toSorted()`.
-
-`size() -> Integer`
-: Returns the number of elements in the iterable.
-
-`sum() -> E`
-: Returns the sum of the elements in the iterable. The elements should support addition (`+`).
-
-`sum( transform: (E) -> R ) -> R`
-: Transforms each element in the iterable with the given closure and returns the sum. The values returned by the closure should support addition (`+`).
-
-`toList() -> List<E>`
-: Converts the iterable to a list.
-: :::{danger}
-  Converting an unordered collection to a list can lead to non-deterministic behavior. Consider using `toSorted()` instead to ensure a deterministic ordering. See {ref}`cache-nondeterministic-inputs` for more information.
-  :::
-
-`toSet() -> Set<E>`
-: Converts the iterable to a set. Duplicate elements are excluded.
-
-`toSorted() -> List<E>`
-: Returns a sorted list of the iterable's elements.
-
-`toSorted( comparator: (E) -> R ) -> List<E>`
-: Returns the iterable as a list sorted according to the given closure.
-: The closure should accept one parameter and transform each element into the value that will be used for comparisons.
-
-`toSorted( comparator: (E,E) -> Integer ) -> List<E>`
-: Returns the iterable as a list sorted according to the given closure.
-: The closure should accept two parameters and return a negative integer, zero, or a positive integer to denote whether the first argument is less than, equal to, or greater than the second.
-
-`toUnique() -> Iterable<E>`
-: Returns a shallow copy of the iterable with duplicate elements excluded.
-
-**`toUnique( comparator: (E) -> R ) -> Iterable<E>`**
-
-`toUnique( comparator: (E,E) -> Integer ) -> Iterable<E>`
-: Returns a shallow copy of the iterable with duplicate elements excluded.
-: The closure should follow the same semantics as the closure parameter of `toSorted()`.
-
-:::{note}
-Iterables in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Iterable.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/Iterable.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
-:::
-
-(stdlib-types-list)=
-
-## List\<E\>
-
-*Implements the {ref}`stdlib-types-iterable` trait.*
-
-A list is an ordered collection of values of type `E`. See {ref}`script-list` for an overview of lists.
-
-The following operations are supported for lists:
-
-`+ : (List<E>, List<E>) -> List<E>`
-: Concatenates two lists.
-
-`* : (List<E>, Integer) -> List<E>`
-: Given a list and an integer *n*, repeats the list *n* times.
-
-`[] : (List<E>, Integer) -> E`
-: Given a list and an index, returns the element at the given index in the list, or `null` if the index is out of range.
-
-`in, !in : (E, List<E>) -> Boolean`
-: Given a value and a list, returns `true` if the list contains the value (or not).
-
-The following methods are available for a list:
-
-`collate( size: Integer, keepRemainder: Boolean = true ) -> List<List<E>>`
-: Collates the list into a list of sub-lists of length `size`. If `keepRemainder` is `true`, any remaining elements are included as a partial sub-list, otherwise they are excluded.
-
-: For example:
-  ```nextflow
-  assert [1, 2, 3, 4, 5, 6, 7].collate(3)        == [[1, 2, 3], [4, 5, 6], [7]]
-  assert [1, 2, 3, 4, 5, 6, 7].collate(3, false) == [[1, 2, 3], [4, 5, 6]]
-  ```
-
-`collate( size: Integer, step: Integer, keepRemainder: Boolean = true ) -> List<List<E>>`
-: Collates the list into a list of sub-lists of length `size`, stepping through the list `step` elements for each sub-list. If `keepRemainder` is `true`, any remaining elements are included as a partial sub-list, otherwise they are excluded.
-
-: For example:
-  ```nextflow
-  assert [1, 2, 3, 4].collate(3, 1)        == [[1, 2, 3], [2, 3, 4], [3, 4], [4]]
-  assert [1, 2, 3, 4].collate(3, 1, false) == [[1, 2, 3], [2, 3, 4]]
-  ```
-
-`find( condition: (E) -> Boolean ) -> E`
-: Returns the first element in the list that satisfies the given condition.
-
-`first() -> E`
-: Returns the first element in the list. Raises an error if the list is empty.
-
-`getIndices() -> List<Integer>`
-: Returns the list of integers from 0 to *n - 1*, where *n* is the number of elements in the list.
-
-`head() -> E`
-: Equivalent to `first()`.
-
-`indexOf( value: E ) -> Integer`
-: Returns the index of the first occurrence of the given value in the list, or -1 if the list does not contain the value.
-
-`init() -> List<E>`
-: Returns a shallow copy of the list with the last element excluded.
-
-`last() -> E`
-: Returns the last element in the list. Raises an error if the list is empty.
-
-`reverse() -> List<E>`
-: Returns a shallow copy of the list with the elements reversed.
-
-`subList( fromIndex: Integer, toIndex: Integer ) -> List<E>`
-: Returns the portion of the list between the given `fromIndex` (inclusive) and `toIndex` (exclusive).
-
-`tail() -> List<E>`
-: Returns a shallow copy of the list with the first element excluded.
-
-`take( n: Integer ) -> List<E>`
-: Returns the first *n* elements of the list.
-
-`takeWhile( condition: (E) -> Boolean ) -> List<E>`
-: Returns the longest prefix of the list where each element satisfies the given condition.
-
-`withIndex() -> List<(E,Integer)>`
-: Returns a list of 2-tuples corresponding to the value and index of each element in the list.
-
-:::{note}
-Lists in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/List.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/List.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
-:::
-
-(stdlib-types-map)=
-
-## Map\<K,V\>
-
-A map associates or "maps" keys of type `K` to values of type `V`. Each key can map to at most one value -- a map cannot contain duplicate keys. See {ref}`script-map` for an overview of maps.
-
-The following operations are supported for maps:
-
-`+ : (Map<K,V>, Map<K,V>) -> Map<K,V>`
-: Concatenates two maps. If a key exists in both maps, the mapping from the right-hand side is used.
-
-`[] : (Map<K,V>, K) -> V`
-: Given a map and a key, returns the value for the given key in the map, or `null` if the key is not in the map.
-
-`in, !in : (K, Map<K,V>) -> Boolean`
-: Given a key and a map, returns `true` if the map contains the key and the corresponding value is *truthy* (e.g. not `null`, `0`, or `false`).
-
-The following methods are available for a map:
-
-`any( condition: (K,V) -> Boolean ) -> Boolean`
-: Returns `true` if any key-value pair in the map satisfies the given condition. The closure should accept two parameters corresponding to the key and value of an entry.
-
-`containsKey( key: K ) -> Boolean`
-: Returns `true` if the map contains a mapping for the given key.
-
-`containsValue( value: V ) -> Boolean`
-: Returns `true` if the map maps one or more keys to the given value.
-
-`each( action: (K,V) -> () )`
-: Invokes the given closure for each key-value pair in the map. The closure should accept two parameters corresponding to the key and value of an entry.
-
-`entrySet() -> Set<(K,V)>`
-: Returns a set of the key-value pairs in the map.
-
-`every( condition: (K,V) -> Boolean ) -> Boolean`
-: Returns `true` if every key-value pair in the map satisfies the given condition. The closure should accept two parameters corresponding to the key and value of an entry.
-
-`isEmpty() -> Boolean`
-: Returns `true` if the map is empty.
-
-`keySet() -> Set<K>`
-: Returns a set of the keys in the map.
-
-`size() -> Integer`
-: Returns the number of key-value pairs in the map.
-
-`subMap( keys: Iterable<K> ) -> Map<K,V>`
-: Returns a sub-map containing the given keys.
-
-`values() -> Bag<V>`
-: Returns a collection of the values in the map.
-
-:::{note}
-Maps in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Map.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Map.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
-:::
-
-(stdlib-types-memoryunit)=
-
-## MemoryUnit
-
-A MemoryUnit represents a quantity of bytes.
-
-A MemoryUnit can be created by adding a unit suffix to an integer (e.g. `1.GB`), or by explicitly casting to `MemoryUnit`:
-
-```nextflow
-// integer with suffix
-oneMegabyte = 1.MB
-
-// integer value (bytes)
-oneKilobyte = 1024 as MemoryUnit
-
-// string value
-oneGigabyte = '1 GB' as MemoryUnit
-```
-
-The following suffixes are available:
-
-| Unit | Description |
-| ---- | ----------- |
-| `B`  | Bytes       |
-| `KB` | Kilobytes   |
-| `MB` | Megabytes   |
-| `GB` | Gigabytes   |
-| `TB` | Terabytes   |
-| `PB` | Petabytes   |
-| `EB` | Exabytes    |
-| `ZB` | Zettabytes  |
-
-:::{note}
-Technically speaking, a kilobyte is equal to 1000 bytes, whereas 1024 bytes is called a "kibibyte" and abbreviated as "KiB", and so on for the other units. In practice, however, kilobyte is commonly understood to mean 1024 bytes, and Nextflow follows this convention in its implementation as well as this documentation.
-:::
-
-Memory units can be compared like numbers, and they support basic arithmetic operations:
-
-```nextflow
-a = 1.GB
-b = 2.GB
-
-assert a < b
-assert a + a == b
-assert b - a == a
-assert a * 2 == b
-assert b / 2 == a
-```
-
-The following methods are available for a `MemoryUnit` object:
-
-`toBytes() -> Integer`
-: Get the memory value in bytes (B).
-
-`toGiga() -> Integer`
-: Get the memory value in gigabytes (rounded down), where 1 GB = 1024 MB.
-
-`toKilo() -> Integer`
-: Get the memory value in kilobytes (rounded down), where 1 KB = 1024 B.
-
-`toMega() -> Integer`
-: Get the memory value in megabytes (rounded down), where 1 MB = 1024 KB.
-
-`toUnit( unit: String ) -> Integer`
-: Get the memory value in terms of a given unit (rounded down). The unit can be one of: `'B'`, `'KB'`, `'MB'`, `'GB'`, `'TB'`, `'PB'`, `'EB'`, `'ZB'`.
-
-:::{note}
-These methods are also available as `getBytes()`, `getGiga()`, `getKilo()`, and `getMega()`.
-:::
-
-(stdlib-types-path)=
-
-## Path
-
-A Path is a handle for hierarchichal paths such as local files and directories, HTTP/FTP URLs, and object storage paths (e.g. Amazon S3).
-
-The `file()` function can be used to get a Path for a given filename or URL:
-
-```nextflow
-def hello = file('hello.txt')
-println hello.text
-```
-
-The `files()` function can be used to get a collection of Paths from a glob pattern:
-
-```nextflow
-def inputs = files('*.txt')
-inputs.each { input ->
-  println "${input.name}: ${input.text}"
-}
-```
-
-The following sections describe the methods that are available for paths.
-
-:::{note}
-Paths in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/nio/file/Path.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/nio/file/Path.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
-:::
-
-<h3>Operations</h3>
-
-The following operations are supported for paths:
-
-`/ : (Path, String) -> Path`
-: Resolves a relative path string against a directory path. Equivalent to `resolve()`.
-
-`<< : (Path, String)`
-: Appends text to a file without replacing existing content. Equivalent to `append()`.
-
-<h3>Getting attributes</h3>
-
-The following methods are useful for getting attributes of a path:
-
-`exists() -> Boolean`
-: Returns `true` if the path exists.
-
-`getBaseName() -> String`
-: Gets the path name without its extension, e.g. `/some/path/file.tar.gz` -> `file.tar`.
-
-`getExtension() -> String`
-: Gets the path extension, e.g. `/some/path/file.txt` -> `txt`.
-
-`getName() -> String`
-: Gets the path name, e.g. `/some/path/file.txt` -> `file.txt`.
-
-`getSimpleName() -> String`
-: Gets the path name without any extension, e.g. `/some/path/file.tar.gz` -> `file`.
-
-`getParent() -> Path`
-: Gets the path parent path, e.g. `/some/path/file.txt` -> `/some/path`.
-
-`getScheme() -> String`
-: Gets the path URI scheme, e.g. `s3://some-bucket/hello.txt` -> `s3`.
-
-`isDirectory() -> Boolean`
-: Returns `true` if the path is a directory.
-
-`isEmpty() -> Boolean`
-: Returns `true` if the path is empty or does not exist.
-
-`isFile() -> Boolean`
-: Returns `true` if the path is a file (i.e. not a directory).
-
-`isHidden() -> Boolean`
-: Returns `true` if the path is hidden.
-
-`isLink() -> Boolean`
-: Returns `true` if the path is a symbolic link.
-
-`lastModified() -> Integer`
-: Returns the path last modified timestamp in Unix time (i.e. milliseconds since January 1, 1970).
-
-`relativize(other: Path) -> Path`
-: Returns the relative path between this path and the given path.
-
-`resolve(other: String) -> Path`
-: Resolves the given path string against this path.
-
-`resolveSibling(other: String) -> Path`
-: Resolves the given path string against this path's parent path.
-
-`size() -> Integer`
-: Gets the file size in bytes.
-
-`toUriString() -> String`
-: Gets the file path along with the protocol scheme:
-  ```nextflow
-  def ref = file('s3://some-bucket/hello.txt')
-
-  assert ref.toString() == '/some-bucket/hello.txt'
-  assert "$ref" == '/some-bucket/hello.txt'
-  assert ref.toUriString() == 's3://some-bucket/hello.txt'
-  ```
-
-<h3>Reading</h3>
-
-The following methods are available for reading files:
-
-`eachByte( action: (byte) -> () )`
-: Iterates over the file, applying the specified closure to each byte.
-
-`eachLine( action: (String) -> () )`
-: Iterates over the file, applying the specified closure to each line.
-
-`getBytes() -> byte[]`
-: Returns the file content as a byte array.
-
-`getText() -> String`
-: Returns the file content as a string.
-
-`newInputStream() -> InputStream`
-: Returns an [InputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/InputStream.html) object to read a binary file.
-
-`newReader() -> Reader`
-: Returns a [Reader](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Reader.html) object to read a text file.
-
-`readLines() -> List<String>`
-: Reads the file line by line and returns the content as a list of strings.
-
-`withInputStream( action: (InputStream) -> () )`
-: Opens a file for reading and lets you access it with an [InputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/InputStream.html) object.
-
-`withReader( action: (Reader) -> () )`
-: Opens a file for reading and lets you access it with a [Reader](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Reader.html) object.
-
-<h3>Writing</h3>
-
-The following methods are available for writing to files:
-
-`append( text: String )`
-: Appends text to a file without replacing existing content.
-
-`newOutputStream() -> OutputStream`
-: Creates an [OutputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/OutputStream.html) object that allows you to write binary data to a file.
-
-`newPrintWriter() -> PrintWriter`
-: Creates a [PrintWriter](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/PrintWriter.html) object that allows you to write formatted text to a file.
-
-`newWriter() -> Writer`
-: Creates a [Writer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Writer.html) object that allows you to save text data to a file.
-
-`setBytes( bytes: byte[] )`
-: Writes a byte array to a file. Equivalent to setting the `bytes` property.
-
-`setText( text: String )`
-: Writes text to a file. Equivalent to setting the `text` property.
-
-`withOutputStream( action: (OutputStream) -> () )`
-: Applies the specified closure to an [OutputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/OutputStream.html) object, closing it when finished.
-
-`withPrintWriter( action: (PrintWriter) -> () )`
-: Applies the specified closure to a [PrintWriter](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/PrintWriter.html) object, closing it when finished.
-
-`withWriter( action: (Writer) -> () )`
-: Applies the specified closure to a [Writer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Writer.html) object, closing it when finished.
-
-`write( text: String )`
-: Writes a string to a file, replacing any existing content.
-
-<h3>Filesystem operations</h3>
-
-The following methods are available for manipulating files and directories in a filesystem:
-
-`copyTo( target: Path )`
-: Copies a source file or directory to a target file or directory.
-
-: *When copying a file to another file:* if the target file already exists, it will be replaced.
-
-  ```nextflow
-  file('/some/path/my_file.txt').copyTo('/another/path/new_file.txt')
-  ```
-
-: *When copying a file to a directory:* the file will be copied into the directory, replacing any file with the same name.
-
-  ```nextflow
-  file('/some/path/my_file.txt').copyTo('/another/path')
-  ```
-
-: *When copying a directory to another directory:* if the target directory already exists, the source directory will be copied into the target directory, replacing any sub-directory with the same name. If the target path does not exist, it will be created automatically.
-
-  ```nextflow
-  file('/any/dir_a').moveTo('/any/dir_b')
-  ```
-
-  The result of the above example depends on the existence of the target directory. If the target directory exists, the source is moved into the target directory, resulting in the path `/any/dir_b/dir_a`. If the target directory does not exist, the source is just renamed to the target name, resulting in the path `/any/dir_b`.
-
-: :::{note}
-  The `copyTo()` function follows the semantics of the Linux command `cp -r <source> <target>`, with the following caveat: while Linux tools often treat paths ending with a slash (e.g. `/some/path/name/`) as directories, and those not (e.g. `/some/path/name`) as regular files, Nextflow (due to its use of the Java files API) views both of these paths as the same file system object. If the path exists, it is handled according to its actual type (i.e. as a regular file or as a directory). If the path does not exist, it is treated as a regular file, with any missing parent directories created automatically.
-  :::
-
-`delete() -> Boolean`
-: Deletes the file or directory at the given path, returning `true` if the operation succeeds, and `false` otherwise:
-
-  ```nextflow
-  myFile = file('some/file.txt')
-  result = myFile.delete()
-  println result ? "OK" : "Cannot delete: $myFile"
-  ```
-
-  If a directory is not empty, it will not be deleted and `delete()` will return `false`.
-
-`deleteDir() -> Boolean`
-: Deletes a directory and all of its contents.
-
-  ```nextflow
-  file('any/path').deleteDir()
-  ```
-
-`getPermissions() -> String`
-: Returns a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation), e.g. `'rw-rw-r--'`.
-
-`list() -> List<String>`
-: Returns the first-level elements (files and directories) of a directory as a list of strings.
-
-`listFiles() -> List<Path>`
-: Returns the first-level elements (files and directories) of a directory as a list of Paths.
-
-`mkdir() -> Boolean`
-: Creates a directory at the given path, returning `true` if the directory is created successfully, and `false` otherwise:
-
-  ```nextflow
-  myDir = file('any/path')
-  result = myDir.mkdir()
-  println result ? "OK" : "Cannot create directory: $myDir"
-  ```
-
-  If the parent directories do not exist, the directory will not be created and `mkdir()` will return `false`.
-
-`mkdirs() -> Boolean`
-: Creates a directory at the given path, including any nonexistent parent directories:
-
-  ```nextflow
-  file('any/path').mkdirs()
-  ```
-
-`mklink( linkName: String, [options] ) -> Path`
-: Creates a *filesystem link* to a given path:
-
-  ```nextflow
-  myFile = file('/some/path/file.txt')
-  myFile.mklink('/user/name/link-to-file.txt')
-  ```
-
-  Returns the Path of the link to create.
-
-  Available options:
-
-  `hard: Boolean`
-  : When `true`, creates a *hard* link, otherwise creates a *soft* (aka *symbolic*) link (default: `false`).
-
-  `overwrite: Boolean`
-  : When `true`, overwrites any existing file with the same name, otherwise throws a [FileAlreadyExistsException](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/nio/file/FileAlreadyExistsException.html) (default: `false`).
-
-`moveTo( target: Path )`
-: Moves a source file or directory to a target file or directory. Follows the same semantics as `copyTo()`.
-
-`renameTo( target: String ) -> Boolean`
-: Rename a file or directory:
-
-  ```nextflow
-  file('my_file.txt').renameTo('new_file_name.txt')
-  ```
-
-`setPermissions( permissions: String ) -> Boolean`
-: Sets a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation):
-
-  ```nextflow
-  myFile.setPermissions('rwxr-xr-x')
-  ```
-
-`setPermissions( owner: Integer, group: Integer, other: Integer ) -> Boolean`
-: Sets a file's permissions using the [numeric notation](http://en.wikipedia.org/wiki/File_system_permissions#Numeric_notation), i.e. as three digits representing the **owner**, **group**, and **other** permissions:
-
-  ```nextflow
-  myFile.setPermissions(7,5,5)
-  ```
-
-The following methods are available for listing and traversing directories:
-
-`eachDir( action: (Path) -> () )`
-: Iterates through first-level directories only.
-
-`eachDirMatch( nameFilter: String, action: (Path) -> () )`
-: Iterates through directories whose names match the given filter.
-
-`eachDirRecurse( action: (Path) -> () )`
-: Iterates through directories depth-first (regular files are ignored).
-
-`eachFile( action: (Path) -> () )`
-: Iterates through first-level files and directories.
-
-`eachFileMatch( nameFilter: String, action: (Path) -> () )`
-: Iterates through files and directories whose names match the given filter.
-
-`eachFileRecurse( action: (Path) -> () )`
-: Iterates through files and directories depth-first.
-
-<h3>Splitting files</h3>
-
-The following methods are available for splitting and counting the records in files:
-
-`countFasta() -> Integer`
-: Counts the number of records in a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file. See the {ref}`operator-splitfasta` operator for available options.
-
-`countFastq() -> Integer`
-: Counts the number of records in a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file. See the {ref}`operator-splitfastq` operator for available options.
-
-`countJson() -> Integer`
-: Counts the number of records in a JSON file. See the {ref}`operator-splitjson` operator for available options.
-
-`countLines() -> Integer`
-: Counts the number of lines in a text file. See the {ref}`operator-splittext` operator for available options.
-
-`splitCsv() -> List<?>`
-: Splits a CSV file into a list of records. See the {ref}`operator-splitcsv` operator for available options.
-
-`splitFasta() -> List<?>`
-: Splits a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file into a list of records. See the {ref}`operator-splitfasta` operator for available options.
-
-`splitFastq() -> List<?>`
-: Splits a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file into a list of records. See the {ref}`operator-splitfastq` operator for available options.
-
-`splitJson() -> List<?>`
-: Splits a JSON file into a list of records. See the {ref}`operator-splitjson` operator for available options.
-
-`splitText() -> List<String>`
-: Splits a text file into a list of lines. See the {ref}`operator-splittext` operator for available options.
-
-(stdlib-types-set)=
-
-## Set\<E\>
-
-*Implements the {ref}`stdlib-types-iterable` trait.*
-
-A set is an unordered collection of values of type `E` which cannot contain duplicates.
-
-A set can be created from a list using the `toSet()` method:
-
-```nextflow
-[1, 2, 2, 3].toSet()
-// -> [1, 2, 3]
-```
-
-The following operations are supported for sets:
-
-`+ : (Set<E>, Iterable<E>) -> Set<E>`
-: Given a set and an iterable, returns a new set containing the elements of both collections.
-
-`- : (Set<E>, Iterable<E>) -> Set<E>`
-: Given a set and an iterable, returns a shallow copy of the set minus the elements of the iterable.
-
-`in, !in : (E, Set<E>) -> Boolean`
-: Given a value and a set, returns `true` if the set contains the value (or not).
-
-The following methods are available for a set:
-
-`intersect( right: Iterable<E> ) -> Set<E>`
-: Returns the intersection of the set and the given iterable.
-
-:::{note}
-Sets in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Set.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Set.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
-:::
-
-(stdlib-types-string)=
-
-## String
-
-A string is an immutable sequence of characters. See {ref}`script-string` for an overview of strings.
-
-The following operations are supported for strings:
-
-`+ : (String, String) -> String`
-: Concatenates two strings.
-
-`* : (String, Integer) -> String`
-: Given a string and an integer *n*, repeats the string *n* times.
-
-`[] : (String, Integer) -> char`
-: Given a string and an index, returns the character at the given index in the string.
-
-`~ : (String) -> Pattern`
-: Creates a regular expression from a string.
-: See [Pattern](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/regex/Pattern.html) in the Java standard library for more information.
-
-`=~ : (String, String) -> Matcher`
-: Given a string and a pattern, creates a matcher that is truthy if the pattern occurs anywhere in the string.
-: See [Matcher](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/regex/Matcher.html) in the Java standard library for more information.
-
-`==~ : (String, String) -> Boolean`
-: Given a string and a pattern, returns `true` if the string matches the pattern exactly.
-
-The following methods are available for a string:
-
-`contains( str: String ) -> Boolean`
-: Returns `true` if the given substring occurs anywhere in the string.
-
-`endsWith( suffix: String ) -> Boolean`
-: Returns `true` if the string ends with the given suffix.
-
-`execute() -> Process`
-: Execute the string as a command. Returns a [Process](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/Process.html) which provides the exit status and standard input/output/error of the executed command.
-
-`indexOf( str: String ) -> Integer`
-: Returns the index within the string of the first occurrence of the given substring. Returns -1 if the string does not contain the substring.
-
-`indexOf( str: String, fromIndex: Integer ) -> Integer`
-: Returns the index within the string of the first occurrence of the given substring, starting the search at the given index. Returns -1 if the string does not contain the substring.
-
-`isBlank() -> Boolean`
-: Returns `true` if the string is empty or contains only whitespace characters.
-
-`isEmpty() -> Boolean`
-: Returns `true` if the string is empty (i.e. `length()` is 0).
-
-`isDouble() -> Boolean`
-: Returns `true` if the string can be parsed as a 64-bit (double precision) floating-point number.
-
-`isFloat() -> Boolean`
-: Returns `true` if the string can be parsed as a 32-bit floating-point number.
-
-`isInteger() -> Boolean`
-: Returns `true` if the string can be parsed as a 32-bit integer.
-
-`isLong() -> Boolean`
-: Returns `true` if the string can be parsed as a 64-bit (long) integer.
-
-`lastIndexOf( str: String ) -> Integer`
-: Returns the index within the string of the last occurrence of the given substring. Returns -1 if the string does not contain the substring.
-
-`lastIndexOf( str: String, fromIndex: Integer ) -> Integer`
-: Returns the index within the string of the last occurrence of the given substring, searching backwards starting at the given index. Returns -1 if the string does not contain the substring.
-
-`length() -> Integer`
-: Returns the length of the string.
-
-`md5() -> String`
-: Returns the MD5 checksum of the string.
-
-`replace( target: String, replacement: String ) -> String`
-: Returns a new string in which each occurrence of the target string is replaced with the given replacement string.
-
-`replaceAll( regex: String, replacement: String ) -> String`
-: Returns a new string in which each occurrence of the given regular expression is replaced with the given replacement string.
-
-`replaceFirst( regex: String, replacement: String ) -> String`
-: Returns a new string in which the first occurrence of the given regular expression is replaced with the given replacement string.
-
-`sha256() -> String`
-: Returns the SHA-256 checksum of the string.
-
-`startsWith( prefix: String ) -> Boolean`
-: Returns `true` if the string ends with the given prefix.
-
-`strip() -> String`
-: Returns a copy of the string with all leading and trailing whitespace removed.
-
-`stripIndent() -> String`
-: Returns a copy of the string with leading spaces on each line removed.
-: The number of spaces to remove is determined by the line with the least number of leading spaces, excluding lines with only whitespace.
-
-`stripLeading() -> String`
-: Returns a copy of the string with all leading whitespace removed.
-
-`stripTrailing() -> String`
-: Returns a copy of the string with all trailing whitespace removed.
-
-`substring( beginIndex: Integer ) -> String`
-: Returns a substring of this string.
-
-`substring( beginIndex: Integer, endIndex: Integer ) -> String`
-: Returns a substring of this string.
-
-`toBoolean() -> Boolean`
-: Returns `true` if the trimmed string is "true", "y", or "1" (ignoring case).
-
-`toDouble() -> Float`
-: Parses the string into a 64-bit (double precision) floating-point number.
-
-`toFloat() -> Float`
-: Parses the string into a 32-bit floating-point number.
-
-`toInteger() -> Integer`
-: Parses the string into a 32-bit integer.
-
-`toLong() -> Integer`
-: Parses the string into a 64-bit (long) integer.
-
-`toLowerCase() -> String`
-: Returns a copy of this string with all characters converted to lower case.
-
-`toUpperCase() -> String`
-: Returns a copy of this string with all characters converted to upper case.
-
-`tokenize( delimiters: String ) -> List<String>`
-: Splits the string into a list of substrings using the given delimiters. Each character in the delimiter string is treated as a separate delimiter.
-
-:::{note}
-Strings in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/String.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
-:::
-
-(stdlib-types-tuple)=
-
-## Tuple
-
-A tuple is a fixed sequence of values, where each value can have its own type. Tuples can be created using the `tuple` function.
-
-The following operations are supported for tuples:
-
-`[] : (Tuple, Integer) -> ?`
-: Given a tuple and an index, returns the tuple element at the index.
-
-(stdlib-types-value)=
-
-## Value\<V\>
-
-A dataflow value (also known as a *value channel*) is an asynchronous value of type `V`. It is used to facilitate dataflow logic in a workflow.
-
-See {ref}`dataflow-page` for an overview of dataflow types.
-
-The following methods are available for a dataflow value:
-
-`flatMap( transform: (V) -> Iterable<R> ) -> Channel<R>`
-: Transforms the dataflow value into a collection with the given closure and emits the resulting values in a dataflow channel.
-
-`map( transform: (V) -> R ) -> Value<R>`
-: Transforms the dataflow value into another dataflow value with the given closure.
-
-`subscribe( action: (V) -> () )`
-: Invokes the given closure on the dataflow value.
-
-`view() -> Value<V>`
-: Prints the dataflow value to standard output.
-
-`view( transform: (V) -> String ) -> Value<V>`
-: Transforms the dataflow value using the given closure and print the result to standard output.
-
-(stdlib-types-versionnumber)=
-
-## VersionNumber
-
-A VersionNumber represents a semantic or calendar version number.
-
-The following methods are available for a VersionNumber:
-
-`getMajor() -> String`
-: Get the major version number, i.e. the first version component.
-
-`getMinor() -> String`
-: Get the minor version number, i.e. the second version component.
-
-`getPatch() -> String`
-: Get the patch version number, i.e. the third version component.
-
-`matches( condition: String ) -> Boolean`
-: Check whether the version satisfies a version requirement.
-
-: The version requirement string can be prefixed with the usual comparison operators:
-  - `=` or `==`: equal to
-  - `<` (`<=`): less than (or equal to)
-  - `>` (`>=`): greater than (or equal to)
-  - `!=` or `<>`: not equal
-
-  For example:
-
-  ```nextflow
-  if( !nextflow.version.matches('>=23.10') ) {
-      error "This workflow requires Nextflow version 23.10 or greater -- You are running version $nextflow.version"
-  }
-  ```
-
-: Multiple constraints can be specified as a comma-separated list, e.g. `>=23.10, <=24.10`.
-
-: Alternatively, the version can be postfixed with `+`, which is similar to `==` but also allows the last version part to be greater. For example, `23.10.1+` is satisfied by `23.10.1` and `23.10.2`, but not `23.11.x` or `23.09.x`. Additionally, `23.10.+` is equivalent to `23.10.0+`. This operator is a useful way to enforce a specific version while allowing for newer patch releases.
diff --git a/docs/reference/stdlib-types.mdx b/docs/reference/stdlib-types.mdx
new file mode 100644
index 0000000000..1544f1612a
--- /dev/null
+++ b/docs/reference/stdlib-types.mdx
@@ -0,0 +1,1252 @@
+---
+title: Types
+description: Types in the Nextflow standard library
+---
+
+# Types
+
+This page describes the standard types in the Nextflow standard library.
+
+## Bag\<E\>
+
+*Implements the [Iterable\<E\>][stdlib-types-iterable] trait.*
+
+A bag is an unordered collection.
+
+The following operations are supported for bags:
+
+##### `+ : (Bag<E>, Bag<E>) -> Bag<E>`
+
+Concatenates two bags.
+
+##### `in, !in : (E, Bag<E>) -> Boolean`
+
+Given a value and a bag, returns `true` if the bag contains the value (or not).
+
+:::note
+Lists in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Collection.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Collection.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## Boolean
+
+A boolean can be `true` or `false`.
+
+The following operations are supported for booleans:
+
+- `&&`: logical AND
+- `||`: logical OR
+- `!`: logical NOT
+
+:::note
+Booleans in Nextflow can be backed by any of the following Java types: `boolean`, `Boolean`.
+:::
+
+## Channel\<E\>
+
+A channel (also known as a *dataflow channel* or *queue channel*) is an asynchronous sequence of values of type `E`. It is used to facilitate dataflow logic in a workflow.
+
+See [Dataflow][dataflow-page] for an overview of dataflow types. See [Operators][operator-page] or the available methods for channels.
+
+## Duration
+
+A Duration represents a duration of time with millisecond precision.
+
+A Duration can be created by adding a unit suffix to an integer (e.g. `1.h`), or by explicitly casting to `Duration`:
+
+```nextflow
+// integer with suffix
+oneDay = 24.h
+
+// integer value (milliseconds)
+oneSecond = 1000 as Duration
+
+// simple string value
+oneHour = '1h' as Duration
+
+// complex string value
+complexDuration = '1day 6hours 3minutes 30seconds' as Duration
+```
+
+The following suffixes are available:
+
+| Unit                            | Description  |
+| ------------------------------- | ------------ |
+| `ms`, `milli`, `millis`         | Milliseconds |
+| `s`, `sec`, `second`, `seconds` | Seconds      |
+| `m`, `min`, `minute`, `minutes` | Minutes      |
+| `h`, `hour`, `hours`            | Hours        |
+| `d`, `day`, `days`              | Days         |
+
+Durations can be compared like numbers, and they support basic arithmetic operations:
+
+```nextflow
+a = 1.h
+b = 2.h
+
+assert a < b
+assert a + a == b
+assert b - a == a
+assert a * 2 == b
+assert b / 2 == a
+```
+
+The following methods are available for a Duration:
+
+##### `toDays() -> Integer`
+
+Get the duration value in days (rounded down).
+
+##### `toHours() -> Integer`
+
+Get the duration value in hours (rounded down).
+
+##### `toMillis() -> Integer`
+
+Get the duration value in milliseconds.
+
+##### `toMinutes() -> Integer`
+
+Get the duration value in minutes (rounded down).
+
+##### `toSeconds() -> Integer`
+
+Get the duration value in seconds (rounded down).
+
+:::note
+These methods are also available as `getDays()`, `getHours()`, `getMillis()`, `getMinutes()`, and `getSeconds()`.
+:::
+
+## Float
+
+A float is a floating-point number (i.e. real number) that can be positive or negative.
+
+The following operations are supported for floats:
+
+- `+, -, *, /`: addition, subtraction, multiplication, division
+- `**`: exponentation
+
+:::note
+Floats in Nextflow can be backed by any of the following Java types: `float`, `double`, `Float`, `Double`.
+:::
+
+## Integer
+
+An integer is a whole number that can be positive or negative.
+
+The following operations are supported for integers:
+
+- `+, -, *, /`: addition, subtraction, multiplication, integer division
+- `%`: remainder of integer division (i.e. modulus)
+- `**`: exponentation
+- `&`, `|`, `^`, `~`: bitwise AND, OR, XOR, NOT
+- `<<`, `>>`: left and right bit-shift
+
+:::note
+Integers in Nextflow can be backed by any of the following Java types: `int`, `long`, `Integer`, `Long`.
+:::
+
+## Iterable\<E\>
+
+*Implemented by the following types: [Bag\<E\>][stdlib-types-bag], [List\<E\>][stdlib-types-list], [Set\<E\>][stdlib-types-set]*
+
+`Iterable` is a trait implemented by collection types that support iteration.
+
+Types that implement `Iterable` can be passed as an `Iterable` parameter of a method, and they can use all of the methods described below.
+
+The following methods are available for iterables:
+
+##### `any( condition: (E) -> Boolean ) -> Boolean`
+
+Returns `true` if any element in the iterable satisfies the given condition.
+
+##### `collect( transform: (E) -> R ) -> Iterable<R>`
+
+Returns a new iterable with each element transformed by the given closure.
+
+##### `collectMany( transform: (E) -> Iterable<R> ) -> Iterable<R>`
+
+Transforms each element in the iterable into a collection with the given closure and concatenates the resulting collections into a list.
+
+##### `contains( value: E ) -> Boolean`
+
+Returns `true` if the iterable contains the given value.
+
+##### `each( action: (E) -> () )`
+
+Invokes the given closure for each element in the iterable.
+
+##### `every( condition: (E) -> Boolean ) -> Boolean`
+
+Returns `true` if every element in the iterable satisfies the given condition.
+
+##### `findAll( condition: (E) -> Boolean ) -> Iterable<E>`
+
+Returns the elements in the iterable that satisfy the given condition.
+
+##### `groupBy( transform: (E) -> K ) -> Map<K,Iterable<E>>`
+
+Collect the elements of an iterable into groups based on a matching key. The closure should return the key for a given element.
+
+##### `inject( accumulator: (E,E) -> E ) -> E`
+
+Apply the given accumulator to each element in the iterable and return the final accumulated value. The closure should accept two parameters, corresponding to the current accumulated value and the current iterable element, and return the next accumulated value.
+
+The first element from the iterable is used as the initial accumulated value.
+
+##### `inject( initialValue: R, accumulator: (R,E) -> R ) -> R`
+
+Apply the given accumulator to each element in the iterable and return the final accumulated value. The closure should accept two parameters, corresponding to the current accumulated value and the current iterable element, and return the next accumulated value.
+
+##### `isEmpty() -> Boolean`
+
+Returns `true` if the iterable is empty.
+
+##### `join( separator: String = '' ) -> String`
+
+Concatenates the string representation of each element in the iterable, with the given string as the separator between each element.
+
+##### `max() -> E`
+
+Returns the maximum element in the iterable.
+
+##### `max( comparator: (E) -> R ) -> E`
+
+Returns the maximum element in the iterable according to the given closure.
+
+The closure should follow the same semantics as the closure parameter of `toSorted()`.
+
+##### `max( comparator: (E,E) -> Integer ) -> E`
+
+Returns the maximum element in the iterable according to the given closure.
+
+The closure should follow the same semantics as the closure parameter of `toSorted()`.
+
+##### `min() -> E`
+
+Returns the minimum element in the iterable.
+
+##### `min( comparator: (E,E) -> Integer ) -> E`
+
+Returns the minimum element in the iterable according to the given closure.
+
+The closure should follow the same semantics as the closure parameter of `toSorted()`.
+
+##### `size() -> Integer`
+
+Returns the number of elements in the iterable.
+
+##### `sum() -> E`
+
+Returns the sum of the elements in the iterable. The elements should support addition (`+`).
+
+##### `sum( transform: (E) -> R ) -> R`
+
+Transforms each element in the iterable with the given closure and returns the sum. The values returned by the closure should support addition (`+`).
+
+##### `toList() -> List<E>`
+
+Converts the iterable to a list.
+
+:::danger
+Converting an unordered collection to a list can lead to non-deterministic behavior. Consider using `toSorted()` instead to ensure a deterministic ordering. See [Non-deterministic process inputs][cache-nondeterministic-inputs] for more information.
+:::
+
+##### `toSet() -> Set<E>`
+
+Converts the iterable to a set. Duplicate elements are excluded.
+
+##### `toSorted() -> List<E>`
+
+Returns a sorted list of the iterable's elements.
+
+##### `toSorted( comparator: (E) -> R ) -> List<E>`
+
+Returns the iterable as a list sorted according to the given closure.
+
+The closure should accept one parameter and transform each element into the value that will be used for comparisons.
+
+##### `toSorted( comparator: (E,E) -> Integer ) -> List<E>`
+
+Returns the iterable as a list sorted according to the given closure.
+
+The closure should accept two parameters and return a negative integer, zero, or a positive integer to denote whether the first argument is less than, equal to, or greater than the second.
+
+##### `toUnique() -> Iterable<E>`
+
+Returns a shallow copy of the iterable with duplicate elements excluded.
+
+**`toUnique( comparator: (E) -> R ) -> Iterable<E>`**
+
+##### `toUnique( comparator: (E,E) -> Integer ) -> Iterable<E>`
+
+Returns a shallow copy of the iterable with duplicate elements excluded.
+
+The closure should follow the same semantics as the closure parameter of `toSorted()`.
+
+:::note
+Iterables in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Iterable.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/Iterable.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## List\<E\>
+
+*Implements the [Iterable\<E\>][stdlib-types-iterable] trait.*
+
+A list is an ordered collection of elements of type `E`. See [Lists][script-list] for an overview.
+
+The following operations are supported for lists:
+
+##### `+ : (List<E>, List<E>) -> List<E>`
+
+Concatenates two lists.
+
+##### `* : (List<E>, Integer) -> List<E>`
+
+Given a list and an integer *n*, repeats the list *n* times.
+
+##### `[] : (List<E>, Integer) -> E`
+
+Given a list and an index, returns the element at the given index in the list, or `null` if the index is out of range.
+
+##### `in, !in : (E, List<E>) -> Boolean`
+
+Given a value and a list, returns `true` if the list contains the value (or not).
+
+The following methods are available for a list:
+
+##### `collate( size: Integer, keepRemainder: Boolean = true ) -> List<List<E>>`
+
+Collates the list into a list of sub-lists of length `size`. If `keepRemainder` is `true`, any remaining elements are included as a partial sub-list, otherwise they are excluded.
+
+For example:
+```nextflow
+assert [1, 2, 3, 4, 5, 6, 7].collate(3)        == [[1, 2, 3], [4, 5, 6], [7]]
+assert [1, 2, 3, 4, 5, 6, 7].collate(3, false) == [[1, 2, 3], [4, 5, 6]]
+```
+
+##### `collate( size: Integer, step: Integer, keepRemainder: Boolean = true ) -> List<List<E>>`
+
+Collates the list into a list of sub-lists of length `size`, stepping through the list `step` elements for each sub-list. If `keepRemainder` is `true`, any remaining elements are included as a partial sub-list, otherwise they are excluded.
+
+For example:
+
+```nextflow
+assert [1, 2, 3, 4].collate(3, 1)        == [[1, 2, 3], [2, 3, 4], [3, 4], [4]]
+assert [1, 2, 3, 4].collate(3, 1, false) == [[1, 2, 3], [2, 3, 4]]
+```
+
+##### `find( condition: (E) -> Boolean ) -> E`
+
+Returns the first element in the list that satisfies the given condition.
+
+##### `first() -> E`
+
+Returns the first element in the list. Raises an error if the list is empty.
+
+##### `getIndices() -> List<Integer>`
+
+Returns the list of integers from 0 to *n - 1*, where *n* is the number of elements in the list.
+
+##### `head() -> E`
+
+Equivalent to `first()`.
+
+##### `indexOf( value: E ) -> Integer`
+
+Returns the index of the first occurrence of the given value in the list, or -1 if the list does not contain the value.
+
+##### `init() -> List<E>`
+
+Returns a shallow copy of the list with the last element excluded.
+
+##### `last() -> E`
+
+Returns the last element in the list. Raises an error if the list is empty.
+
+##### `reverse() -> List<E>`
+
+Returns a shallow copy of the list with the elements reversed.
+
+##### `subList( fromIndex: Integer, toIndex: Integer ) -> List<E>`
+
+Returns the portion of the list between the given `fromIndex` (inclusive) and `toIndex` (exclusive).
+
+##### `tail() -> List<E>`
+
+Returns a shallow copy of the list with the first element excluded.
+
+##### `take( n: Integer ) -> List<E>`
+
+Returns the first *n* elements of the list.
+
+##### `takeWhile( condition: (E) -> Boolean ) -> List<E>`
+
+Returns the longest prefix of the list where each element satisfies the given condition.
+
+##### `withIndex() -> List<(E,Integer)>`
+
+Returns a list of 2-tuples corresponding to the value and index of each element in the list.
+
+:::note
+Lists in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/List.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/List.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## Map\<K,V\>
+
+A map associates or "maps" keys of type `K` to values of type `V`. Each key can map to at most one value -- a map cannot contain duplicate keys. See [Maps][script-map] for an overview.
+
+The following operations are supported for maps:
+
+`+ : (Map<K,V>, Map<K,V>) -> Map<K,V>`
+
+Concatenates two maps. If a key exists in both maps, the mapping from the right-hand side is used.
+
+##### `[] : (Map<K,V>, K) -> V`
+
+Given a map and a key, returns the value for the given key in the map, or `null` if the key is not in the map.
+
+##### `in, !in : (K, Map<K,V>) -> Boolean`
+
+Given a key and a map, returns `true` if the map contains the key and the corresponding value is *truthy* (e.g. not `null`, `0`, or `false`).
+
+The following methods are available for a map:
+
+##### `any( condition: (K,V) -> Boolean ) -> Boolean`
+
+Returns `true` if any key-value pair in the map satisfies the given condition. The closure should accept two parameters corresponding to the key and value of an entry.
+
+##### `containsKey( key: K ) -> Boolean`
+
+Returns `true` if the map contains a mapping for the given key.
+
+##### `containsValue( value: V ) -> Boolean`
+
+Returns `true` if the map maps one or more keys to the given value.
+
+##### `each( action: (K,V) -> () )`
+
+Invokes the given closure for each key-value pair in the map. The closure should accept two parameters corresponding to the key and value of an entry.
+
+##### `entrySet() -> Set<(K,V)>`
+
+Returns a set of the key-value pairs in the map.
+
+##### `every( condition: (K,V) -> Boolean ) -> Boolean`
+
+Returns `true` if every key-value pair in the map satisfies the given condition. The closure should accept two parameters corresponding to the key and value of an entry.
+
+##### `isEmpty() -> Boolean`
+
+Returns `true` if the map is empty.
+
+##### `keySet() -> Set<K>`
+
+Returns a set of the keys in the map.
+
+##### `size() -> Integer`
+
+Returns the number of key-value pairs in the map.
+
+##### `subMap( keys: Iterable<K> ) -> Map<K,V>`
+
+Returns a sub-map containing the given keys.
+
+##### `values() -> Bag<V>`
+
+Returns a collection of the values in the map.
+
+:::note
+Maps in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Map.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Map.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## MemoryUnit
+
+A MemoryUnit represents a quantity of bytes.
+
+A MemoryUnit can be created by adding a unit suffix to an integer (e.g. `1.GB`), or by explicitly casting to `MemoryUnit`:
+
+```nextflow
+// integer with suffix
+oneMegabyte = 1.MB
+
+// integer value (bytes)
+oneKilobyte = 1024 as MemoryUnit
+
+// string value
+oneGigabyte = '1 GB' as MemoryUnit
+```
+
+The following suffixes are available:
+
+| Unit | Description |
+| ---- | ----------- |
+| `B`  | Bytes       |
+| `KB` | Kilobytes   |
+| `MB` | Megabytes   |
+| `GB` | Gigabytes   |
+| `TB` | Terabytes   |
+| `PB` | Petabytes   |
+| `EB` | Exabytes    |
+| `ZB` | Zettabytes  |
+
+:::note
+Technically speaking, a kilobyte is equal to 1000 bytes, whereas 1024 bytes is called a "kibibyte" and abbreviated as "KiB", and so on for the other units. In practice, however, kilobyte is commonly understood to mean 1024 bytes, and Nextflow follows this convention in its implementation as well as this documentation.
+:::
+
+Memory units can be compared like numbers, and they support basic arithmetic operations:
+
+```nextflow
+a = 1.GB
+b = 2.GB
+
+assert a < b
+assert a + a == b
+assert b - a == a
+assert a * 2 == b
+assert b / 2 == a
+```
+
+The following methods are available for a `MemoryUnit` object:
+
+##### `toBytes() -> Integer`
+
+Get the memory value in bytes (B).
+
+##### `toGiga() -> Integer`
+
+Get the memory value in gigabytes (rounded down), where 1 GB = 1024 MB.
+
+##### `toKilo() -> Integer`
+
+Get the memory value in kilobytes (rounded down), where 1 KB = 1024 B.
+
+##### `toMega() -> Integer`
+
+Get the memory value in megabytes (rounded down), where 1 MB = 1024 KB.
+
+##### `toUnit( unit: String ) -> Integer`
+
+Get the memory value in terms of a given unit (rounded down). The unit can be one of: `'B'`, `'KB'`, `'MB'`, `'GB'`, `'TB'`, `'PB'`, `'EB'`, `'ZB'`.
+
+:::note
+These methods are also available as `getBytes()`, `getGiga()`, `getKilo()`, and `getMega()`.
+:::
+
+## Path
+
+A Path is a handle for hierarchichal paths such as local files and directories, HTTP/FTP URLs, and object storage paths (e.g. Amazon S3).
+
+The `file()` function can be used to get a Path for a given filename or URL:
+
+```nextflow
+def hello = file('hello.txt')
+println hello.text
+```
+
+The `files()` function can be used to get a collection of Paths from a glob pattern:
+
+```nextflow
+def inputs = files('*.txt')
+inputs.each { input ->
+  println "${input.name}: ${input.text}"
+}
+```
+
+The following sections describe the methods that are available for paths.
+
+:::note
+Paths in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/nio/file/Path.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/nio/file/Path.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+<h3>Operations</h3>
+
+The following operations are supported for paths:
+
+##### `/ : (Path, String) -> Path`
+
+Resolves a relative path string against a directory path. Equivalent to `resolve()`.
+
+##### `<< : (Path, String)`
+
+Appends text to a file without replacing existing content. Equivalent to `append()`.
+
+<h3>Getting attributes</h3>
+
+The following methods are useful for getting attributes of a path:
+
+##### `exists() -> Boolean`
+
+Returns `true` if the path exists.
+
+##### `getBaseName() -> String`
+
+Gets the path name without its extension, e.g. `/some/path/file.tar.gz` -> `file.tar`.
+
+##### `getExtension() -> String`
+
+Gets the path extension, e.g. `/some/path/file.txt` -> `txt`.
+
+##### `getName() -> String`
+
+Gets the path name, e.g. `/some/path/file.txt` -> `file.txt`.
+
+##### `getSimpleName() -> String`
+
+Gets the path name without any extension, e.g. `/some/path/file.tar.gz` -> `file`.
+
+##### `getParent() -> Path`
+
+Gets the path parent path, e.g. `/some/path/file.txt` -> `/some/path`.
+
+##### `getScheme() -> String`
+
+Gets the path URI scheme, e.g. `s3://some-bucket/hello.txt` -> `s3`.
+
+##### `isDirectory() -> Boolean`
+
+Returns `true` if the path is a directory.
+
+##### `isEmpty() -> Boolean`
+
+Returns `true` if the path is empty or does not exist.
+
+##### `isFile() -> Boolean`
+
+Returns `true` if the path is a file (i.e. not a directory).
+
+##### `isHidden() -> Boolean`
+
+Returns `true` if the path is hidden.
+
+##### `isLink() -> Boolean`
+
+Returns `true` if the path is a symbolic link.
+
+##### `lastModified() -> Integer`
+
+Returns the path last modified timestamp in Unix time (i.e. milliseconds since January 1, 1970).
+
+##### `relativize(other: Path) -> Path`
+
+Returns the relative path between this path and the given path.
+
+##### `resolve(other: String) -> Path`
+
+Resolves the given path string against this path.
+
+##### `resolveSibling(other: String) -> Path`
+
+Resolves the given path string against this path's parent path.
+
+##### `size() -> Integer`
+
+Gets the file size in bytes.
+
+##### `toUriString() -> String`
+
+Gets the file path along with the protocol scheme:
+
+```nextflow
+def ref = file('s3://some-bucket/hello.txt')
+
+assert ref.toString() == '/some-bucket/hello.txt'
+assert "$ref" == '/some-bucket/hello.txt'
+assert ref.toUriString() == 's3://some-bucket/hello.txt'
+```
+
+<h3>Reading</h3>
+
+The following methods are available for reading files:
+
+##### `eachByte( action: (byte) -> () )`
+
+Iterates over the file, applying the specified closure to each byte.
+
+##### `eachLine( action: (String) -> () )`
+
+Iterates over the file, applying the specified closure to each line.
+
+##### `getBytes() -> byte[]`
+
+Returns the file content as a byte array.
+
+##### `getText() -> String`
+
+Returns the file content as a string.
+
+##### `newInputStream() -> InputStream`
+
+Returns an [InputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/InputStream.html) object to read a binary file.
+
+##### `newReader() -> Reader`
+
+Returns a [Reader](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Reader.html) object to read a text file.
+
+##### `readLines() -> List<String>`
+
+Reads the file line by line and returns the content as a list of strings.
+
+##### `withInputStream( action: (InputStream) -> () )`
+
+Opens a file for reading and lets you access it with an [InputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/InputStream.html) object.
+
+##### `withReader( action: (Reader) -> () )`
+
+Opens a file for reading and lets you access it with a [Reader](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Reader.html) object.
+
+<h3>Writing</h3>
+
+The following methods are available for writing to files:
+
+##### `append( text: String )`
+
+Appends text to a file without replacing existing content.
+
+##### `newOutputStream() -> OutputStream`
+
+Creates an [OutputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/OutputStream.html) object that allows you to write binary data to a file.
+
+##### `newPrintWriter() -> PrintWriter`
+
+Creates a [PrintWriter](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/PrintWriter.html) object that allows you to write formatted text to a file.
+
+##### `newWriter() -> Writer`
+
+Creates a [Writer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Writer.html) object that allows you to save text data to a file.
+
+##### `setBytes( bytes: byte[] )`
+
+Writes a byte array to a file. Equivalent to setting the `bytes` property.
+
+##### `setText( text: String )`
+
+Writes text to a file. Equivalent to setting the `text` property.
+
+##### `withOutputStream( action: (OutputStream) -> () )`
+
+Applies the specified closure to an [OutputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/OutputStream.html) object, closing it when finished.
+
+##### `withPrintWriter( action: (PrintWriter) -> () )`
+
+Applies the specified closure to a [PrintWriter](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/PrintWriter.html) object, closing it when finished.
+
+##### `withWriter( action: (Writer) -> () )`
+
+Applies the specified closure to a [Writer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Writer.html) object, closing it when finished.
+
+##### `write( text: String )`
+
+Writes a string to a file, replacing any existing content.
+
+<h3>Filesystem operations</h3>
+
+The following methods are available for manipulating files and directories in a filesystem:
+
+##### `copyTo( target: Path )`
+
+Copies a source file or directory to a target file or directory.
+
+*When copying a file to another file:* if the target file already exists, it will be replaced.
+
+```nextflow
+file('/some/path/my_file.txt').copyTo('/another/path/new_file.txt')
+```
+
+*When copying a file to a directory:* the file will be copied into the directory, replacing any file with the same name.
+
+```nextflow
+file('/some/path/my_file.txt').copyTo('/another/path')
+```
+
+*When copying a directory to another directory:* if the target directory already exists, the source directory will be copied into the target directory, replacing any sub-directory with the same name. If the target path does not exist, it will be created automatically.
+
+```nextflow
+file('/any/dir_a').moveTo('/any/dir_b')
+```
+
+The result of the above example depends on the existence of the target directory. If the target directory exists, the source is moved into the target directory, resulting in the path `/any/dir_b/dir_a`. If the target directory does not exist, the source is just renamed to the target name, resulting in the path `/any/dir_b`.
+
+
+:::note
+The `copyTo()` function follows the semantics of the Linux command `cp -r <source> <target>`, with the following caveat: while Linux tools often treat paths ending with a slash (e.g. `/some/path/name/`) as directories, and those not (e.g. `/some/path/name`) as regular files, Nextflow (due to its use of the Java files API) views both of these paths as the same file system object. If the path exists, it is handled according to its actual type (i.e. as a regular file or as a directory). If the path does not exist, it is treated as a regular file, with any missing parent directories created automatically.
+:::
+
+##### `delete() -> Boolean`
+
+Deletes the file or directory at the given path, returning `true` if the operation succeeds, and `false` otherwise:
+
+```nextflow
+myFile = file('some/file.txt')
+result = myFile.delete()
+println result ? "OK" : "Cannot delete: $myFile"
+```
+
+If a directory is not empty, it will not be deleted and `delete()` will return `false`.
+
+##### `deleteDir() -> Boolean`
+
+Deletes a directory and all of its contents.
+
+```nextflow
+file('any/path').deleteDir()
+```
+
+##### `getPermissions() -> String`
+
+Returns a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation), e.g. `'rw-rw-r--'`.
+
+##### `list() -> List<String>`
+
+Returns the first-level elements (files and directories) of a directory as a list of strings.
+
+##### `listFiles() -> List<Path>`
+
+Returns the first-level elements (files and directories) of a directory as a list of Paths.
+
+##### `mkdir() -> Boolean`
+
+Creates a directory at the given path, returning `true` if the directory is created successfully, and `false` otherwise:
+
+```nextflow
+myDir = file('any/path')
+result = myDir.mkdir()
+println result ? "OK" : "Cannot create directory: $myDir"
+```
+
+If the parent directories do not exist, the directory will not be created and `mkdir()` will return `false`.
+
+##### `mkdirs() -> Boolean`
+
+Creates a directory at the given path, including any nonexistent parent directories:
+
+```nextflow
+file('any/path').mkdirs()
+```
+
+##### `mklink( linkName: String, [options] ) -> Path`
+
+Creates a *filesystem link* to a given path:
+
+```nextflow
+myFile = file('/some/path/file.txt')
+myFile.mklink('/user/name/link-to-file.txt')
+```
+
+Returns the Path of the link to create.
+
+Available options:
+
+###### `hard: Boolean`
+
+When `true`, creates a *hard* link, otherwise creates a *soft* (aka *symbolic*) link (default: `false`).
+
+###### `overwrite: Boolean`
+
+When `true`, overwrites any existing file with the same name, otherwise throws a [FileAlreadyExistsException](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/nio/file/FileAlreadyExistsException.html) (default: `false`).
+
+##### `moveTo( target: Path )`
+
+Moves a source file or directory to a target file or directory. Follows the same semantics as `copyTo()`.
+
+##### `renameTo( target: String ) -> Boolean`
+
+Rename a file or directory:
+
+```nextflow
+file('my_file.txt').renameTo('new_file_name.txt')
+```
+
+##### `setPermissions( permissions: String ) -> Boolean`
+
+Sets a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation):
+
+```nextflow
+myFile.setPermissions('rwxr-xr-x')
+```
+
+##### `setPermissions( owner: Integer, group: Integer, other: Integer ) -> Boolean`
+
+Sets a file's permissions using the [numeric notation](http://en.wikipedia.org/wiki/File_system_permissions#Numeric_notation), i.e. as three digits representing the **owner**, **group**, and **other** permissions:
+
+```nextflow
+myFile.setPermissions(7,5,5)
+```
+
+The following methods are available for listing and traversing directories:
+
+##### `eachDir( action: (Path) -> () )`
+
+Iterates through first-level directories only.
+
+##### `eachDirMatch( nameFilter: String, action: (Path) -> () )`
+
+Iterates through directories whose names match the given filter.
+
+##### `eachDirRecurse( action: (Path) -> () )`
+
+Iterates through directories depth-first (regular files are ignored).
+
+##### `eachFile( action: (Path) -> () )`
+
+Iterates through first-level files and directories.
+
+##### `eachFileMatch( nameFilter: String, action: (Path) -> () )`
+
+Iterates through files and directories whose names match the given filter.
+
+##### `eachFileRecurse( action: (Path) -> () )`
+
+Iterates through files and directories depth-first.
+
+<h3>Splitting files</h3>
+
+The following methods are available for splitting and counting the records in files:
+
+##### `countFasta() -> Integer`
+
+Counts the number of records in a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file. See the [splitFasta][operator-splitfasta] operator for available options.
+
+##### `countFastq() -> Integer`
+
+Counts the number of records in a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file. See the [splitFastq][operator-splitfastq] operator for available options.
+
+##### `countJson() -> Integer`
+
+Counts the number of records in a JSON file. See the [splitJson][operator-splitjson] operator for available options.
+
+##### `countLines() -> Integer`
+
+Counts the number of lines in a text file. See the [splitText][operator-splittext] operator for available options.
+
+##### `splitCsv() -> List<?>`
+
+Splits a CSV file into a list of records. See the [splitCsv][operator-splitcsv] operator for available options.
+
+##### `splitFasta() -> List<?>`
+
+Splits a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file into a list of records. See the [splitFasta][operator-splitfasta] operator for available options.
+
+##### `splitFastq() -> List<?>`
+
+Splits a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file into a list of records. See the [splitFastq][operator-splitfastq] operator for available options.
+
+##### `splitJson() -> List<?>`
+
+Splits a JSON file into a list of records. See the [splitJson][operator-splitjson] operator for available options.
+
+##### `splitText() -> List<String>`
+
+Splits a text file into a list of lines. See the [splitText][operator-splittext] operator for available options.
+
+## Set\<E\>
+
+*Implements the [Iterable\<E\>][stdlib-types-iterable] trait.*
+
+A set is an unordered collection of values of type `E` which cannot contain duplicates.
+
+A set can be created from a list using the `toSet()` method:
+
+```nextflow
+[1, 2, 2, 3].toSet()
+// -> [1, 2, 3]
+```
+
+The following operations are supported for sets:
+
+##### `+ : (Set<E>, Iterable<E>) -> Set<E>`
+
+Given a set and an iterable, returns a new set containing the elements of both collections.
+
+##### `- : (Set<E>, Iterable<E>) -> Set<E>`
+
+Given a set and an iterable, returns a shallow copy of the set minus the elements of the iterable.
+
+##### `in, !in : (E, Set<E>) -> Boolean`
+
+Given a value and a set, returns `true` if the set contains the value (or not).
+
+The following methods are available for a set:
+
+##### `intersect( right: Iterable<E> ) -> Set<E>`
+
+Returns the intersection of the set and the given iterable.
+
+:::note
+Sets in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Set.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Set.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## String
+
+A string is an immutable sequence of characters. See [Strings][script-string] for an overview of strings.
+
+The following operations are supported for strings:
+
+##### `+ : (String, String) -> String`
+
+Concatenates two strings.
+
+##### `* : (String, Integer) -> String`
+
+Given a string and an integer *n*, repeats the string *n* times.
+
+##### `[] : (String, Integer) -> char`
+
+Given a string and an index, returns the character at the given index in the string.
+
+##### `~ : (String) -> Pattern`
+
+Creates a regular expression from a string.
+
+See [Pattern](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/regex/Pattern.html) in the Java standard library for more information.
+
+##### `=~ : (String, String) -> Matcher`
+
+Given a string and a pattern, creates a matcher that is truthy if the pattern occurs anywhere in the string.
+
+See [Matcher](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/regex/Matcher.html) in the Java standard library for more information.
+
+##### `==~ : (String, String) -> Boolean`
+
+Given a string and a pattern, returns `true` if the string matches the pattern exactly.
+
+The following methods are available for a string:
+
+##### `contains( str: String ) -> Boolean`
+
+Returns `true` if the given substring occurs anywhere in the string.
+
+##### `endsWith( suffix: String ) -> Boolean`
+
+Returns `true` if the string ends with the given suffix.
+
+##### `execute() -> Process`
+
+Execute the string as a command. Returns a [Process](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/Process.html) which provides the exit status and standard input/output/error of the executed command.
+
+##### `indexOf( str: String ) -> Integer`
+
+Returns the index within the string of the first occurrence of the given substring. Returns -1 if the string does not contain the substring.
+
+##### `indexOf( str: String, fromIndex: Integer ) -> Integer`
+
+Returns the index within the string of the first occurrence of the given substring, starting the search at the given index. Returns -1 if the string does not contain the substring.
+
+##### `isBlank() -> Boolean`
+
+Returns `true` if the string is empty or contains only whitespace characters.
+
+##### `isEmpty() -> Boolean`
+
+Returns `true` if the string is empty (i.e. `length()` is 0).
+
+##### `isDouble() -> Boolean`
+
+Returns `true` if the string can be parsed as a 64-bit (double precision) floating-point number.
+
+##### `isFloat() -> Boolean`
+
+Returns `true` if the string can be parsed as a 32-bit floating-point number.
+
+##### `isInteger() -> Boolean`
+
+Returns `true` if the string can be parsed as a 32-bit integer.
+
+##### `isLong() -> Boolean`
+
+Returns `true` if the string can be parsed as a 64-bit (long) integer.
+
+##### `lastIndexOf( str: String ) -> Integer`
+
+Returns the index within the string of the last occurrence of the given substring. Returns -1 if the string does not contain the substring.
+
+##### `lastIndexOf( str: String, fromIndex: Integer ) -> Integer`
+
+Returns the index within the string of the last occurrence of the given substring, searching backwards starting at the given index. Returns -1 if the string does not contain the substring.
+
+##### `length() -> Integer`
+
+Returns the length of the string.
+
+##### `md5() -> String`
+
+Returns the MD5 checksum of the string.
+
+##### `replace( target: String, replacement: String ) -> String`
+
+Returns a new string in which each occurrence of the target string is replaced with the given replacement string.
+
+##### `replaceAll( regex: String, replacement: String ) -> String`
+
+Returns a new string in which each occurrence of the given regular expression is replaced with the given replacement string.
+
+##### `replaceFirst( regex: String, replacement: String ) -> String`
+
+Returns a new string in which the first occurrence of the given regular expression is replaced with the given replacement string.
+
+##### `sha256() -> String`
+
+Returns the SHA-256 checksum of the string.
+
+##### `startsWith( prefix: String ) -> Boolean`
+
+Returns `true` if the string ends with the given prefix.
+
+##### `strip() -> String`
+
+Returns a copy of the string with all leading and trailing whitespace removed.
+
+##### `stripIndent() -> String`
+
+Returns a copy of the string with leading spaces on each line removed.
+
+The number of spaces to remove is determined by the line with the least number of leading spaces, excluding lines with only whitespace.
+
+##### `stripLeading() -> String`
+
+Returns a copy of the string with all leading whitespace removed.
+
+##### `stripTrailing() -> String`
+
+Returns a copy of the string with all trailing whitespace removed.
+
+##### `substring( beginIndex: Integer ) -> String`
+
+Returns a substring of this string.
+
+##### `substring( beginIndex: Integer, endIndex: Integer ) -> String`
+
+Returns a substring of this string.
+
+##### `toBoolean() -> Boolean`
+
+Returns `true` if the trimmed string is "true", "y", or "1" (ignoring case).
+
+##### `toDouble() -> Float`
+
+Parses the string into a 64-bit (double precision) floating-point number.
+
+##### `toFloat() -> Float`
+
+Parses the string into a 32-bit floating-point number.
+
+##### `toInteger() -> Integer`
+
+Parses the string into a 32-bit integer.
+
+##### `toLong() -> Integer`
+
+Parses the string into a 64-bit (long) integer.
+
+##### `toLowerCase() -> String`
+
+Returns a copy of this string with all characters converted to lower case.
+
+##### `toUpperCase() -> String`
+
+Returns a copy of this string with all characters converted to upper case.
+
+##### `tokenize( delimiters: String ) -> List<String>`
+
+Splits the string into a list of substrings using the given delimiters. Each character in the delimiter string is treated as a separate delimiter.
+
+:::note
+Strings in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/String.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## Tuple
+
+A tuple is a fixed sequence of values, where each value can have its own type. Tuples can be created using the `tuple` function.
+
+The following operations are supported for tuples:
+
+##### `[] : (Tuple, Integer) -> ?`
+
+Given a tuple and an index, returns the tuple element at the index.
+
+## Value\<V\>
+
+A dataflow value (also known as a *value channel*) is an asynchronous value of type `V`. It is used to facilitate dataflow logic in a workflow.
+
+See [Dataflow][dataflow-page] for an overview of dataflow types.
+
+The following methods are available for a dataflow value:
+
+##### `flatMap( transform: (V) -> Iterable<R> ) -> Channel<R>`
+
+Transforms the dataflow value into a collection with the given closure and emits the resulting values in a dataflow channel.
+
+##### `map( transform: (V) -> R ) -> Value<R>`
+
+Transforms the dataflow value into another dataflow value with the given closure.
+
+##### `subscribe( action: (V) -> () )`
+
+Invokes the given closure on the dataflow value.
+
+##### `view() -> Value<V>`
+
+Prints the dataflow value to standard output.
+
+##### `view( transform: (V) -> String ) -> Value<V>`
+
+Transforms the dataflow value using the given closure and print the result to standard output.
+
+## VersionNumber
+
+A VersionNumber represents a semantic or calendar version number.
+
+The following methods are available for a VersionNumber:
+
+##### `getMajor() -> String`
+
+Get the major version number, i.e. the first version component.
+
+##### `getMinor() -> String`
+
+Get the minor version number, i.e. the second version component.
+
+##### `getPatch() -> String`
+
+Get the patch version number, i.e. the third version component.
+
+##### `matches( condition: String ) -> Boolean`
+
+Check whether the version satisfies a version requirement.
+
+
+The version requirement string can be prefixed with the usual comparison operators:
+  - `=` or `==`: equal to
+  - `<` (`<=`): less than (or equal to)
+  - `>` (`>=`): greater than (or equal to)
+  - `!=` or `<>`: not equal
+
+  For example:
+
+  ```nextflow
+  if( !nextflow.version.matches('>=23.10') ) {
+      error "This workflow requires Nextflow version 23.10 or greater -- You are running version $nextflow.version"
+  }
+  ```
+
+
+Multiple constraints can be specified as a comma-separated list, e.g. `>=23.10, <=24.10`.
+
+
+Alternatively, the version can be postfixed with `+`, which is similar to `==` but also allows the last version part to be greater. For example, `23.10.1+` is satisfied by `23.10.1` and `23.10.2`, but not `23.11.x` or `23.09.x`. Additionally, `23.10.+` is equivalent to `23.10.0+`. This operator is a useful way to enforce a specific version while allowing for newer patch releases.
+
+
+[cache-nondeterministic-inputs]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#non-deterministic-process-inputs
+[dataflow-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[channel-factory]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx
+[operator-page]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx
+[operator-splitfasta]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splitfasta
+[operator-splitfastq]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splitfastq
+[operator-splitjson]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splitjson
+[operator-splittext]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splittext
+[operator-splitcsv]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splitcsv
+[script-list]: /nextflow_docs/nextflow_repo/docs/script.mdx#lists
+[script-map]: /nextflow_docs/nextflow_repo/docs/script.mdx#maps
+[script-strings]: /nextflow_docs/nextflow_repo/docs/script.mdx#strings
+[stdlib-types-bag]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#bage
+[stdlib-types-iterable]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#iterablee
+[stdlib-types-list]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#liste
+[stdlib-types-set]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#sete
diff --git a/docs/reference/stdlib.md b/docs/reference/stdlib.md
deleted file mode 100644
index 6bdf3ebd70..0000000000
--- a/docs/reference/stdlib.md
+++ /dev/null
@@ -1,12 +0,0 @@
-(stdlib-page)=
-
-# Standard library
-
-This section describes the Nextflow standard library, which consists of built-in namespaces and types.
-
-```{toctree}
-:maxdepth: 1
-stdlib-namespaces
-stdlib-types
-stdlib-groovy
-```
diff --git a/docs/reference/stdlib.mdx b/docs/reference/stdlib.mdx
new file mode 100644
index 0000000000..a53a1379e8
--- /dev/null
+++ b/docs/reference/stdlib.mdx
@@ -0,0 +1,7 @@
+import DocCardList from "@theme/DocCardList";
+
+# Standard library
+
+This section describe the Nextflow standard library, which consists of built-in namespaces and types.
+
+<DocCardList />
diff --git a/docs/reference/syntax.md b/docs/reference/syntax.mdx
similarity index 88%
rename from docs/reference/syntax.md
rename to docs/reference/syntax.mdx
index 02319d2ba7..f11c1537ff 100644
--- a/docs/reference/syntax.md
+++ b/docs/reference/syntax.mdx
@@ -1,5 +1,3 @@
-(syntax-page)=
-
 # Syntax
 
 This page provides a comprehensive description of the Nextflow language.
@@ -52,7 +50,7 @@ workflow {
 }
 ```
 
-:::{warning}
+:::warning
 Statements and script declarations can not be mixed at the same level.
 :::
 
@@ -66,7 +64,7 @@ The first line of a script can be a [shebang](https://en.wikipedia.org/wiki/Sheb
 
 ### Feature flag
 
-A feature flag declaration is an assignment. The target should be a valid {ref}`feature flag <config-feature-flags>` and the source should be a literal (i.e. number, string, boolean):
+A feature flag declaration is an assignment. The target should be a valid [feature flag][config-feature-flags] and the source should be a literal (i.e. number, string, boolean):
 
 ```nextflow
 nextflow.preview.recursion = true
@@ -131,8 +129,6 @@ params.message = 'Hello world!'
 
 Parameters supplied via command line options, params files, and config files take precedence over parameter definitions in a script.
 
-(syntax-workflow)=
-
 ### Workflow
 
 A workflow can be a *named workflow* or an *entry workflow*.
@@ -193,8 +189,6 @@ In order for a script to be executable, it must either define an entry workflow
 
 Entry workflow definitions are ignored when a script is included as a module. This way, the same script can be included as a module or executed as a pipeline.
 
-(syntax-process)=
-
 ### Process
 
 A process consists of a name and a body. The process body consists of one or more [statements](#statements). A minimal process definition must return a string:
@@ -215,7 +209,7 @@ process greet {
     errorStrategy 'retry'
     tag { "${greeting}/${name}" }
 
-    input: 
+    input:
     val greeting
     val name
 
@@ -240,13 +234,13 @@ process greet {
 
 - Sections must be defined in the order shown above, with the exception of the output section, which can also be specified after the script and stub.
 
-Each section may contain one or more statements. For directives, inputs, and outputs, these statements must be [function calls](#function-call). See {ref}`process-reference` for the set of available input qualifiers, output qualifiers, and directives.
+Each section may contain one or more statements. For directives, inputs, and outputs, these statements must be [function calls](#function-call). See [Process reference][process-reference] for the set of available input qualifiers, output qualifiers, and directives.
 
 The script section can be substituted with an exec section:
 
 ```nextflow
 process greet {
-    input: 
+    input:
     val greeting
     val name
 
@@ -260,9 +254,7 @@ process greet {
 
 The script and stub sections must return a string in the same manner as a [function](#function).
 
-See {ref}`process-page` for more information on the semantics of each process section.
-
-(syntax-process-typed)=
+See [Processes][process-page] for more information on the semantics of each process section.
 
 ### Process (typed)
 
@@ -270,7 +262,7 @@ A typed process is a process that uses static types for inputs and/or outputs:
 
 ```nextflow
 process greet {
-    input: 
+    input:
     greeting: String
     name: String
 
@@ -292,25 +284,27 @@ process greet {
 
 Typed processes may specify the following sections:
 
-`input:`
-: Consists of one or more process inputs. Each input has a name and type.
+##### `input:`
+
+Consists of one or more process inputs. Each input has a name and type.
 
-`stage:`
-: Consists of one or more stage directives. See {ref}`process-reference-typed` for the set of available stage directives.
+##### `stage:`
 
-`output:`
-: Consists of one or more *output statements*. An output statement can be a [variable name](#variable), an [assignment](#assignment), or an [expression statement](#expression-statement). An output statement must be the only output if it is an expression statement.  See {ref}`process-reference-typed` for the set of available output functions.
+Consists of one or more stage directives. See [Inputs and outputs (typed)][inputs-and-outputs-typed] for the set of available stage directives.
 
-`topic:`
-: Consists of one or more *topic statements*. A topic statement is a right-shift expression with an output value on the left side and a string on the right side.
+##### `output:`
 
-:::{note}
+Consists of one or more *output statements*. An output statement can be a [variable name](#variable), an [assignment](#assignment), or an [expression statement](#expression-statement). An output statement must be the only output if it is an expression statement.  See [Inputs and outputs (typed)][inputs-and-outputs-typed] for the set of available output functions.
+
+##### `topic:`
+
+Consists of one or more *topic statements*. A topic statement is a right-shift expression with an output value on the left side and a string on the right side.
+
+:::note
 Typed processes use the same behavior as legacy processes for all other sections.
 :::
 
-See {ref}`process-typed-page` for more information on the semantics of typed processes.
-
-(syntax-function)=
+See [Process (typed)][process-reference-typed] for more information on the semantics of typed processes.
 
 ### Function
 
@@ -360,7 +354,7 @@ enum Day {
 
 Enum values in the above example can be accessed as `Day.MONDAY`, `Day.TUESDAY`, and so on.
 
-:::{note}
+:::note
 Enum types cannot be included across modules at this time.
 :::
 
@@ -379,7 +373,7 @@ output {
 }
 ```
 
-Only one output block may be defined in a script. See {ref}`workflow-output-def` for the set of available output directives.
+Only one output block may be defined in a script. See [Workflow outputs][workflow-output-def] for the set of available output directives.
 
 ## Statements
 
@@ -567,7 +561,7 @@ def isEven2(n) {
 }
 ```
 
-:::{note}
+:::note
 If the last statement is not a return or expression statement (implicit return), it is equivalent to appending an empty return.
 :::
 
@@ -579,8 +573,9 @@ A throw statement consists of the `throw` keyword followed by an expression that
 throw new Exception('something failed!')
 ```
 
-:::{note}
-In general, the appropriate way to raise an error is to use the {ref}`error <stdlib-namespaces-global>` function:
+:::note
+In general, the appropriate way to raise an error is to use the [error][stdlib-namespaces-global] function:
+
 ```nextflow
 error 'something failed!'
 ```
@@ -657,7 +652,7 @@ def x = null
 x = 42
 ```
 
-:::{note}
+:::note
 Using a null value in certain expressions (e.g. the object of a property expression or method call) will lead to a "null reference" error. It is best to avoid the use of `null` where possible.
 :::
 
@@ -690,7 +685,7 @@ A *slashy string* is enclosed by slashes instead of quotes:
 /no escape!/
 ```
 
-:::{note}
+:::note
 A slashy string cannot be empty because it would become a line comment.
 :::
 
@@ -803,7 +798,7 @@ println result
 // -> 14
 ```
 
-See {ref}`standard library <stdlib-page>` and {ref}`operator <operator-page>` for more examples of how closures are used in practice.
+See [standard library][stdlib-page] and [operator][operator-page] for more examples of how closures are used in practice.
 
 ### Index expression
 
@@ -895,7 +890,7 @@ If the type is implicitly available in the script, the *fully-qualified type nam
 new Date()
 ```
 
-See {ref}`stdlib-page` for the set of types that are available in Nextflow scripts.
+See [Standard library][stdlib-page] for the set of types that are available in Nextflow scripts.
 
 ### Unary expressions
 
@@ -1007,7 +1002,21 @@ Compound expressions are evaluated in the following order:
 
 The following legacy features were excluded from this page because they are deprecated:
 
-- The `addParams` and `params` clauses of include declarations. See {ref}`module-params` for more information.
-- The `when:` section of a process definition. See {ref}`process-when` for more information.
-- The `shell:` section of a process definition. See {ref}`process-shell` for more information.
-- The implicit `it` closure parameter. See {ref}`script-closure` for more information.
+- The `addParams` and `params` clauses of include declarations. See [Module parameters][module-params] for more information.
+- The `when:` section of a process definition. See [When][process-when] for more information.
+- The `shell:` section of a process definition. See [Shell][process-shell] for more information.
+- The implicit `it` closure parameter. See [Closures][script-closure] for more information.
+
+[config-feature-flags]: /nextflow_docs/nextflow_repo/docs/reference/feature-flags.mdx
+[module-params]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-parameters
+[operator-page]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx
+[process-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[process-reference]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx
+[inputs-and-outputs-typed]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#inputs-and-outputs-typed
+[process-reference-typed]: /nextflow_docs/nextflow_repo/docs/process-typed.mdx
+[process-shell]: /nextflow_docs/nextflow_repo/docs/process.mdx#shell
+[process-when]: /nextflow_docs/nextflow_repo/docs/process.mdx#when
+[script-closure]: /nextflow_docs/nextflow_repo/docs/script.mdx#closures
+[stdlib-namespaces-global]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-namespaces.mdx
+[stdlib-page]: /nextflow_docs/nextflow_repo/docs/reference/stdlib.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
diff --git a/docs/reports.mdx b/docs/reports.mdx
new file mode 100644
index 0000000000..c0a040faa5
--- /dev/null
+++ b/docs/reports.mdx
@@ -0,0 +1,483 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Reports
+
+## Execution log
+
+The `nextflow log` command shows information about executed pipelines in the current folder:
+
+```bash
+nextflow log <RUN_NAME> [options]
+```
+
+:::note
+Both the [execution report](#execution-report) and the [trace file](#trace-file) must be specified when the pipeline is first called. By contrast, the `log` option is useful after a pipeline has already run and is available for every executed pipeline.
+:::
+
+By default, `log` prints the list of executed pipelines:
+
+```console
+$ nextflow log
+TIMESTAMP            RUN NAME         SESSION ID                            COMMAND
+2016-08-01 11:44:51  grave_poincare   18cbe2d3-d1b7-4030-8df4-ae6c42abaa9c  nextflow run hello
+2016-08-01 11:44:55  small_goldstine  18cbe2d3-d1b7-4030-8df4-ae6c42abaa9c  nextflow run hello -resume
+2016-08-01 11:45:09  goofy_kilby      0a1f1589-bd0e-4cfc-b688-34a03810735e  nextflow run rnatoy -with-docker
+```
+
+Specifying a run name or session id prints tasks executed by that pipeline run:
+
+```console
+$ nextflow log goofy_kilby
+/Users/../work/0b/be0d1c4b6fd6c778d509caa3565b64
+/Users/../work/ec/3100e79e21c28a12ec2204304c1081
+/Users/../work/7d/eb4d4471d04cec3c69523aab599fd4
+/Users/../work/8f/d5a26b17b40374d37338ccfe967a30
+/Users/../work/94/dfdfb63d5816c9c65889ae34511b32
+```
+
+### Customizing fields
+
+By default, only the task execution paths are printed. A custom list of fields to print can be provided via the `-f` (`-fields`) option:
+
+```console
+$ nextflow log goofy_kilby -f hash,name,exit,status
+0b/be0d1c  buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank)  0  COMPLETED
+ec/3100e7  mapping (ggal_gut)                                       0  COMPLETED
+7d/eb4d44  mapping (ggal_liver)                                     0  COMPLETED
+8f/d5a26b  makeTranscript (ggal_liver)                              0  COMPLETED
+94/dfdfb6  makeTranscript (ggal_gut)                                0  COMPLETED
+```
+
+The fields accepted by the `-f` options are the ones in the [trace file report][trace-file], as well as: script, stdout, stderr, env. List available fields using the `-l` (`-list-fields`) option.
+
+The `script` field is useful for examining script commands run in each task:
+
+```console
+$ nextflow log goofy_kilby -f name,status,script
+align_genome      COMPLETED
+   bowtie --index /data/genome input.fastq > output
+...
+```
+
+### Templates
+
+The `-t` option allows a template (string or file) to be specified. This makes it possible to create complex custom reports in any text-based format. For example, you could save this Markdown snippet to a file:
+
+```md
+## $name
+
+script:
+
+    $script
+
+exit status: $exit
+task status: $status
+task folder: $folder
+```
+
+Then, the following command will output a markdown file containing the script, exit status and folder of all executed tasks:
+
+```bash
+nextflow log goofy_kilby -t my-template.md > execution-report.md
+```
+
+### Filtering
+
+The `filter` option makes it possible to select which entries to include in the log report. Any valid groovy boolean expression on the log fields can be used to define the filter condition. For example:
+
+```bash
+nextflow log goofy_kilby -filter 'name =~ /hello.*/ && status == "FAILED"'
+```
+
+## Execution report
+
+Nextflow can create an HTML execution report: a single document which includes many useful metrics about a workflow execution. The report is organised in the three main sections: `Summary`, `Resources` and `Tasks` (see below for details).
+
+To enable the creation of this report add the `-with-report` command line option when launching the pipeline execution. For example:
+
+```bash
+nextflow run main.nf -with-report [file name]
+```
+
+The report file name can be specified as an optional parameter following the report option.
+
+### Summary
+
+The `Summary` section reports the execution status, the launch command, overall execution time and some other workflow metadata. You can see an example below:
+
+![Report summary](_static/report-summary-min.png)
+
+### Resource Usage
+
+The `Resources` section plots the distribution of resource usage for each workflow process using the interactive [plotly.js](https://plot.ly/javascript/) plotting library.
+
+Plots are shown for CPU, memory, job duration and disk I/O. They have two (or three) tabs with the raw values and a percentage representation showing what proportion of the requested resources were used. These plots are very helpful to check that task resources are used efficiently.
+
+![Usage CPUs](_static/report-resource-cpu.png)
+
+See the [Understanding task resource metrics][metrics-page] guide to learn more about how resource usage is computed in Nextflow.
+
+### Tasks
+
+The `Tasks` section lists all executed tasks, reporting for each of them the status, the actual command script, and many other metrics. You can see an example below:
+
+![Tasks](_static/report-tasks-min.png)
+
+:::note
+Nextflow collects these metrics through a background process for each job in the target environment. Make sure the following tools are available in the environment where tasks are executed: `awk`, `date`, `grep`, `ps`, `sed`, `tail`, `tee`. Moreover, some of these metrics are not reported when running on Mac OS X. See the corresponding note in the [trace file](#trace-file) section.
+:::
+
+:::warning
+A common problem when using a third party container image is that it does not include one or more of the above utilities, resulting in an empty execution report.
+:::
+
+See [Report scope][config-report] to learn more about the execution report configuration details.
+
+## Trace file
+
+Nextflow creates an execution tracing file that contains some useful information about each process executed in your pipeline script, including: submission time, start time, completion time, cpu and memory used.
+
+In order to create the execution trace file add the `-with-trace` command line option when launching the pipeline execution. For example:
+
+```bash
+nextflow run main.nf -with-trace
+```
+
+It will create a file named `trace.txt` in the current directory. The content looks similar the above example:
+
+| task_id | hash      | native_id | name           | status    | exit | submit                  | duration | walltime | %cpu   | rss      | vmem     | rchar    | wchar    |
+| ------- | --------- | --------- | -------------- | --------- | ---- | ----------------------- | -------- | -------- | ------ | -------- | -------- | -------- | -------- |
+| 19      | 45/ab752a | 2032      | blast (1)      | COMPLETED | 0    | 2014-10-23 16:33:16.288 | 1m       | 5s       | 0.0%   | 29.8 MB  | 354 MB   | 33.3 MB  | 0        |
+| 20      | 72/db873d | 2033      | blast (2)      | COMPLETED | 0    | 2014-10-23 16:34:17.211 | 30s      | 10s      | 35.7%  | 152.8 MB | 428.1 MB | 192.7 MB | 1 MB     |
+| 21      | 53/d13188 | 2034      | blast (3)      | COMPLETED | 0    | 2014-10-23 16:34:17.518 | 29s      | 20s      | 4.5%   | 289.5 MB | 381.6 MB | 33.3 MB  | 0        |
+| 22      | 26/f65116 | 2035      | blast (4)      | COMPLETED | 0    | 2014-10-23 16:34:18.459 | 30s      | 9s       | 6.0%   | 122.8 MB | 353.4 MB | 33.3 MB  | 0        |
+| 23      | 88/bc00e4 | 2036      | blast (5)      | COMPLETED | 0    | 2014-10-23 16:34:18.507 | 30s      | 19s      | 5.0%   | 195 MB   | 395.8 MB | 65.3 MB  | 121 KB   |
+| 24      | 74/2556e9 | 2037      | blast (6)      | COMPLETED | 0    | 2014-10-23 16:34:18.553 | 30s      | 12s      | 43.6%  | 140.7 MB | 432.2 MB | 192.7 MB | 182.7 MB |
+| 28      | b4/0f9613 | 2041      | exonerate (1)  | COMPLETED | 0    | 2014-10-23 16:38:19.657 | 1m 30s   | 1m 11s   | 94.3%  | 611.6 MB | 693.8 MB | 961.2 GB | 6.1 GB   |
+| 32      | af/7f2f57 | 2044      | exonerate (4)  | COMPLETED | 0    | 2014-10-23 16:46:50.902 | 1m 1s    | 38s      | 36.6%  | 115.8 MB | 167.8 MB | 364 GB   | 5.1 GB   |
+| 33      | 37/ab1fcc | 2045      | exonerate (5)  | COMPLETED | 0    | 2014-10-23 16:47:51.625 | 30s      | 12s      | 59.6%  | 696 MB   | 734.6 MB | 354.3 GB | 420.4 MB |
+| 31      | d7/eabe51 | 2042      | exonerate (3)  | COMPLETED | 0    | 2014-10-23 16:45:50.846 | 3m 1s    | 2m 6s    | 130.1% | 703.3 MB | 760.9 MB | 1.1 TB   | 28.6 GB  |
+| 36      | c4/d6cc15 | 2048      | exonerate (6)  | COMPLETED | 0    | 2014-10-23 16:48:48.718 | 3m 1s    | 2m 43s   | 116.6% | 682.1 MB | 743.6 MB | 868.5 GB | 42 GB    |
+| 30      | 4f/1ad1f0 | 2043      | exonerate (2)  | COMPLETED | 0    | 2014-10-23 16:45:50.961 | 10m 2s   | 9m 16s   | 95.5%  | 706.2 MB | 764 MB   | 1.6 TB   | 172.4 GB |
+| 52      | 72/41d0c6 | 2055      | similarity (1) | COMPLETED | 0    | 2014-10-23 17:13:23.543 | 30s      | 352ms    | 0.0%   | 35.6 MB  | 58.3 MB  | 199.3 MB | 7.9 MB   |
+| 57      | 9b/111b5e | 2058      | similarity (6) | COMPLETED | 0    | 2014-10-23 17:13:23.655 | 30s      | 488ms    | 0.0%   | 108.2 MB | 158 MB   | 317.1 MB | 9.8 MB   |
+| 53      | 3e/bca30f | 2061      | similarity (2) | COMPLETED | 0    | 2014-10-23 17:13:23.770 | 30s      | 238ms    | 0.0%   | 6.7 MB   | 29.6 MB  | 190 MB   | 91.2 MB  |
+| 54      | 8b/d45b47 | 2062      | similarity (3) | COMPLETED | 0    | 2014-10-23 17:13:23.808 | 30s      | 442ms    | 0.0%   | 108.1 MB | 158 MB   | 832 MB   | 565.6 MB |
+| 55      | 51/ac19c6 | 2064      | similarity (4) | COMPLETED | 0    | 2014-10-23 17:13:23.873 | 30s      | 6s       | 0.0%   | 112.7 MB | 162.8 MB | 4.9 GB   | 3.9 GB   |
+| 56      | c3/ec5f4a | 2066      | similarity (5) | COMPLETED | 0    | 2014-10-23 17:13:23.948 | 30s      | 616ms    | 0.0%   | 10.4 MB  | 34.6 MB  | 238 MB   | 8.4 MB   |
+| 98      | de/d6c0a6 | 2099      | matrix (1)     | COMPLETED | 0    | 2014-10-23 17:14:27.139 | 30s      | 1s       | 0.0%   | 4.8 MB   | 42 MB    | 240.6 MB | 79 KB    |
+
+### Trace fields
+
+The following table shows the fields that can be included in the execution report:
+
+##### `task_id`
+
+Task ID.
+
+##### `hash`
+
+Task hash code.
+
+##### `native_id`
+
+Task ID given by the underlying execution system e.g. POSIX process PID when executed locally, job ID when executed by a grid engine, etc.
+
+##### `process`
+
+Nextflow process name.
+
+##### `tag`
+
+User provided identifier associated this task.
+
+##### `name`
+
+Task name.
+
+##### `status`
+
+Task status. Possible values are: `NEW`, `SUBMITTED`, `RUNNING`, `COMPLETED`, `FAILED`, and `ABORTED`.
+
+##### `exit`
+
+POSIX process exit status.
+
+##### `module`
+
+Environment module used to run the task.
+
+##### `container`
+
+Docker image name used to execute the task.
+
+##### `cpus`
+
+The cpus number request for the task execution.
+
+##### `time`
+
+The time request for the task execution
+
+##### `disk`
+
+The disk space request for the task execution.
+
+##### `memory`
+
+The memory request for the task execution.
+
+##### `attempt`
+
+Attempt at which the task completed.
+
+##### `submit`
+
+Timestamp when the task has been submitted.
+
+##### `start`
+
+Timestamp when the task execution has started.
+
+##### `complete`
+
+Timestamp when task execution has completed.
+
+##### `duration`
+
+Time elapsed to complete since the submission.
+
+##### `realtime`
+
+Task execution time i.e. delta between completion and start timestamp.
+
+##### `error_action`
+
+Task execution time i.e. delta between completion and start timestamp.
+
+##### `queue`
+
+The queue that the executor attempted to run the process on.
+
+##### `%cpu`
+
+Percentage of CPU used by the process.
+
+##### `%mem`
+
+Percentage of memory used by the process.
+
+##### `rss`
+
+Real memory (resident set) size of the process. Equivalent to `ps -o rss` .
+
+##### `vmem`
+
+Virtual memory size of the process. Equivalent to `ps -o vsize` .
+
+##### `peak_rss`
+
+Peak of real memory. This data is read from field `VmHWM` in `/proc/$pid/status` file.
+
+##### `peak_vmem`
+
+Peak of virtual memory. This data is read from field `VmPeak` in `/proc/$pid/status` file.
+
+##### `rchar`
+
+Number of bytes the process read, using any read-like system call from files, pipes, tty, etc. This data is read from file `/proc/$pid/io`.
+
+##### `wchar`
+
+Number of bytes the process wrote, using any write-like system call. This data is read from file `/proc/$pid/io`.
+
+##### `syscr`
+
+Number of read-like system call invocations that the process performed. This data is read from file `/proc/$pid/io`.
+
+##### `syscw`
+
+Number of write-like system call invocations that the process performed. This data is read from file `/proc/$pid/io`.
+
+##### `read_bytes`
+
+Number of bytes the process directly read from disk. This data is read from file `/proc/$pid/io`.
+
+##### `write_bytes`
+
+Number of bytes the process originally dirtied in the page-cache (assuming they will go to disk later). This data is read from file `/proc/$pid/io`.
+
+##### `vol_ctxt`
+
+Number of voluntary context switches. This data is read from field `voluntary_ctxt_switches` in `/proc/$pid/status` file.
+
+##### `inv_ctxt`
+
+Number of involuntary context switches. This data is read from field `nonvoluntary_ctxt_switches` in `/proc/$pid/status` file.
+
+##### `env`
+
+The variables defined in task execution environment.
+
+##### `workdir`
+
+The directory path where the task was executed.
+
+##### `script`
+
+The task command script.
+
+##### `scratch`
+
+The value of the process `scratch` directive.
+
+##### `error_action`
+
+The action applied on error task failure.
+
+##### `hostname`
+
+<AddedInVersion version="25.05.0-edge" />
+
+The host on which the task was executed. Supported only for the Kubernetes executor yet. Activate with `k8s.fetchNodeName = true` in the Nextflow config file.
+
+##### `cpu_model`
+
+<AddedInVersion version="22.07.0-edge" />
+
+The name of the CPU model used to execute the task. This data is read from file `/proc/cpuinfo`.
+
+:::note
+These metrics provide an estimation of the resources used by running tasks. They are not an alternative to low-level performance analysis tools, and they may not be completely accurate, especially for very short-lived tasks (running for less than a few seconds).
+:::
+
+Trace report layout and other configuration settings can be specified by using the `nextflow.config` configuration file. See [Trace scope][config-trace] to learn more.
+
+## Execution timeline
+
+Nextflow can render an HTML timeline for all processes executed in your pipeline. An example of the execution timeline is shown below:
+
+![Execution timeline](_static/timeline-min.png)
+
+Each bar represents a process run in the pipeline execution. The bar length represents the task duration time (wall-time). The colored area in each bar represents the real execution time. The grey area to the *left* of the colored area represents the task scheduling wait time. The grey area to the *right* of the colored area represents the task termination time (clean-up and file un-staging). The numbers on the x-axis represent the time in absolute units e.g. minutes, hours, etc.
+
+Each bar displays two numbers: the task duration time and the virtual memory size peak.
+
+As each process can spawn many tasks, colors are used to identify those tasks belonging to the same process.
+
+To enable the creation of the execution timeline add the `-with-timeline` command line option when launching the pipeline execution. For example:
+
+```bash
+nextflow run main.nf -with-timeline [file name]
+```
+
+The report file name can be specified as an optional parameter following the timeline option.
+
+## Workflow diagram
+
+A Nextflow pipeline can be represented as a direct acyclic graph (DAG). The vertices in the graph represent the pipeline's processes and operators, while the edges represent the data dependencies (i.e. channels) between them.
+
+To render the workflow DAG, run your pipeline with the `-with-dag` option. By default, it creates a file named `dag-<timestamp>.html` with the workflow DAG rendered as a [Mermaid](https://mermaid.js.org/) diagram.
+
+The workflow DAG can be rendered in a different format by specifying an output file name with a different extension based on the desired format. For example:
+
+```bash
+nextflow run main.nf -with-dag flowchart.png
+```
+
+<ChangedInVersion version="23.10.0">
+The default output format was changed from DOT to HTML.
+</ChangedInVersion>
+
+The following file formats are supported:
+
+##### `dot`
+
+Graphviz [DOT](http://www.graphviz.org/content/dot-language) file
+
+##### `gexf`
+
+Graph Exchange XML file (Gephi)
+
+##### `html`
+
+HTML file with Mermaid diagram
+
+<ChangedInVersion version="23.10.0">
+The HTML format was changed to render a Mermaid diagram instead of a Cytoscape diagram.
+</ChangedInVersion>
+
+##### `mmd`
+
+Mermaid diagram
+
+##### `pdf`
+
+*Requires [Graphviz](http://www.graphviz.org) to be installed*
+
+Graphviz PDF file
+
+##### `png`
+
+*Requires [Graphviz](http://www.graphviz.org) to be installed*
+
+Graphviz PNG file
+
+##### `svg`
+
+*Requires [Graphviz](http://www.graphviz.org) to be installed*
+
+Graphviz SVG file
+
+Here is the Mermaid diagram produced by Nextflow for the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline (using the [Mermaid Live Editor](https://mermaid-js.github.io/mermaid-live-editor/edit) with the `default` theme):
+
+```bash
+nextflow run rnaseq-nf -preview -with-dag
+```
+
+```mermaid
+%%{
+    init: {
+        'theme': 'base',
+        'themeVariables': {
+            'primaryColor': '#B6ECE2',
+            'primaryTextColor': '#160F26',
+            'primaryBorderColor': '#065647',
+            'lineColor': '#545555',
+            'clusterBkg': '#BABCBD22',
+            'clusterBorder': '#DDDEDE',
+            'fontFamily': 'degular'
+        }
+    }
+}%%
+flowchart TB
+    subgraph " "
+    v0["Channel.fromFilePairs"]
+    v1["transcriptome"]
+    v7["config"]
+    end
+    subgraph RNASEQ
+    v2([INDEX])
+    v3([FASTQC])
+    v4([QUANT])
+    end
+    v8([MULTIQC])
+    subgraph " "
+    v9[" "]
+    end
+    v5(( ))
+    v0 --> v3
+    v0 --> v4
+    v1 --> v2
+    v2 --> v4
+    v3 --> v5
+    v4 --> v5
+    v7 --> v8
+    v5 --> v8
+    v8 --> v9
+```
+
+[metrics-page]: /nextflow_docs/nextflow_repo/docs/tutorials/metrics.mdx
+[config-report]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#report
+[config-trace]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#trace
+[trace-file]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
diff --git a/docs/script.md b/docs/script.mdx
similarity index 89%
rename from docs/script.md
rename to docs/script.mdx
index ea57222b61..bab179ea8c 100644
--- a/docs/script.md
+++ b/docs/script.mdx
@@ -1,16 +1,14 @@
-(script-page)=
-
 # Scripts
 
-Nextflow is a workflow language that runs on the Java virtual machine (JVM). Nextflow's syntax is very similar to [Groovy](https://groovy-lang.org/), a scripting language for the JVM. However, Nextflow is specialized for writing computational pipelines in a declarative manner. See {ref}`syntax-page` for a full description of the Nextflow language.
+Nextflow is a workflow language that runs on the Java virtual machine (JVM). Nextflow's syntax is very similar to [Groovy](https://groovy-lang.org/), a scripting language for the JVM. However, Nextflow is specialized for writing computational pipelines in a declarative manner. See [Syntax][syntax-page] for a full description of the Nextflow language.
 
-Nextflow scripts can also make full use of the Java and Groovy standard libraries. See {ref}`stdlib-page` for more information.
+Nextflow scripts can also make full use of the Java and Groovy standard libraries. See [Standard library][stdlib-page] for more information.
 
-:::{warning}
+:::warning
 Nextflow uses UTF-8 as the default character encoding for source files. Make sure to use UTF-8 encoding when editing Nextflow scripts with your preferred text editor.
 :::
 
-:::{warning}
+:::warning
 Nextflow scripts have a maximum size of 64 KiB. To avoid this limit for large pipelines, consider moving pipeline components into separate files and including them as modules.
 :::
 
@@ -43,12 +41,10 @@ def str = "Hi"
 println str
 ```
 
-:::{warning}
-Variables can also be declared without `def` in some cases. However, this practice is discouraged outside of simple code snippets because it can lead to a {ref}`race condition <cache-global-var-race-condition>`.
+:::warning
+Variables can also be declared without `def` in some cases. However, this practice is discouraged outside of simple code snippets because it can lead to a [race condition][cache-global-var-race-condition].
 :::
 
-(script-list)=
-
 ## Lists
 
 Lists are defined using square brackets:
@@ -69,9 +65,7 @@ In order to get the length of the list use the `size` method:
 println myList.size()
 ```
 
-See {ref}`stdlib-types-list` for the set of available list operations.
-
-(script-map)=
+See [List\<E\>][stdlib-types-list] for the set of available list operations.
 
 ## Maps
 
@@ -105,13 +99,11 @@ def new_scores = scores + ["Pete": 3, "Cedric": 120]
 
 When adding two maps, the first map is copied and then appended with the keys from the second map. Any conflicting keys are overwritten by the second map.
 
-:::{tip}
+:::tip
 Copying a map with the `+` operator is a safer way to modify maps in Nextflow, specifically when passing maps through channels. This way, a new instance of the map will be created, and any references to the original map won't be affected.
 :::
 
-See {ref}`stdlib-types-map` for the set of available map operations.
-
-(script-tuples)=
+See [Map\<K,V\>][stdlib-types-map] for the set of available map operations.
 
 ## Tuples
 
@@ -152,16 +144,14 @@ coords.each { x, y ->
 
 Tuples are immutable -- once a tuple is created, its elements cannot be modified.
 
-See {ref}`stdlib-types-tuple` for the set of available tuple operations.
-
-(script-operators)=
+See [Tuple][stdlib-types-tuple] for the set of available tuple operations.
 
 ## Operators
 
 Operators are symbols that perform specific functions on one or more values, and generally make code easier to read. This section highlights some of the most commonly used operators.
 
-:::{note}
-Operators in this context are different from *channel operators*, which are specialized functions for working with channels. See {ref}`dataflow-page` for more information.
+:::note
+Operators in this context are different from *channel operators*, which are specialized functions for working with channels. See [Dataflow][dataflow-page] for more information.
 :::
 
 The `==` and `!=` operators can be used to test whether any two values are equal (or not equal):
@@ -172,7 +162,7 @@ assert [2, 2] != [4]
 assert 'two plus two' != 'four'
 ```
 
-:::{tip}
+:::tip
 The `assert` keyword simply tests a condition and raises an error if the condition is false. Every assert that you see on this page will succeed if executed.
 :::
 
@@ -246,12 +236,10 @@ def counts = ['A': 1, 'B', 2]
 assert counts['C'] ?: 0 == 0    // x is "truthy" if !!x == true
 ```
 
-:::{tip}
+:::tip
 The `?:` operator is also known as the [elvis operator](https://en.wikipedia.org/wiki/Elvis_operator).
 :::
 
-(script-string)=
-
 ## Strings
 
 Strings can be defined by enclosing text in single or double quotes (`'` or `"` characters):
@@ -268,8 +256,6 @@ def a = "world"
 print "hello " + a + "\n"
 ```
 
-(string-interpolation)=
-
 ### String interpolation
 
 There is an important difference between single-quoted and double-quoted strings: Double-quoted strings support variable interpolations, while single-quoted strings do not.
@@ -303,7 +289,7 @@ def text = """
     """
 ```
 
-:::{note}
+:::note
 Like before, multi-line strings inside double quotes support variable interpolation, while single-quoted multi-line strings do not.
 :::
 
@@ -323,7 +309,7 @@ def result = myLongCmdline.execute().text
 
 In the preceding example, `blastp` and its `-in`, `-out`, `-db` and `-html` switches and their arguments are effectively a single line.
 
-:::{warning}
+:::warning
 Do not put any spaces after the backslash when using backslashes to continue a multi-line command. Spaces after the backslash will be interpreted as an escaped space and will make your script incorrect. It will also print this warning:
 
 ```
@@ -331,8 +317,6 @@ unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltEx
 ```
 :::
 
-(script-regexp)=
-
 ## Regular expressions
 
 Regular expressions are the Swiss Army knife of text processing. They provide the ability to match and extract patterns from strings.
@@ -403,8 +387,6 @@ println patch   // 3
 println flavor  // beta
 ```
 
-(script-closure)=
-
 ## Closures
 
 A closure is a function that can be used like a regular value. Typically, closures are passed as arguments to *higher-order functions* to express computations in a declarative manner.
@@ -490,7 +472,7 @@ def result = counts.values().inject { sum, v -> sum + v }
 
 This way, the closure is fully "self-contained" because it doesn't access or mutate any variables outside of its scope.
 
-:::{note}
+:::note
 When a closure takes a single parameter, the parameter can be omitted, in which case the implicit `it` parameter will be used:
 
 ```nextflow
@@ -531,4 +513,15 @@ workflow {
 }
 ```
 
-See {ref}`workflow-page`, {ref}`process-page`, and {ref}`module-page`  for more information about how to use these features in your Nextflow scripts.
+See [Workflows][workflow-page], [Processes][process-page], and [Modules][module-page] for more information about how to use these features in your Nextflow scripts.
+
+[cache-global-var-race-condition]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#race-condition-on-a-global-variable
+[channel-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[module-page]: /nextflow_docs/nextflow_repo/docs/module.mdx
+[process-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[stdlib-page]: /nextflow_docs/nextflow_repo/docs/reference/stdlib.mdx
+[stdlib-types-list]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#liste
+[stdlib-types-map]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#mapkv
+[stdlib-types-tuple]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#tuple
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[workflow-page]: /nextflow_docs/nextflow_repo/docs/workflow.mdx
diff --git a/docs/secrets.mdx b/docs/secrets.mdx
new file mode 100644
index 0000000000..2ad49fede0
--- /dev/null
+++ b/docs/secrets.mdx
@@ -0,0 +1,115 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Secrets
+
+<AddedInVersion version="22.10.0">
+</AddedInVersion>
+
+Nextflow has built-in support for pipeline secrets, allowing users to safely provide sensitive information to a pipeline run.
+
+## How it works
+
+This feature allows you to decouple the use of secrets in your pipelines from the pipeline code and configuration files. Secrets are managed by Nextflow and stored separately into a local store only accessible to the secrets owner.
+
+When a pipeline is launched, Nextflow injects the secrets into the run without leaking them into temporary execution files. Secrets are provided to tasks as environment variables.
+
+Secrets can be used with the local executor and grid executors (e.g., Slurm or Grid Engine). Secrets can be used with the AWS Batch executor when launched from [Seqera Platform](https://seqera.io/blog/pipeline-secrets-secure-handling-of-sensitive-information-in-tower/).
+
+## Command line
+
+The Nextflow [secrets][cli-secrets] sub-command can be used to manage secrets:
+
+```bash
+# create a new secret
+nextflow secrets set FOO "Hello world"
+
+# list all secrets
+nextflow secrets list
+
+# get the value of secret FOO
+nextflow secrets get FOO
+
+# delete the secret FOO
+nextflow secrets delete FOO
+```
+
+## Configuration file
+
+Secrets can be used in configuration files using the built-in `secrets` variable. For example:
+
+```groovy
+aws {
+  accessKey = secrets.MY_ACCESS_KEY
+  secretKey = secrets.MY_SECRET_KEY
+}
+```
+
+The above snippet accesses the secrets `MY_ACCESS_KEY` and `MY_SECRET_KEY` and assigns them to the corresponding AWS config settings.
+
+:::warning
+Secrets should not be assigned to pipeline parameters, as they can be leaked by the pipeline.
+:::
+
+<AddedInVersion version="25.10.0" />
+
+Nextflow supports the use of secrets provided by plugins (e.g., AWS secrets) in configuration. However, due to the way that plugins are loaded, there are specific considerations when using config secrets:
+
+- **Initial config load**: Nextflow first loads the configuration _without_ secrets enabled. Any reference to a secret will return the empty string `''`.
+
+- **Plugin resolution**: Plugins are resolved after the initial configuration load. This is because the configuration can specify additional plugins.
+
+- **Config reloading**: If secrets are accessed during configuration and the initial load succeeds, Nextflow will reload the configuration with secrets enabled.
+
+As a result, config secrets must be used in a way that does not cause the config resolution to fail when secrets are not present.
+
+For example:
+
+```groovy
+includeConfig secrets.MY_SECRET
+    ? "https://example.com/extra.config?secret=${secrets.MY_SECRET}"
+    : '/dev/null'
+```
+
+The above snippet includes a secured config only if the secret is present. Otherwise, it includes `/dev/null`, which is equivalent to including an empty file.
+The reference to `secrets.MY_SECRET` in the condition causes the config to be reloaded with secrets enabled, including secrets from plugins such as AWS secrets.
+
+## Pipeline script
+
+<AddedInVersion version="24.04.0" />
+
+Secrets can be accessed in the pipeline script using the built-in `secrets` variable. For example:
+
+```nextflow
+workflow {
+    println "The secret is: ${secrets.MY_SECRET}"
+}
+```
+
+:::warning
+The above example is only meant to demonstrate how to access a secret, not how to use it. In practice, sensitive information should not be printed to the console or output files.
+:::
+
+## Process directive
+
+Secrets can be accesses by processes using the [secret][process-secret] directive. For example:
+
+```nextflow
+process my_task {
+    secret 'MY_ACCESS_KEY'
+    secret 'MY_SECRET_KEY'
+
+    script:
+    """
+    your_command --access \$MY_ACCESS_KEY --secret \$MY_SECRET_KEY
+    """
+}
+```
+
+In the above example, the secrets `MY_ACCESS_KEY` and `MY_SECRET_KEY` are injected into the process script as environment variables.
+
+:::warning
+Secrets are made available as environment variables in the process script. To prevent evaluation in the Nextflow script context, escape variable names with a backslash (e.g., `\$MY_ACCESS_KEY`) as shown above.
+:::
+
+[cli-secrets]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#secrets
+[process-secret]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#secret
\ No newline at end of file
diff --git a/docs/sharing.md b/docs/sharing.mdx
similarity index 90%
rename from docs/sharing.md
rename to docs/sharing.mdx
index 58c836c2ae..7c749fc25f 100644
--- a/docs/sharing.md
+++ b/docs/sharing.mdx
@@ -1,16 +1,14 @@
-(sharing-page)=
-
 # Sharing pipelines
 
 Nextflow seamlessly integrates with popular Git providers, including [BitBucket](http://bitbucket.org/), [GitHub](http://github.com), and [GitLab](http://gitlab.com) for managing Nextflow pipelines as version-controlled Git repositories. This feature allows you to easily use other people's Nextflow pipelines and publish your own pipelines.
 
-:::{note}
+:::note
 Nextflow is not meant to completely replace the [Git](https://git-scm.com/) tool. You may still need `git` to create new repositories or commit changes, etc.
 :::
 
 ## Git configuration
 
-You can configure your credentials for various Git providers in the Git configuration file, located at `$HOME/.nextflow/scm`. See {ref}`git-page` for more information.
+You can configure your credentials for various Git providers in the Git configuration file, located at `$HOME/.nextflow/scm`. See [Git][git-page] for more information.
 
 ## Using a local repository
 
@@ -34,7 +32,7 @@ Nextflow only requires that the main script in your pipeline project is called `
 manifest.mainScript = 'my_very_long_script_name.nf'
 ```
 
-To learn more about this and other project metadata information, that can be defined in the Nextflow configuration file, read the {ref}`Manifest <config-manifest>` section on the Nextflow configuration page.
+To learn more about this and other project metadata information, that can be defined in the Nextflow configuration file, read the [Manifest][config-manifest] section on the Nextflow configuration page.
 
 Once you have uploaded your pipeline project to GitHub other people can execute it simply using the project name or the repository URL.
 
@@ -50,7 +48,7 @@ or
 nextflow run http://github.com/acme/hello
 ```
 
-See the {ref}`CLI <cli-page>` page to learn how to use the Nextflow command line to run pipelines and manage pipeline projects.
+See [Command line][cli-page] to learn how to use the Nextflow command line to run pipelines and manage pipeline projects.
 
 ## Managing dependencies
 
@@ -87,14 +85,12 @@ conda.enabled = true
 
 This way, when you launch your pipeline, Nextflow will automatically download the necessary dependencies to run your tasks based on this configuration.
 
-Read the {ref}`container-page` page to learn more about how to use containers with Nextflow, and the {ref}`conda-page` page for Conda packages.
+Read the [Containers][container-page] page to learn more about how to use containers with Nextflow, and the [Conda environments][conda-page] page for Conda packages.
 
-:::{tip}
+:::tip
 For maximal reproducibility, make sure to define a specific version for each tool. Otherwise, your pipeline might use different versions across subsequent runs, which can introduce subtle differences to your results.
 :::
 
-(bundling-executables)=
-
 #### The `bin` directory
 
 As for custom scripts, you can include executable scripts in the `bin` directory of your pipeline repository. When configured correctly, these scripts can be executed like a regular command from any process script (i.e. without modifying the `PATH` environment variable or using an absolute path), and changing the script will cause the task to be re-executed on a resumed run (i.e. just like changing the process script itself).
@@ -105,7 +101,7 @@ To configure a custom script:
 2. Specify a portable shebang (see note below for details).
 3. Make the script executable. For example: `chmod a+x bin/my_script.py`
 
-:::{tip}
+:::tip
 To maximize the portability of your bundled script, use `env` to dynamically resolve the location of the interpreter instead of hard-coding it in the shebang line.
 
 For example, shebang definitions `#!/usr/bin/python` and `#!/usr/local/bin/python` both hard-code specific paths to the Python interpreter. Instead, the following approach is more portable:
@@ -115,8 +111,6 @@ For example, shebang definitions `#!/usr/bin/python` and `#!/usr/local/bin/pytho
 ```
 :::
 
-(lib-directory)=
-
 #### The `lib` directory
 
 The `lib` directory can be used to add utility code or external libraries without cluttering the pipeline scripts. The `lib` directory in the Nextflow project root is added to the classpath by default. Classes defined in the `lib` directory will be available in pipeline scripts. Functions defined outside of classes will not be available in pipeline scripts.
@@ -171,7 +165,7 @@ Found sequence 'DNA[ACGTTGCAATGCCGTA]' with melting temperaure 48.0°C
 Found sequence 'DNA[GCGTACGGTACGTTAC]' with melting temperaure 50.0°C
 ```
 
-:::{note}
+:::note
 Package declarations in the `lib` directory are ignored. The package of a class is determined by the directory structure within the `lib` directory.
 
 For example, if the above example were defined in `lib/utils/DNASequence.groovy`, the class would need to be referenced in pipeline scripts as `utils.DNASequence`.
@@ -222,4 +216,12 @@ env {
 
 Similarly, if you use an HPC scheduler like SLURM or a cloud batch service like AWS Batch to execute tasks in a distributed manner, you can use a configuration profile to define the settings for a given environment.
 
-See {ref}`config-page` for more information about Nextflow configuration and {ref}`executor-page` for more information about executors.
+See [Configuration][config-page] for more information about Nextflow configuration and [Executors][executor-page] for more information about executors.
+
+[git-page]: /nextflow_docs/nextflow_repo/docs/git.mdx
+[config-manifest]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#manifest
+[cli-page]: /nextflow_docs/nextflow_repo/docs/cli.mdx
+[container-page]: /nextflow_docs/nextflow_repo/docs/container.mdx
+[conda-page]: /nextflow_docs/nextflow_repo/docs/conda.mdx
+[config-page]: /nextflow_docs/nextflow_repo/docs/config.mdx
+[executor-page]: /nextflow_docs/nextflow_repo/docs/executor.mdx
diff --git a/docs/spack.mdx b/docs/spack.mdx
new file mode 100644
index 0000000000..2256e64f04
--- /dev/null
+++ b/docs/spack.mdx
@@ -0,0 +1,180 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Spack environments
+
+<AddedInVersion version="23.02.0-edge" />
+
+[Spack](https://spack.io/) is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. Spack is not tied to a particular language; you can build a software stack in Python or R, link to libraries written in C, C++, or Fortran, and easily swap compilers or target specific CPU microarchitectures.
+
+Nextflow has built-in support for Spack that allows the configuration of workflow dependencies using Spack recipes and environment files.
+
+This allows Nextflow applications to build packages from source on the compute infrastructure in use, whilst taking advantage of the configuration flexibility provided by Nextflow. At shared compute facilities where Spack has been configured by the administrators, this may result in optimized builds without user intervention. With appropriate options, this also permits end users to customize binary optimizations by themselves.
+
+## Prerequisites
+
+This feature requires the [Spack](https://spack.io) package manager to be installed on your system.
+
+## How it works
+
+Nextflow automatically creates and activates the Spack environment(s) given the dependencies specified by each process.
+
+Dependencies are specified by using the [spack][process-spack] directive, providing either the names of the required Spack packages, the path of a Spack environment yaml file or the path of an existing Spack environment directory.
+
+:::note
+Spack always installs the software packages in its own directories, regardless of the Nextflow specifications. The Spack environment created by Nextflow only contains symbolic links pointing to the appropriate package locations, and therefore it is relatively small in size.
+:::
+
+You can specify the directory where the Spack environment is stored using the `spack.cacheDir` configuration property (see [spack][config-spack] for more information). When using a computing cluster, make sure to use a shared file system path accessible from all compute nodes.
+
+:::warning
+The Spack environment feature is not supported by executors that use remote object storage as the work directory, e.g. AWS Batch.
+:::
+
+### Enabling Spack environment
+
+The use of Spack recipes specified using the [spack][process-spack] directive needs to be enabled explicitly by setting the option shown below in the pipeline configuration file (i.e. `nextflow.config`):
+
+```groovy
+spack.enabled = true
+```
+
+Alternatively, it can be specified by setting the variable `NXF_SPACK_ENABLED=true` in your environment or by using the `-with-spack` command line option.
+
+### Use Spack package names
+
+Spack package names can specified using the `spack` directive. Multiple package names can be specified by separating them with a blank space. For example:
+
+```nextflow
+process hello {
+  spack 'bwa samtools py-multiqc'
+
+  script:
+  '''
+  your_command --here
+  '''
+}
+```
+
+Using the above definition, a Spack environment that includes BWA, Samtools, and MultiQC tools is created and activated when the process is executed.
+
+The usual Spack package syntax and naming conventions can be used. The version of a package can be specified after the package name like so: `bwa@0.7.15`.
+
+Spack is able to infer the local CPU microarchitecture and optimize the build accordingly. If you really need to customize this option, you can use the [arch][process-arch] directive.
+
+Read the Spack documentation for more details about [package specifications](https://spack.readthedocs.io/en/latest/basic_usage.html#specs-dependencies).
+
+### Use Spack environment files
+
+Spack environments can also be defined using one or more Spack environment files. A Spack environment file is a YAML file that lists the required packages and channels. For example:
+
+```yaml
+spack:
+  specs:
+  - star@2.5.4a
+  - bwa@0.7.15
+
+  concretizer:
+    unify: true
+```
+
+Here, the `concretizer` option is a sensible default for Spack environments.
+
+:::note
+When creating a Spack environment, Nextflow always enables the corresponding Spack view. This is required by Nextflow to locate executables at pipeline runtime.
+:::
+
+As mentioned above, Spack is able to guess the target CPU microarchitecture and optimize the build accordingly. If you really need to customize this option, we advise to use the [arch][process-arch] directive rather than the available options for the Spack environment file.
+
+Read the Spack documentation for more details about how to create [environment files](https://spack.readthedocs.io/en/latest/environments.html).
+
+The path of an environment file can be specified using the `spack` directive:
+
+```nextflow
+process hello {
+  spack '/some/path/my-env.yaml'
+
+  script:
+  '''
+  your_command --here
+  '''
+}
+```
+
+:::warning
+The environment file name **must** have a `.yaml` extension or else it won't be properly recognized.
+:::
+
+### Use existing Spack environments
+
+If you already have a local Spack environment, you can use it in your workflow specifying the installation directory of such environment by using the `spack` directive:
+
+```nextflow
+process hello {
+  spack '/path/to/an/existing/env/directory'
+
+  script:
+  '''
+  your_command --here
+  '''
+}
+```
+
+## Best practices
+
+### Building Spack packages for Nextflow pipelines
+
+Spack builds most software package from their source codes, and it does this for a request package and for all its required dependencies. As a result, Spack builds can last for long, even several hours. This can represent an inconvenience, in that it can significantly lengthen the duration of Nextflow processes. Here we briefly discuss two strategies to mitigate this aspect, and render the usage of Spack more effective.
+
+1. Use a Spack yaml file, and pre-build the environment outside of Nextflow, prior to running the pipeline.
+   Building packages outside of the Nextflow pipeline will work since Spack always installs packages in its own directories,
+   and only creates symbolic links in the environment. This sequence of commands will do the trick in most cases:
+
+   ```bash
+   spack env create myenv /path/to/spack.yaml
+   spack env activate myenv
+   spack env view enable
+   spack concretize -f
+   spack install -y
+   spack env deactivate
+   ```
+
+2. Use the Nextflow stub functionality prior to running the pipeline for production.
+   Nextflow will run the stub pipeline, skipping process executions but still setting up the required software packages.
+   This option is useful if it is not possible to write a Spack yaml file for the environment.
+   The stub functionality is described in the [Stub][process-stub] section of the Processes page.
+
+### Configuration file
+
+When the `spack` directive is used in any `process` definition within the pipeline script, Spack is required for the pipeline execution.
+
+Specifying the Spack environments in a separate configuration [profile][config-profiles] is therefore
+recommended to allow the execution via a command line option and to enhance the pipeline portability. For example:
+
+```groovy
+profiles {
+  spack {
+    process.spack = 'samtools'
+  }
+
+  docker {
+    process.container = 'biocontainers/samtools'
+    docker.enabled = true
+  }
+}
+```
+
+The above configuration snippet allows the execution either with Spack or Docker by specifying `-profile spack` or `-profile docker` when running the pipeline script.
+
+:::note
+Nextflow does not allow for fine-grained configuration of the Spack package manager. Instead, this has to be performed directly on the host Spack installation. For more information see the [Spack documentation](https://spack.readthedocs.io).
+:::
+
+## Advanced settings
+
+Spack advanced configuration settings are described in the [spack][config-spack] section on the Nextflow configuration page.
+
+[config-profiles]: /nextflow_docs/nextflow_repo/docs/config.mdx#config-profiles
+[config-spack]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#spack
+[process-arch]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#arch
+[process-spack]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#spack
+[process-stub]: /nextflow_docs/nextflow_repo/docs/process.mdx#stub
diff --git a/docs/strict-syntax.mdx b/docs/strict-syntax.mdx
new file mode 100644
index 0000000000..9e53124243
--- /dev/null
+++ b/docs/strict-syntax.mdx
@@ -0,0 +1,610 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Preparing for strict syntax
+
+This page explains how to update Nextflow scripts and config files to adhere to the [Nextflow language specification][syntax-page], also known as the _strict syntax_.
+
+:::note
+If you are still using DSL1, see [Migrating from DSL1][dsl1-page] to learn how to migrate your Nextflow pipelines to DSL2 before consulting this guide.
+:::
+
+<AddedInVersion version="25.02.0-edge">
+The strict syntax can be enabled in Nextflow by setting the environment variable `NXF_SYNTAX_PARSER=v2`.
+</AddedInVersion>
+
+
+## Overview
+
+The strict syntax is a subset of DSL2. While DSL2 allows any Groovy syntax, the strict syntax allows only a subset of Groovy syntax for Nextflow scripts and config files. This new specification enables more specific error reporting, ensures more consistent code, and will allow the Nextflow language to evolve independently of Groovy.
+
+The strict syntax will eventually become the only way to write Nextflow code, and new language features will be implemented only in the strict syntax, with few exceptions. Therefore, it is important to prepare for the strict syntax in order to maintain compatibility with future versions of Nextflow and be able to use new language features.
+
+This page outlines the key differences between DSL2 and the strict syntax. The extent of required changes will vary depending on the amount of custom Groovy code used within your scripts and config files.
+
+## Removed syntax
+
+### Import declarations
+
+In Groovy, the `import` declaration can be used to import external classes:
+
+```groovy
+import groovy.json.JsonSlurper
+
+def json = new JsonSlurper().parseText(json_file.text)
+```
+
+In the strict syntax, use the fully qualified name to reference the class:
+
+```nextflow
+def json = new groovy.json.JsonSlurper().parseText(json_file.text)
+```
+
+### Class declarations
+
+Some users use classes in Nextflow to define helper functions or custom types. Helper functions should be defined as standalone functions in Nextflow. Custom types should be moved to the `lib` directory.
+
+:::note
+Enums, a special type of class, are supported, but they cannot be included across modules at this time.
+:::
+
+:::note
+Record types will be addressed in a future version of the Nextflow language specification.
+:::
+
+### Mixing script declarations and statements
+
+In the strict syntax, a script may contain any of the following top-level declarations:
+
+- Feature flags
+- Include declarations
+- Parameter declarations
+- Workflows
+- Processes
+- Functions
+- Output block
+
+Alternatively, a script may contain only statements, also known as a _code snippet_:
+
+```nextflow
+println 'Hello world!'
+```
+
+Code snippets are treated as an implicit entry workflow:
+
+```nextflow
+workflow {
+    println 'Hello world!'
+}
+```
+
+Script declarations and statements cannot be mixed at the same level. All statements must reside within script declarations unless the script is a code snippet:
+
+```nextflow
+process hello {
+    // ...
+}
+
+// incorrect -- move into entry workflow
+// println 'Hello world!'
+
+// correct
+workflow {
+    println 'Hello world!'
+}
+```
+
+:::note
+Mixing statements and script declarations was necessary in DSL1 and optional in DSL2. However, it is no longer supported in the strict syntax in order to simplify the language and to ensure that top-level statements are not executed when the script is included as a module.
+:::
+
+### Assignment expressions
+
+In Groovy, variables can be assigned in an expression:
+
+```groovy
+hello(x = 1, y = 2)
+```
+
+In the strict syntax, assignments are allowed only as statements:
+
+```nextflow
+x = 1
+y = 2
+hello(x, y)
+```
+
+In Groovy, variables can be incremented and decremented in an expression:
+
+```groovy
+hello(x++, y--)
+```
+
+In the strict syntax, use `+=` and `-=` instead:
+
+```nextflow
+x += 1
+y -= 1
+hello(x, y)
+```
+
+### For and while loops
+
+In Groovy, loop statements, such as `for` and `while`, are supported:
+
+```groovy
+for (rseqc_module in ['read_distribution', 'inner_distance', 'tin']) {
+    if (rseqc_modules.contains(rseqc_module))
+        rseqc_modules.remove(rseqc_module)
+}
+```
+
+In the strict syntax, use higher-order functions, such as the `each` method, instead:
+
+```nextflow
+['read_distribution', 'inner_distance', 'tin'].each { rseqc_module ->
+    if (rseqc_modules.contains(rseqc_module))
+        rseqc_modules.remove(rseqc_module)
+}
+```
+
+Lists, maps, and sets provide several functions (e.g., `collect`, `find`, `findAll`, `inject`) for iteration. See [Groovy standard library](https://docs.groovy-lang.org/latest/html/groovy-jdk/overview-summary.html) for more information.
+
+### Switch statements
+
+In Groovy, switch statements are used for pattern matching on a value:
+
+```groovy
+switch (aligner) {
+case 'bowtie2':
+    // ...
+    break
+case 'bwamem':
+    // ...
+    break
+case 'dragmap':
+    // ...
+    break
+case 'snap':
+    // ...
+    break
+default:
+    // ...
+}
+```
+
+In the strict syntax, use if-else statements instead:
+
+```nextflow
+if (aligner == 'bowtie2') {
+    // ...
+} else if (aligner == 'bwamem') {
+    // ...
+} else if (aligner == 'dragmap') {
+    // ...
+} else if (aligner == 'snap') {
+    // ...
+} else {
+    // ...
+}
+```
+
+### Spread operator
+
+In Groovy, the _spread_ operator can be used to flatten a nested list:
+
+```groovy
+ch.map { meta, bambai -> [meta, *bambai] }
+```
+
+In the strict syntax, enumerate the list elements explicitly:
+
+```groovy
+// alternative 1
+ch.map { meta, bambai -> [meta, bambai[0], bambai[1]] }
+
+// alternative 2
+ch.map { meta, bambai ->
+    def (bam, bai) = bambai
+    [meta, bam, bai]
+}
+```
+
+### Implicit environment variables
+
+In Nextflow DSL1 and DSL2, environment variables can be referenced directly in strings:
+
+```nextflow
+println "PWD = ${PWD}"
+```
+
+In the strict syntax, use `System.getenv()` instead:
+
+```nextflow
+println "PWD = ${System.getenv('PWD')}"
+```
+
+<AddedInVersion version="24.11.0-edge">
+The `env()` function should be used instead of `System.getenv()`:
+
+```nextflow
+println "PWD = ${env('PWD')}"
+```
+</AddedInVersion>
+
+## Restricted syntax
+
+The following patterns are still supported but have been restricted. That is, some syntax variants have been removed.
+
+### Include declarations
+
+In Nextflow DSL2, include declarations can have an `addParams` or `params` clause as described in [Module parameters][module-params]:
+
+```nextflow
+params.message = 'Hola'
+params.target = 'Mundo'
+
+include { sayHello } from './some/module' addParams(message: 'Ciao')
+
+workflow {
+    sayHello()
+}
+```
+
+In the strict syntax, these clauses are no longer supported. Params should be passed to workflows, processes, and functions as explicit inputs:
+
+```nextflow
+include { sayHello } from './some/module'
+
+params.message = 'Hola'
+params.target = 'Mundo'
+
+workflow {
+    sayHello('Ciao', params.target)
+}
+```
+
+Where the `sayHello` workflow is defined as follows:
+
+```nextflow
+workflow sayHello {
+    take:
+    message
+    target
+
+    main:
+    // ...
+}
+```
+
+### Variable declarations
+
+In Groovy, variables can be declared in many different ways:
+
+```groovy
+def a = 1
+final b = 2
+def c = 3, d = 4
+def (e, f) = [5, 6]
+String str = 'hello'
+def Map meta = [:]
+```
+
+In the strict syntax, variables must be declared with `def` and must not specify a type:
+
+```nextflow
+def a = 1
+def b = 2
+def (c, d) = [3, 4]
+def (e, f) = [5, 6]
+def str = 'hello'
+def meta = [:]
+```
+
+< AddedInVersion version="25.10.0" />
+
+Local variables can be declared with a type annotation:
+
+```nextflow
+def a: Integer = 1
+def b: Integer = 2
+def (c: Integer, d: Integer) = [3, 4]
+def (e: Integer, f: Integer) = [5, 6]
+def str: String = 'hello'
+def meta: Map = [:]
+```
+
+Groovy-style type annotations are still supported. However, the language server and `nextflow lint` will automatically convert them to Nextflow-style type annotations when formatting code. Groovy-style type annotations will not be supported in a future version.
+
+### Strings
+
+Groovy supports a wide variety of strings, including multi-line strings, dynamic strings, slashy strings, multi-line dynamic slashy strings, and more.
+
+The strict syntax supports single- and double-quoted strings, multi-line strings, and slashy strings.
+
+Slashy strings cannot be interpolated:
+
+```nextflow
+def id = 'SRA001'
+assert 'SRA001.fastq' ~= /${id}\.f(?:ast)?q/
+```
+
+Use a double-quoted string instead:
+
+```nextflow
+def id = 'SRA001'
+assert 'SRA001.fastq' ~= "${id}\\.f(?:ast)?q"
+```
+
+Slashy strings cannot span multiple lines:
+
+```groovy
+/
+Patterns in the code,
+Symbols dance to match and find,
+Logic unconfined.
+/
+```
+
+Use a multi-line string instead:
+
+```nextflow
+"""
+Patterns in the code,
+Symbols dance to match and find,
+Logic unconfined.
+"""
+```
+
+Dollar slashy strings are not supported:
+
+```groovy
+$/
+echo "Hello world!"
+/$
+```
+
+Use a multi-line string instead:
+
+```nextflow
+"""
+echo "Hello world!"
+"""
+```
+
+### Type conversions
+
+In Groovy, there are two ways to perform type conversions or _casts_:
+
+```groovy
+def map = (Map) readJson(json)  // soft cast
+def map = readJson(json) as Map // hard cast
+```
+
+In the strict syntax, only hard casts are supported. Use an explicit method to cast a value to a different type if one is available. For example, to parse a string as a number:
+
+```groovy
+def x = '42' as Integer
+def x = '42'.toInteger()    // preferred
+```
+
+### Process env inputs and outputs
+
+In Nextflow DSL2, the name of a process `env` input/output can be specified with or without quotes:
+
+```nextflow
+process my_task {
+    input:
+    env FOO
+    env 'BAR'
+
+    // ...
+}
+```
+
+In the strict syntax, the name must be specified with quotes:
+
+```nextflow
+process my_task {
+    input:
+    env 'FOO'
+    env 'BAR'
+
+    // ...
+}
+```
+
+### Implicit process script section
+
+In Nextflow DSL1 and DSL2, the process `script:` section label can almost always be omitted:
+
+```nextflow
+process greet {
+    input:
+    val greeting
+
+    """
+    echo '${greeting}!'
+    """
+}
+```
+
+In the strict syntax, the `script:` label can be omitted only if there are no other sections:
+
+```nextflow
+process hello {
+    """
+    echo 'Hello world!'
+    """
+}
+
+process greet {
+    input:
+    val greeting
+
+    script:
+    """
+    echo '${greeting}!'
+    """
+}
+```
+
+### Workflow onComplete/onError handlers
+
+[Workflow handlers][workflow-handlers] (i.e. `workflow.onComplete` and `workflow.onError`) can be defined in several different ways in a script, but are typically defined as top-level statements and without an equals sign:
+
+```nextflow
+workflow.onComplete {
+    println "Pipeline completed at: $workflow.complete"
+    println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
+}
+```
+
+The strict syntax does not allow statements to be mixed with script declarations, so workflow handlers must be defined in the entry workflow:
+
+```nextflow
+workflow {
+    // ...
+
+    workflow.onComplete = {
+        println "Pipeline completed at: $workflow.complete"
+        println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
+    }
+}
+```
+
+:::note
+A more concise syntax for workflow handlers will be addressed in a future version of the Nextflow language specification.
+:::
+
+## Deprecated syntax
+
+The following patterns are deprecated, and the strict syntax reports warnings for them. These warnings will become errors in the future.
+
+### Process shell section
+
+The process `shell` section is deprecated. Use the `script` section instead. The strict syntax provides error checking to help distinguish between Nextflow variables and Bash variables.
+
+## Best practices
+
+The following patterns are discouraged. The language server reports informative messages for these patterns, which are disabled by default. Enable them by setting the error reporiting mode (**Nextflow > Error reporting mode** in the extension settings) to `paranoid`. These messages may become warnings or errors in the future.
+
+### Implicit closure parameter
+
+In Groovy, a closure with no parameters is assumed to have a single parameter named `it`:
+
+```nextflow
+ch.map { it * 2 }
+```
+
+As a best practice, the closure parameter should be explicitly declared:
+
+```nextflow
+ch.map { v -> v * 2 }   // correct
+ch.map { it -> it * 2 } // also correct
+```
+
+### Using params outside the entry workflow
+
+While params can be used anywhere in the pipeline code, they are only intended to be used in the entry workflow.
+
+As a best practice, processes and workflows should receive params as explicit inputs:
+
+```nextflow
+process myproc {
+    input:
+    val myproc_args
+
+    // ...
+}
+
+workflow myflow {
+    take:
+    myflow_args
+
+    // ...
+}
+
+workflow {
+    myproc(params.myproc_args)
+    myflow(params.myflow_args)
+}
+```
+
+### Process when section
+
+The process [when][process-when] section is discouraged. As a best practice, conditional logic should be implemented in the calling workflow (e.g. using an `if` statement or [filter][operator-filter] operator) instead of the process definition.
+
+## Configuration syntax
+
+<AddedInVersion version="25.02.0-edge">
+The strict config syntax can be enabled in Nextflow by setting the environment variable `NXF_SYNTAX_PARSER=v2`.
+</AddedInVersion>
+
+See [Configuration][config-syntax] for a comprehensive description of the configuration language.
+
+Currently, Nextflow parses config files as Groovy scripts, allowing the use of scripting constructs like variables, helper functions, try-catch blocks, and conditional logic for dynamic configuration:
+
+```groovy
+def getHostname() {
+    // ...
+}
+
+def hostname = getHostname()
+if (hostname == 'small') {
+    params.max_memory = 32.GB
+    params.max_cpus = 8
+}
+else if (hostname == 'large') {
+    params.max_memory = 128.GB
+    params.max_cpus = 32
+}
+```
+
+The strict config syntax does not support functions, and only allows statements (e.g., variables and if statements) within closures. The same dynamic configuration can be achieved by using a dynamic include:
+
+```groovy
+includeConfig ({
+    def hostname = // ...
+    if (hostname == 'small')
+        return 'small.config'
+    else if (hostname == 'large')
+        return 'large.config'
+    else
+        return '/dev/null'
+}())
+```
+
+The include source is a closure that is immediately invoked. It includes a different config file based on the return value of the closure. Including `/dev/null` is equivalent to including nothing.
+
+Each conditional configuration is defined in a separate config file:
+
+```groovy
+// small.config
+params.max_memory = 32.GB
+params.max_cpus = 8
+
+// large.config
+params.max_memory = 128.GB
+params.max_cpus = 32
+```
+
+## Preserving Groovy code
+
+There are two ways to preserve Groovy code:
+
+- Move the code to the `lib` directory
+- Create a plugin
+
+Any Groovy code can be moved into the `lib` directory, which supports the full Groovy language. This approach is useful for temporarily preserving some Groovy code until it can be updated later and incorporated into a Nextflow script. See [The `lib` directory][lib-directory] for more information.
+
+For Groovy code that is complicated or if it depends on third-party libraries, it may be better to create a plugin. Plugins can define custom functions that can be included by Nextflow scripts like a module. Furthermore, plugins can be easily re-used across different pipelines. See [Developing plugins][plugins-dev-page] for more information on how to develop plugins.
+
+[config-syntax]: /nextflow_docs/nextflow_repo/docs/config.mdx#syntax
+[dsl1-page]: /nextflow_docs/nextflow_repo/docs/migrations/dsl1.mdx
+[lib-directory]: /nextflow_docs/nextflow_repo/docs/sharing.mdx#the-lib-directory
+[module-params]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-parameters
+[operator-filter]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#filter
+[plugins-dev-page]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx
+[process-when]: /nextflow_docs/nextflow_repo/docs/process.mdx#when
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[workflow-handlers]: /nextflow_docs/nextflow_repo/docs/notifications.mdx#workflow-handlers
diff --git a/docs/tutorials/data-lineage.md b/docs/tutorials/data-lineage.mdx
similarity index 91%
rename from docs/tutorials/data-lineage.md
rename to docs/tutorials/data-lineage.mdx
index af0687062e..d5efb3f8e5 100644
--- a/docs/tutorials/data-lineage.md
+++ b/docs/tutorials/data-lineage.mdx
@@ -1,10 +1,8 @@
-(data-lineage-page)=
-
 # Getting started with data lineage
 
 Data lineage in Nextflow provides comprehensive tracking of workflow runs, task executions, and output files. This feature helps you verify the integrity and reproducibility of your pipeline results by maintaining a complete history of computations and intermediate data.
 
-:::{warning}
+:::warning
 Data lineage is an experimental feature added in Nextflow 25.04. The functionality may change in future releases.
 :::
 
@@ -18,7 +16,7 @@ Data lineage tracks the complete history of your Nextflow runs, including:
 
 Each lineage record has a unique identifier called a *lineage ID* (LID) that you can use to access and query the data.
 
-:::{note}
+:::note
 The data model for every lineage record is defined in the Nextflow [source code](https://github.com/nextflow-io/nextflow/tree/master/modules/nf-lineage/src/main/nextflow/lineage/model).
 :::
 
@@ -36,11 +34,11 @@ By default, lineage data is stored in the `.lineage` directory in your current w
 lineage.store.location = '<PATH_TO_STORAGE>'
 ```
 
-:::{tip}
+:::tip
 For global configuration, add these settings to `$HOME/.nextflow/config`.
 :::
 
-See the {ref}`config-lineage` configuration scope for details.
+See the [lineage][config-lineage] configuration scope for details.
 
 ## Generate lineage metadata
 
@@ -54,13 +52,13 @@ Nextflow will automatically record the workflow run, task executions, and output
 
 ## Explore lineage
 
-Now that you have generated some lineage metadata, you can explore it from the command line using the {ref}`cli-lineage` command.
+Now that you have generated some lineage metadata, you can explore it from the command line using the [lineage][cli-lineage] command.
 
 First, use the `list` subcommand to list the workflow runs in the lineage store:
 
 ```console
 $ nextflow lineage list
-TIMESTAMP               RUN NAME                SESSION ID                              LINEAGE ID                            
+TIMESTAMP               RUN NAME                SESSION ID                              LINEAGE ID
 2025-05-09 13:28:30 CDT peaceful_blackwell      065bdc6b-89b4-42ee-92c1-2a5af37f2c50    lid://16b31030474f2e96c55f4940bca3ab64
 ```
 
@@ -95,7 +93,7 @@ Every workflow run is represented in the lineage store as a `WorkflowRun` record
 
 The output files of a workflow run can be accessed as `lid://<WORKFLOW_RUN_HASH>/<PATH>`, where `<PATH>` is the file path relative to the workflow output directory.
 
-:::{note}
+:::note
 Files must be published to the workflow output directory as defined by the `outputDir` config option (or `-output-dir` command line option) in order to be recorded as workflow outputs in the lineage store.
 :::
 
@@ -242,13 +240,13 @@ $ nextflow lineage find type=TaskRun workflowRun=lid://16b31030474f2e96c55f4940b
 
 You can use any field defined in the [lineage data model](https://github.com/nextflow-io/nextflow/tree/master/modules/nf-lineage/src/main/nextflow/lineage/model).
 
-:::{tip}
+:::tip
 Since the `find` and `view` subcommands always output JSON, you can use JSON processing tools such as [jq](https://jqlang.org/) to further query and transform results.
 :::
 
 ## Compare task runs
 
-Task run LIDs are based on the standard {ref}`task hash <cache-resume-task-hash>`, which makes it easy to compare two task runs in the lineage metadata. For example, if a task is unexpectedly re-executed during a resumed run, as long as lineage is enabled for both the initial and resumed runs, the two tasks can be compared without any additional runs.
+Task run LIDs are based on the standard [task hash][cache-resume-task-hash], which makes it easy to compare two task runs in the lineage metadata. For example, if a task is unexpectedly re-executed during a resumed run, as long as lineage is enabled for both the initial and resumed runs, the two tasks can be compared without any additional runs.
 
 This section builds on the above [`rnaseq-nf` example](#generate-lineage-metadata) to demonstrate how to compare two task runs in the event of a cache invalidation.
 
@@ -329,7 +327,7 @@ $ nextflow lineage view lid://9410d13abeec617640b5fe9735ba12fc#output
 
 This view can be used to traverse output files directly instead of inferring LIDs from the workflow output directory.
 
-See {ref}`workflow-output-def` for more information about the `output` block.
+See [Workflow outputs][workflow-output-def] for more information about the `output` block.
 
 ## Use lineage in a Nextflow script
 
@@ -349,4 +347,10 @@ It should produce the following output:
 [id:gut, quant:/results/gut/quant, fastqc:/results/gut/fastqc]
 ```
 
-The `fromLineage` channel factory can also be used to query lineage records in a similar manner as the `find` subcommand. See {ref}`channel-from-lineage` for details.
+The `fromLineage` channel factory can also be used to query lineage records in a similar manner as the `find` subcommand. See [fromLineage][channel-from-lineage] for details.
+
+[cache-resume-task-hash]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#task-cache
+[channel-from-lineage]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#fromlineage
+[cli-lineage]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lineage
+[config-lineage]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#lineage
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
\ No newline at end of file
diff --git a/docs/tutorials/flux.mdx b/docs/tutorials/flux.mdx
new file mode 100644
index 0000000000..c404666a2c
--- /dev/null
+++ b/docs/tutorials/flux.mdx
@@ -0,0 +1,148 @@
+# Using Nextflow with Flux
+
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+<AddedInVersion version="22.11.0-edge" />
+
+## Overview
+
+The [Flux Framework](https://flux-framework.org/) is a modern resource manager that can span the space between cloud and HPC. If your center does not provide Flux, you can [build Flux yourself](https://flux-framework.readthedocs.io/en/latest/quickstart.html#building-the-code) and launch it as a job using your resource manager of choice (e.g. SLURM or a cloud provider).
+
+In the [`docker/flux`](https://github.com/nextflow-io/nextflow/tree/master/docker/flux) directory we provide a [Dockerfile for interacting with Flux](https://github.com/nextflow-io/nextflow/tree/master/docker/flux/.devcontainer/Dockerfile) along with a [VSCode Developer Container](https://code.visualstudio.com/docs/devcontainers/containers) environment that you can put at the root of the project to be provided with a Flux agent and the dependencies needed to build Nextflow. There are two ways to use this:
+
+- Build a container from scratch and bind your code to it (e.g. for development or testing)
+- Use VSCode and DevContainers to create a more seamless environment
+
+Both strategies are described below. For this tutorial, you will generally want to prepare a pipeline to use the `flux` executor, create an environment with Flux, start a Flux instance, and interact with it.
+
+## Prepare your pipeline
+
+To run your pipeline with Flux, you'll want to specify it in your config. Here is an example `nextflow.config`:
+
+```groovy
+manifest {
+    mainScript = 'demo.nf'
+    homePage = 'https://github.com/nextflow-io/nextflow/tree/master/docker/flux'
+    description = 'Demo using Nextflow with Flux'
+}
+
+process {
+    executor = 'flux'
+}
+```
+
+For additional Flux settings, see the [Flux executor][flux-executor] section.
+
+Here is an example pipeline that we will use:
+
+```nextflow
+workflow {
+    breakfast = channel.of '🥞️', '🥑️', '🥧️', '🍵️', '🍞️'
+    haveMeal(breakfast)
+}
+
+process haveMeal {
+    debug true
+    input:
+    val food
+    script:
+    """
+    printf '$food for breakfast!'
+    """
+}
+```
+
+## Prepare your environment
+
+You can either build the Docker image from the root of the Nextflow repository:
+
+```console
+$ docker build -f docker/flux/.devcontainer/Dockerfile --platform linux/amd64 -o type=docker -t nextflow-flux .
+```
+
+And then shell into the container for a development environment. You'll need to bind the present working directory to `/code` to see your local changes in the container:
+
+```console
+$ docker run -it -v $PWD:/code nextflow-flux
+```
+
+You can also move the `.devcontainer` directory to the root of your repository, and open it in VSCode:
+
+```console
+$ cp -R docker/flux/.devcontainer .devcontainer
+```
+
+Then open in VSCode, and select **Re-open in container**:
+
+```console
+$ code .
+```
+
+Then you should be able to open a terminal (**Terminal** -> **New Terminal**) to interact with the command line. Try running `make` again! Whichever of these two approaches you take, you should be in a container environment with the `flux` command available.
+
+## Start a Flux instance
+
+Once in your container, you can start an interactive Flux instance (from which you can submit jobs on the command line to test with Nextflow) as follows:
+
+```console
+$ flux start --test-size=4
+```
+
+### Getting familiar with Flux
+
+Here is an example of submitting a job and getting the log for it.
+
+First submit the job:
+
+```console
+$ flux submit echo "HELLO MOTO"
+ƒEzWqspb
+```
+
+Then get the log for it:
+
+```console
+$ flux job attach ƒEzWqspb
+HELLO MOTO
+```
+
+Try submitting a longer job:
+
+```console
+$ flux submit sleep 60
+```
+
+And then seeing it in the jobs listing.
+
+```console
+$ flux jobs
+       JOBID USER     NAME       ST NTASKS NNODES     TIME INFO
+   ƒ4tkMUAAT root     sleep       R      1      1   2.546s ab6634a491bb
+```
+
+## Submitting with Nextflow
+
+Prepare your `nextflow.config` and `demo.nf` in the same directory.
+
+```console
+$ ls .
+demo.nf    nextflow.config
+```
+
+Finally, run the pipeline with Flux:
+
+```console
+$ nextflow -c nextflow.config run demo.nf
+
+N E X T F L O W  ~  version 22.10.0
+Launching `demo.nf` [clever_blackwell] DSL2 - revision: f8cda838cb
+executor >  flux (5)
+[4c/f162db] process > haveMeal (3) [100%] 5 of 5 ✔
+🥞️ for breakfast!
+🍞️ for breakfast!
+🍵️ for breakfast!
+🥑️ for breakfast!
+🥧️ for breakfast!
+```
+
+[flux-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#flux-executor
\ No newline at end of file
diff --git a/docs/tutorials/metrics.md b/docs/tutorials/metrics.mdx
similarity index 88%
rename from docs/tutorials/metrics.md
rename to docs/tutorials/metrics.mdx
index d3d56d0ba1..c2afcced7f 100644
--- a/docs/tutorials/metrics.md
+++ b/docs/tutorials/metrics.mdx
@@ -1,15 +1,12 @@
-(metrics-page)=
-
 # Understanding task resource metrics
 
-This tutorial explains how resource usage metrics are computed from execution reports. See {ref}`Execution report <execution-report>` for more information about how to enable them.
+This tutorial explains how resource usage metrics are computed from execution reports. See [Execution report][execution-report] for more information about how to enable them.
 
 ## CPU Usage
 
 CPU Usage plots report how CPU resources are used by each process.
 
-```{image} ../_static/report-resource-cpu-noheader.png
-```
+![CPU usage](../_static/report-resource-cpu-noheader.png)
 
 **Raw Usage** tabs are expected to show 100% core usage if processes perform one task of pure computation. If tasks are distributed over, 2, 3, or 4 CPUs, the raw usage will be 200%, 300%, or 400%, respectively. **% Allocated** tabs rescale raw usage values relative to the number of CPUs that are set with the `cpus` directive. If the `cpus` directive is not set, CPUs are set to `1` and **% Allocated** tabs will show the same values **Raw Usage** tabs.
 
@@ -17,12 +14,12 @@ For example, using the [stress](https://people.seas.harvard.edu/~apw/stress/) pr
 
 ```nextflow
 process cpu_usage_ex1 {
-  cpus 2
+    cpus 2
 
-  script:
-  """
-  stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
-  """
+    script:
+    """
+    stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
+    """
 }
 
 workflow{
@@ -30,7 +27,7 @@ workflow{
 }
 ```
 
-:::{tip}
+:::tip
 See [Linux stress command with examples](https://www.geeksforgeeks.org/linux-stress-command-with-examples/) for more information about the stress command.
 :::
 
@@ -38,14 +35,14 @@ CPU usage decreases if processes spend some time performing pure computation and
 
 ```nextflow
 process cpu_usage_ex2 {
-  cpus 1
-
-  script:
-  """
-  stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
-  stress -c 1 -t 5 # compute square-root of random numbers during 5s using 1 CPU
-  sleep 5 # use no CPU during 5s
-  """
+    cpus 1
+
+    script:
+    """
+    stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
+    stress -c 1 -t 5 # compute square-root of random numbers during 5s using 1 CPU
+    sleep 5 # use no CPU during 5s
+    """
 }
 
 workflow{
@@ -63,13 +60,13 @@ CPU usage increases if a single step is forked on multiple CPUs:
 
 ```nextflow
 process cpu_usage_ex3 {
-  cpus 2
+    cpus 2
 
-  script:
-  """
-  stress -c 2 -t 10 # compute square-root of random numbers during 10 s using 2 CPUs
-  sleep 10 # use no CPU during 10s
-  """
+    script:
+    """
+    stress -c 2 -t 10 # compute square-root of random numbers during 10 s using 2 CPUs
+    sleep 10 # use no CPU during 10s
+    """
 }
 
 workflow{
@@ -93,6 +90,7 @@ Peak usage during process executions is reported for both physical and virtual m
 
 The relationship is:
 
+
 $$
 vmem \geq RSS + Swap
 $$
@@ -253,20 +251,17 @@ workflow{
 
 The **Virtual (RAM + Disk swap)** tab shows that both `malloc` and `malloc_fill` use the same amount of virtual memory (~1 GiB):
 
-```{image} ../_static/report-resource-memory-vmem.png
-```
+![Memory vmem](../_static/report-resource-memory-vmem.png)
 
 However, the **Physical (RAM)** tab shows that `malloc_fill` uses ~1 GiB of RAM while `malloc` uses ~0 GiB of RAM:
 
-```{image} ../_static/report-resource-memory-ram.png
-```
+![Memory ram](../_static/report-resource-memory-ram.png)
 
 The **% RAM Allocated** tab shows that `malloc` and `malloc_fill` used 0% and 67% of resources set in the `memory` directive, respectively:
 
-```{image} ../_static/report-resource-memory-pctram.png
-```
+![Memory pctram](../_static/report-resource-memory-pctram.png)
 
-:::{warning}
+:::warning
 Memory and storage metrics are reported in bytes. For example, 1 KB = $1024$ bytes, 1 MB = $1024^2$ bytes, and 1 GB = $1024^3$ bytes.
 :::
 
@@ -274,8 +269,7 @@ Memory and storage metrics are reported in bytes. For example, 1 KB = $1024$ byt
 
 **Job Duration** plots report how long each process took to run. It has two tabs. The **Raw Usage** tab shows the job duration and the **% Allocated** tab shows the time that was requested relative to what was requested using the `time` directive. Job duration is sometimes known as elapsed real time, real time or wall time.
 
-```{image} ../_static/report-resource-job-duration.png
-```
+![Job duration](../_static/report-resource-job-duration.png)
 
 ## I/O Usage
 
@@ -306,10 +300,10 @@ workflow{
 
 The **Read** tab shows that ~1 Gib and ~256 Mb are read:
 
-```{image} ../_static/report-resource-io-read.png
-```
+![Resources io read](../_static/report-resource-io-read.png)
 
 The **Write** tab shows that ~1 Gib and ~256 Mb are written:
 
-```{image} ../_static/report-resource-io-write.png
-```
+![Resources io write](../_static/report-resource-io-write.png)
+
+[execution-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#execution-report
diff --git a/docs/tutorials/workflow-outputs.md b/docs/tutorials/workflow-outputs.mdx
similarity index 87%
rename from docs/tutorials/workflow-outputs.md
rename to docs/tutorials/workflow-outputs.mdx
index a9d3adf750..bfce516bd3 100644
--- a/docs/tutorials/workflow-outputs.md
+++ b/docs/tutorials/workflow-outputs.mdx
@@ -1,8 +1,6 @@
-(migrating-workflow-outputs)=
-
 # Migrating to workflow outputs
 
-The {ref}`workflow output definition <workflow-output-def>` is a new way to define the top-level outputs of a workflow. It is a replacement for the {ref}`publishDir <process-publishdir>` directive. This tutorial describes these changes and explains how to migrate from `publishDir` to workflow outputs using the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline as an example.
+The [workflow output definition][workflow-output-def] is a new way to define the top-level outputs of a workflow. It is a replacement for the [publishDir][process-publishdir] directive. This tutorial describes these changes and explains how to migrate from `publishDir` to workflow outputs using the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline as an example.
 
 ## Overview
 
@@ -10,7 +8,7 @@ In Nextflow DSL1, pipelines were defined in a single script and there was no con
 
 Nextflow DSL2 introduced workflows and modules, making it easier to develop large and complex pipelines. However, DSL2 retained the same process-based publishing syntax and became unwieldy for several reasons:
 
-- **Mismatch with reusable modules**: Publishing rules often depend on how a process is used in a pipeline. This made it impractical to set `publishDir` in a reusable way for processes that are shared across many pipelines. Publishing rules could be defined in the configuration, but this approach requires extensive use of {ref}`process selectors <config-process-selectors>`, which are difficult to use for large pipelines.
+- **Mismatch with reusable modules**: Publishing rules often depend on how a process is used in a pipeline. This made it impractical to set `publishDir` in a reusable way for processes that are shared across many pipelines. Publishing rules could be defined in the configuration, but this approach requires extensive use of [process selectors][config-process-selectors], which are difficult to use for large pipelines.
 
 - **Fragmented outputs**: It is difficult to get a concise view of a workflow's outputs when publishing rules are separated across many different modules.
 
@@ -30,7 +28,7 @@ Workflow outputs were introduced to address these problems by providing a unifie
 
 ## Timeline
 
-Nextflow {ref}`24.04 <workflow-outputs-first-preview>` introduced the workflow output definition as a preview feature. It has since undergone multiple revisions, with the third preview currently available in Nextflow {ref}`25.04 <workflow-outputs-third-preview>`.
+Nextflow [24.04][workflow-outputs-first-preview] introduced the workflow output definition as a preview feature. It has since undergone multiple revisions, with the third preview currently available in Nextflow [25.04][workflow-outputs-third-preview].
 
 Nextflow 25.10 will finalize workflow outputs and bring them out of preview. The `publishDir` directive will continue to be supported, but will be deprecated. It may be removed in a future release.
 
@@ -38,7 +36,7 @@ Nextflow 25.10 will finalize workflow outputs and bring them out of preview. The
 
 This section describes how to migrate from `publishDir` to workflow outputs using the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline as an example. To view the completed migration, see the [`preview-25-04`](https://github.com/nextflow-io/rnaseq-nf/tree/preview-25-04) branch of the rnaseq-nf repository.
 
-See {ref}`rnaseq-nf-page` for an introduction to the rnaseq-nf pipeline.
+See [Getting started with rnaseq-nf][rnaseq-nf-page] for an introduction to the `rnaseq-nf` pipeline.
 
 ### Replacing `publishDir` with workflow outputs
 
@@ -71,7 +69,7 @@ output {
 }
 ```
 
-:::{note}
+:::note
 Each output assigned in the `publish:` section must be declared in the `output` block, and vice versa.
 :::
 
@@ -193,7 +191,7 @@ output {
 
 Preserving the sample ID in each output channel allows you to customize the publish path without trying to parse the file name. The dynamic path is applied to each channel value to determine the target name for the given file.
 
-:::{note}
+:::note
 The closure parameters for the dynamic publish path must match the structure of the published channel.
 :::
 
@@ -291,3 +289,10 @@ $ cat results/samples.csv
 ```
 
 In the future, if you add a tool with per-sample outputs, you only need to join the tool output into the `samples_ch` channel and update the output `path` directive accordingly. This approach keeps the output definition concise as you add more tools to the pipeline. Additionally, a single unified index file for all per-sample outputs is easier for downstream pipelines to consume, rather than cross-referencing multiple related index files.
+
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[process-publishdir]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#publishdir
+[rnaseq-nf-page]: /nextflow_docs/nextflow_repo/docs/tutorials/rnaseq-nf.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-outputs-first-preview]: /nextflow_docs/nextflow_repo/docs/migrations/24-04.mdx#workflow-outputs-first-preview
+[workflow-outputs-third-preview]: /nextflow_docs/nextflow_repo/docs/migrations/25-04.mdx
diff --git a/docs/updating-nextflow.md b/docs/updating-nextflow.mdx
similarity index 80%
rename from docs/updating-nextflow.md
rename to docs/updating-nextflow.mdx
index c4b148fb49..874a99542a 100644
--- a/docs/updating-nextflow.md
+++ b/docs/updating-nextflow.mdx
@@ -1,5 +1,3 @@
-(updating-nextflow-page)=
-
 # Updating Nextflow
 
 This page describes Nextflow release cadence, how to self-update Nextflow, and how select your version of Nextflow.
@@ -10,29 +8,27 @@ A stable version of Nextflow is released in the 4th and 10th month of each year.
 
 Nextflow uses [Calendar Versioning](https://calver.org). Versions are numbered as `<year>.<month>.<patch>`. For example, `23.10.1` corresponds to the first patch of the October 2023 stable release.
 
-See {ref}`migrations-page` for a list of migration guides for each stable release. See the [changelog](https://github.com/nextflow-io/nextflow/blob/master/changelog.txt) for an exhaustive list of changes across all releases.
+See [Migration notes][migrations-page] for a list of migration guides for each stable release. See the [changelog](https://github.com/nextflow-io/nextflow/blob/master/changelog.txt) for an exhaustive list of changes across all releases.
 
 ## Self-update
 
 To update to the latest stable release of Nextflow, run the `self-update` command:
 
-```{code-block} bash
-:class: copyable
+```bash
 nextflow self-update
 ```
 
 To use the latest edge release, set `NXF_EDGE=1` when updating Nextflow:
 
-```{code-block} bash
-:class: copyable
+```bash
 NXF_EDGE=1 nextflow self-update
 ```
 
-:::{note}
+:::note
 When updating from an edge release to a stable release, you must explicitly set `NXF_EDGE=0`.
 :::
 
-:::{warning}
+:::warning
 Nextflow will update its executable during the self-update process. The update can fail if the Nextflow executable is in a directory with restricted permissions.
 :::
 
@@ -40,29 +36,28 @@ Nextflow will update its executable during the self-update process. The update c
 
 The `NXF_VER` environment variable can be used to define which version of Nextflow to use. To switch to a specific version of Nextflow for a single run, set the `NXF_VER` environment variable in your execution command. For example:
 
-```{code-block} bash
-:class: copyable
+```bash
 NXF_VER=23.10.0 nextflow info
 ```
 
 To set a specific version of Nextflow for a terminal session, export the `NXF_VER` environment variable. For example:
 
-```{code-block} bash
-:class: copyable
+```bash
 export NXF_VER=23.10.0
 ```
 
 To set a specific version of Nextflow for your user profile, add the above `NXF_VER` export command to your shell configuration file, such as `~/.bashrc` or `~/.zshrc`, and restart your session.
 
-:::{tip}
+:::tip
 You can use `NXF_VER` to switch to an edge release. For example:
 
-```{code-block} bash
-:class: copyable
+```bash
 NXF_VER=24.06.0-edge nextflow info
 ```
 :::
 
-:::{warning}
+:::warning
 Nextflow will update its executable during the self-update process. The update can fail if the Nextflow executable is in a directory with restricted permissions.
 :::
+
+[migrations-page]: /nextflow_docs/nextflow_repo/docs/migrations/index.mdx
diff --git a/docs/updating-spot-retries.mdx b/docs/updating-spot-retries.mdx
new file mode 100644
index 0000000000..75b0802fd1
--- /dev/null
+++ b/docs/updating-spot-retries.mdx
@@ -0,0 +1,84 @@
+# Spot Instance failures and retries
+
+This page describes changes in how Nextflow handles Spot Instance failures and retries on AWS and Google Cloud, the impact of those changes, and how to configure spot retry behavior for your pipelines. These changes apply to Nextflow 24.10 and later.
+
+## Retry behavior
+
+Up to version 24.10, Nextflow would silently retry Spot Instance failures up to `5` times when using AWS Batch or Google Batch. These retries were controlled by cloud-specific configuration parameters (e.g., `aws.batch.maxSpotAttempts`) and happened in cloud infrastructure without explicit visibility to Nextflow.
+
+### Before Nextflow 24.10
+
+By default, Nextflow would instruct AWS and Google to automatically retry jobs lost to Spot reclamation up to `5` times. Retries were handled by the cloud provider _within_ a Nextflow task. It was often unclear that tasks were restarted as there was no explicit message. Task runtimes and associated cloud costs were increased because they included the runtime of the reclaimed and retried tasks. Due to the high likelihood of reclamation before completion, long-running tasks running on Spot Instances frequently required retries, leading to inefficient allocation of resources and higher costs.
+
+### After Nextflow 24.10
+
+The default Spot reclamation retry setting changed to `0` on AWS and Google. By default, no _internal_ retries are attempted on these platforms. Spot reclamations lead to an immediate failure, exposed to Nextflow in the same way as other generic failures (for example, returning `exit code 1` on AWS). Nextflow treats these failures like any other job failure, unless a retry strategy is configured.
+
+## Impact on existing workflows
+
+If you rely on silent Spot retries (the previous default behavior), you may now see more tasks fail with the following characteristics:
+
+- **AWS**: Generic failure with `exit code 1`. You may see messages indicating the host machine was terminated.
+
+- **Google**: Spot reclamation typically produces a specific code, but is now surfaced as a recognizable task failure in Nextflow logs.
+
+Since the default for Spot retries is now `0`, you must actively enable a retry strategy if you want Nextflow to handle reclaimed Spot Instances automatically.
+
+## Possible actions
+
+There are four possible actions.
+
+### Do nothing
+
+If you do not configure anything, you will observe more pipeline failures when Spot Instances are reclaimed. This approach provides clearer visibility into failures. Failed tasks can be re-run with the `-resume` option. However, frequent task reclamation may lead to a higher failure rate and each retry requires manual intervention.
+
+:::note
+If you resume the pipeline using the resume option, it will pick up at the point the pipeline was interrupted and start with a retry of that task.
+:::
+
+### Re-enable Spot retries
+
+You can re-enable Spot retries for each provider in your Nextflow config:
+
+```groovy
+aws.batch.maxSpotAttempts = 5
+google.batch.maxSpotAttempts = 5
+```
+
+The above example sets the maximum number of Spot retries to `5` for both AWS and Google.
+
+### Make Spot failures visible and retry them
+
+You can set `maxRetries` to enable Nextflow-level retries for any failure:
+
+```groovy
+process.maxRetries = 5
+```
+
+The above example sets retries to `5` for any failures across all providers.
+
+### Use Fusion Snapshots
+
+*This option is only available for AWS Batch.*
+
+If you have long-running tasks where progress lost due to Spot reclamation is costly, consider [Fusion Snapshots](https://docs.seqera.io/fusion/guide/snapshots) (if supported by your environment). Fusion Snapshots allow you to resume a partially completed task on a new machine if a Spot Instance is reclaimed, thereby reducing wasted compute time.
+
+Key features of Fusion Snapshots:
+
+- Jobs do not need to start from scratch after reclamation.
+- Especially useful for tasks that take many hours or days to complete.
+- May significantly reduce costs and run times in high-reclamation environments.
+
+See [Fusion Snapshots for AWS Batch](https://docs.seqera.io/fusion/guide/snapshots) for more information.
+
+## Best practices
+
+Best practices for Spot Instance failures and retries:
+
+- **Evaluate job duration**: If your tasks are very long (multiple hours or more), Spot Instances can cause repeated interruptions. Consider using on-demand instances or Fusion Snapshots.
+
+- **Set sensible retry limits**: If you enable Spot retries, choose a retry count that balances the cost savings of Spot usage against the overhead of restarting tasks.
+
+- **Monitor logs and exit codes**: Failures due to Spot reclamation will now appear in Nextflow logs. Monitor failures and fine-tune your strategy.
+
+- **Consider partial usage of Spot**: Some workflows may mix on-demand instances for critical or long tasks and Spot Instances for shorter, less critical tasks. This can optimize cost while minimizing wasted compute time.
diff --git a/docs/vscode.md b/docs/vscode.mdx
similarity index 94%
rename from docs/vscode.md
rename to docs/vscode.mdx
index ac3a716edf..a02fefad8b 100644
--- a/docs/vscode.md
+++ b/docs/vscode.mdx
@@ -1,5 +1,3 @@
-(vscode-page)=
-
 # VS Code integration
 
 The [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) provides language support for Nextflow pipelines in [VS Code](https://code.visualstudio.com/).
@@ -18,8 +16,8 @@ The extension highlights source code in red for errors and yellow for warnings.
 
 To view all diagnostics for the workspace, open the **Problems** tab. Here, you can search for diagnostics by diagnostic message, filename, and so on.
 
-:::{note}
-The language server parses scripts and config files according to the {ref}`Nextflow language specification <syntax-page>`, which is more strict than the Nextflow CLI. See {ref}`strict-syntax-page` for more information.
+:::note
+The language server parses scripts and config files according to the [Nextflow language specification][syntax-page], which is more strict than the Nextflow CLI. See [Preparing for strict syntax][strict-syntax-page] for more information.
 :::
 
 ### Hover hints
@@ -85,10 +83,11 @@ Report issues at [nextflow-io/vscode-language-nextflow](https://github.com/nextf
 
 - The language server provides limited support for Groovy scripts in the `lib` directory. Errors in Groovy scripts are not reported as diagnostics, and changing a Groovy script does not automatically re-compile the Nextflow scripts that reference it. Edit the Nextflow script or close and re-open it to refresh the diagnostics.
 
-(vscode-language-server)=
-
 ## Language server
 
 The Nextflow language server implements the [Language Server Protocol (LSP)](https://microsoft.github.io/language-server-protocol/) for Nextflow scripts and config files. It is distributed as a standalone Java application and can be integrated with any editor that functions as an LSP client.
 
 Currently, only the VS Code integration is officially supported, but community contributions for other editors are welcome. Visit the [GitHub issues](https://github.com/nextflow-io/language-server/issues) page for the latest updates on community-led integrations.
+
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
diff --git a/docs/wave.mdx b/docs/wave.mdx
new file mode 100644
index 0000000000..98747257f8
--- /dev/null
+++ b/docs/wave.mdx
@@ -0,0 +1,216 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Wave containers
+
+<AddedInVersion version="22.10.0" />
+
+[Wave](https://seqera.io/wave/) is a container provisioning service integrated with Nextflow. With Wave, you can build, upload, and manage the container images required by your data analysis workflows automatically and on-demand during pipeline execution.
+
+## Getting started
+
+### Wave configuration
+
+Wave can be used in any Nextflow pipeline by adding the following snippet to your `nextflow.config` file:
+
+```groovy
+wave {
+  enabled = true
+}
+
+tower {
+  accessToken = '<your access token>'
+}
+```
+
+:::note
+The Seqera Platform access token is not mandatory, but it is recommended in order to access private container repositories and pull public containers without being affected by service rate limits. Credentials should be made available to Wave using the [credentials manager](https://docs.seqera.io/platform/latest/credentials/overview) in Seqera Platform.
+:::
+
+## Use cases
+
+### Authenticate private repositories
+
+Wave allows the use of private repositories in your Nextflow pipelines. The repository access keys must be provided in the form of [Seqera Platform credentials](https://docs.seqera.io/platform/latest/credentials/overview/).
+
+Once the credentials have been created, simply specify your [personal access token](https://docs.seqera.io/platform/23.3.0/api/overview#authentication) in your pipeline configuration file. If the credentials were created in a Seqera Platform organization workspace, specify the workspace ID as well in the config file as shown below:
+
+```groovy
+tower {
+  accessToken = '<your access token>'
+  workspaceId = '<your workspace id>'
+}
+```
+
+### Build module containers
+
+Wave can build and provision container images on-demand for your Nextflow pipelines.
+
+To enable this feature, add the Dockerfile of the container to be built in the [module directory][module-directory] where the pipeline process is defined. When Wave is enabled, it automatically uses the Dockerfile to build the required container, upload to the registry, and it uses the container to carry out the tasks defined in the module.
+
+:::tip
+Make sure the process does not declare a `container` directive, otherwise it will take precedence over the Dockerfile definition.
+:::
+
+If a process uses a `container` directive and you still want to build the container using the Dockerfile provided in the module directory, add the following setting to the pipeline config file:
+
+```groovy
+wave.strategy = ['dockerfile','container']
+```
+
+This setting instructs Wave to prioritize the module Dockerfile over process `container` directives.
+
+:::warning
+When building containers, Wave currently does not support `ADD`, `COPY`, or any other Dockerfile commands that access files in the host file system.
+:::
+
+### Build Conda based containers
+
+Wave allows the provisioning of containers based on the [`conda`][process-conda] directive used by the processes in your pipeline. This is a quick alternative to building Conda packages in the local computer. Moreover, this enables the use of Conda packages in your pipeline when deploying to cloud-native platforms such as AWS Batch and Kubernetes, which do not allow the easy use of the Conda package manager.
+
+With Wave enabled in your pipeline, simply define the `conda` requirements in the pipeline processes, provided the same process does not also specify a `container` directive or a Dockerfile.
+
+In the latter case, add the following setting to your pipeline configuration:
+
+```groovy
+wave.strategy = ['conda']
+```
+
+The above setting instructs Wave to use the `conda` directive to provision the pipeline containers and ignore the `container` directive and any Dockerfile(s).
+
+:::tip
+Some configuration options in the `conda` scope are used when Wave is used to build Conda-based containers.
+For example, the Conda channels and their priority can be set with `conda.channels`:
+
+```groovy
+wave.strategy = 'conda'
+conda.channels = 'conda-forge,bioconda'
+```
+:::
+
+Packages from the [Python Package Index](https://pypi.org/) can also be added to a Conda `environment.yml` file. See [Conda and PyPI][conda-pypi] for more information.
+
+### Build Singularity native images
+
+<AddedInVersion version="23.09.0-edge" />
+
+Nextflow can build Singularity native images on-demand either using `Singularityfile`,
+Conda packages or Spack packages. The Singularity images are automatically uploaded in a container registry OCI compliant
+of your choice and stored as a [ORAS artefact](https://oras.land/).
+
+:::note
+This feature requires Singularity (or Apptainer) version supporting the pull of images using the `oras:` pseudo-protocol.
+:::
+
+For example to enable the provisioning of Singularity images in your pipeline use the following configuration snippet:
+
+```groovy
+singularity.enabled = true
+wave.enabled = true
+wave.freeze = true
+wave.strategy = ['conda']
+wave.build.repository = 'docker.io/user/repo'
+```
+
+In the above configuration replace `docker.io/user/repo` with a repository of your choice where Singularity image files
+should be uploaded.
+
+:::note
+When using a private repository, the repository access keys must be provided via the Seqera Platform credentials manager (see [Use cases](#use-cases)).
+
+Moreover the access to the repository must be granted in the compute nodes by using the command singularity remote login. See Singularity documentation for further details.
+:::
+
+:::note
+In order to build Singularity native images, both `singularity.ociAutoPull` and `singularity.ociMode` need to be disabled in the configuration. See [singularity][config-singularity] for more information.
+:::
+
+### Push to a private repository
+
+Containers built by Wave are uploaded to the Wave default repository hosted on AWS ECR at `195996028523.dkr.ecr.eu-west-1.amazonaws.com/wave/build`. The images in this repository are automatically deleted 1 week after the date of their push.
+
+If you want to store Wave containers in your own container repository use the following settings in the Nextflow configuration file:
+
+```groovy
+wave.build.repository = 'example.com/your/build-repo'
+wave.build.cacheRepository = 'example.com/your/cache-repo'
+```
+
+The first repository is used to store the built container images. The second one is used to store the individual image layers for caching purposes.
+
+The repository access keys must be provided as Seqera Platform credentials (see
+[Authenticate private repositories](#authenticate-private-repositories) above).
+
+### Mirroring containers
+
+Wave allows mirroring, i.e., copying containers used by your pipeline into a container registry of your choice. This allows the pipeline to pull containers from the target registry rather than the original registry.
+
+Mirroring is useful to create an on-demand cache of container images that are co-located in the same region where the pipeline
+is executed, and therefore optimising cost and network efficiency.
+
+Include the following settings in your Nextflow configuration to enable this capability:
+
+```groovy
+wave.enabled = true
+wave.mirror = true
+wave.build.repository = '<YOUR REGISTRY>'
+tower.accessToken = '<YOUR ACCESS TOKEN>'
+```
+
+In the above snippet, replace `<YOUR REGISTRY>` with a container registry of your choice. For example, `quay.io` (no prefix or suffix is needed).
+The container will be copied with the same name, tag, and checksum in the specified registry. For example, if the source
+container is `quay.io/biocontainers/bwa:0.7.13--1` and the build repository setting is `example.com`, the resulting container
+name is `example.com/biocontainers/bwa:0.7.13--1`.
+
+:::tip
+When using a path prefix in the target registry name, it will be prepended to the resulting container name. For example,
+having `quay.io/biocontainers/bwa:0.7.13--1` as source container and `example.com/library` as build repository, the resulting
+container will be named `example.com/library/biocontainers/bwa:0.7.13--1`.
+:::
+
+The credentials to allow the push of containers to the target repository need to be provided via the Seqera Platform
+credentials manager. The account used for this is specified by the `tower.accessToken` in the configuration above.
+
+### Container security scanning
+
+Wave enables the scanning of containers used in your pipelines for security vulnerabilities.
+If any issues are detected, it will trigger an execution error and provide a report.
+
+To enable this capability add the following settings to your Nextflow configuration file:
+
+```groovy
+wave.enabled = true
+wave.scan.mode = 'required'
+tower.accessToken = '<YOUR ACCESS TOKEN>'
+```
+
+Nextflow will only allow the use of containers with no security
+vulnerabilities when using these settings. You can define the level of accepted vulnerabilities using `wave.scan.allowedLevels`. For example:
+
+```groovy
+wave.scan.allowedLevels = 'low,medium'
+```
+
+The above setting will allow the use of containers with *low* and *medium* vulnerabilities. Accepted values are `low`, `medium`, `high`, and `critical`. See [common vulnerabilities scoring system](https://en.wikipedia.org/wiki/Common_Vulnerability_Scoring_System) for more information about these levels.
+
+:::note
+Wave's security scanning applies to any container used in your pipeline, whether it was built by Wave or simply accessed through it. The security scan automatically expires after one week. If a container is accessed again after 7 days or more, the scan will be re-executed.
+:::
+
+### Run pipelines using Fusion file system
+
+Wave containers allow you to run your containerized workflow with [Fusion][fusion-page].
+
+This enables the use of an object storage bucket such as AWS S3 or Google Cloud Storage as your pipeline work directory, simplifying and speeding up many operations on local, AWS Batch, Google Batch or Kubernetes executions.
+
+See [Fusion][fusion-page] for more information.
+
+## Advanced settings
+
+Wave advanced configuration settings are described in the [Wave][config-wave] section on the Nextflow configuration page.
+
+[conda-pypi]: /nextflow_docs/nextflow_repo/docs/conda.mdx#python-packages-from-pypi
+[config-singularity]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#singularity
+[config-wave]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#wave
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[module-directory]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-directory
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
diff --git a/docs/workflow.mdx b/docs/workflow.mdx
new file mode 100644
index 0000000000..5b9069727b
--- /dev/null
+++ b/docs/workflow.mdx
@@ -0,0 +1,735 @@
+import { AddedInVersion, ChangedInVersion, DeprecatedInVersion } from '@site/src/components/VersionedAdmonitions';
+
+# Workflows
+
+In Nextflow, a **workflow** is a function that is specialized for composing processes and dataflow logic (i.e. channels and operators).
+
+See [Workflow][syntax-workflow] for a full description of the workflow syntax.
+
+:::note
+Workflows were introduced in DSL2. If you are still using DSL1, see [Migrating from DSL1][dsl1-page] for more information about how to migrate your Nextflow pipelines to DSL2.
+:::
+
+## Entry workflow
+
+A script can define up to one *entry workflow*, which does not have a name and serves as the entrypoint of the script:
+
+```nextflow
+workflow {
+    channel.of('Bonjour', 'Ciao', 'Hello', 'Hola')
+        .map { v -> "$v world!" }
+        .view()
+}
+```
+
+## Parameters
+
+Parameters can be declared in a Nextflow script with the `params` block or with *legacy* parameter declarations.
+
+### Params block
+
+<AddedInVersion version="25.10.0" />
+
+:::note
+This feature requires the [strict syntax][strict-syntax-page] to be enabled (`NXF_SYNTAX_PARSER=v2`).
+:::
+
+A script can declare parameters using the `params` block:
+
+```nextflow
+params {
+    // Path to input data.
+    input: Path
+
+    // Whether to save intermediate files.
+    save_intermeds: Boolean = false
+}
+```
+
+The following types can be used for parameters:
+
+- [Boolean][stdlib-types-boolean]
+- [Float][stdlib-types-float]
+- [Integer][stdlib-types-integer]
+- [Path][stdlib-types-path]
+- [String][stdlib-types-string]
+
+Parameters can be used in the entry workflow:
+
+```nextflow
+workflow {
+    analyze(params.input, params.save_intermeds)
+}
+```
+
+:::note
+As a best practice, parameters should only be used directly in the entry workflow and passed to workflows and processes as explicit inputs.
+:::
+
+The default value can be overridden by the command line, params file, or config file. Parameters from multiple sources are resolved in the order described in [Pipeline parameters][cli-params]. Parameters specified on the command line are converted to the appropriate type based on the corresponding type annotation.
+
+A parameter that doesn't specify a default value is a *required* param. If a required param is not given a value at runtime, the run will fail.
+
+### Legacy parameters
+
+Parameters can be declared by assigning a `params` property to a default value:
+
+```nextflow
+params.input = '/some/data/file'
+params.save_intermeds = false
+
+workflow {
+    if( params.input )
+        analyze(params.input, params.save_intermeds)
+    else
+        analyze(fake_input(), params.save_intermeds)
+}
+```
+
+The default value can be overridden by the command line, params file, or config file. Parameters from multiple sources are resolved in the order described in [Pipeline parameters][cli-params].
+
+## Named workflows
+
+A *named workflow* is a workflow that can be called by other workflows:
+
+```nextflow
+workflow my_workflow {
+    hello()
+    bye( hello.out.collect() )
+}
+
+workflow {
+    my_workflow()
+}
+```
+
+The above example defines a workflow named `my_workflow` which is called by the entry workflow. Both `hello` and `bye` could be any other process or workflow.
+
+### Takes and emits
+
+The `take:` section is used to declare the inputs of a named workflow:
+
+```nextflow
+workflow my_workflow {
+    take:
+    data1
+    data2
+
+    main:
+    hello(data1, data2)
+    bye(hello.out)
+}
+```
+
+Inputs can be specified like arguments when calling the workflow:
+
+```nextflow
+workflow {
+    my_workflow( channel.of('/some/data') )
+}
+```
+
+The `emit:` section is used to declare the outputs of a named workflow:
+
+```nextflow
+workflow my_workflow {
+    main:
+    hello(data)
+    bye(hello.out)
+
+    emit:
+    bye.out
+}
+```
+
+When calling the workflow, the output can be accessed using the `out` property, i.e. `my_workflow.out`.
+
+If an output is assigned to a name, the name can be used to reference the output from the calling workflow. For example:
+
+```nextflow
+workflow my_workflow {
+    main:
+    hello(data)
+    bye(hello.out)
+
+    emit:
+    my_data = bye.out
+}
+```
+
+The result of the above workflow can be accessed using `my_workflow.out.my_data`.
+
+:::note
+Every output must be assigned to a name when multiple outputs are declared.
+:::
+
+## Calling processes and workflows
+
+Processes and workflows are called like functions, passing their inputs as arguments:
+
+```nextflow
+process hello {
+    output:
+    path 'hello.txt', emit: txt
+
+    script:
+    """
+    your_command > hello.txt
+    """
+}
+
+process bye {
+    input:
+    path 'hello.txt'
+
+    output:
+    path 'bye.txt', emit: txt
+
+    script:
+    """
+    another_command hello.txt > bye.txt
+    """
+}
+
+workflow hello_bye {
+    take:
+    data
+
+    main:
+    hello()
+    bye(data)
+}
+
+workflow {
+    data = channel.fromPath('/some/path/*.txt')
+    hello_bye(data)
+}
+```
+
+Processes and workflows have a few extra rules for how they can be called:
+
+- Processes and workflows can only be called by workflows
+
+- A given process or workflow can only be called once in a given workflow. To use a process or workflow multiple times in the same workflow, use [Module aliases][module-aliases].
+
+The "return value" of a process or workflow call is the process outputs or workflow emits, respectively. The return value can be assigned to a variable or passed into another call:
+
+```nextflow
+workflow hello_bye {
+    take:
+    data
+
+    main:
+    bye_out = bye(hello(data))
+
+    emit:
+    bye_out
+}
+
+workflow {
+    data = channel.fromPath('/some/path/*.txt')
+    bye_out = hello_bye(data)
+}
+```
+
+Named outputs can be accessed as properties of the return value:
+
+```nextflow
+workflow hello_bye {
+    take:
+    data
+
+    main:
+    hello_out = hello(data)
+    bye_out = bye(hello_out.txt)
+
+    emit:
+    bye = bye_out.txt
+}
+
+workflow {
+    data = channel.fromPath('/some/path/*.txt')
+    flow_out = hello_bye(data)
+    bye_out = flow_out.bye
+}
+```
+
+As a convenience, process and workflow outputs can also be accessed without first assigning to a variable, by using the `.out` property of the process or workflow name:
+
+```nextflow
+workflow hello_bye {
+    take:
+    data
+
+    main:
+    hello(data)
+    bye(hello.out)
+
+    emit:
+    bye = bye.out
+}
+
+workflow {
+    data = channel.fromPath('/some/path/*.txt')
+    hello_bye(data)
+    hello_bye.out.bye.view()
+}
+```
+
+:::note
+Process named outputs are defined using the `emit` option on a process output. See [naming process outputs][process-naming-outputs] for more information.
+:::
+
+:::note
+Process and workflow outputs can also be accessed by index (e.g., `hello.out[0]`, `hello.out[1]`, etc.). As a best practice, multiple outputs should be accessed by name.
+:::
+
+Workflows can be composed in the same way:
+
+```nextflow
+workflow flow1 {
+    take:
+    data
+
+    main:
+    tick(data)
+    tack(tick.out)
+
+    emit:
+    tack.out
+}
+
+workflow flow2 {
+    take:
+    data
+
+    main:
+    tick(data)
+    tock(tick.out)
+
+    emit:
+    tock.out
+}
+
+workflow {
+    data = channel.fromPath('/some/path/*.txt')
+    flow1(data)
+    flow2(flow1.out)
+}
+```
+
+:::note
+The same process can be called in different workflows without using an alias, like `tick` in the above example, which is used in both `flow1` and `flow2`. The workflow call stack determines the *fully qualified process name*, which is used to distinguish the different process calls, i.e. `flow1:tick` and `flow2:tick` in the above example.
+:::
+
+:::tip
+The fully qualified process name can be used as a [process selector][config-process-selectors] in a Nextflow configuration file, and it takes priority over the simple process name.
+:::
+
+## Special operators
+
+The following operators have a special meaning when used in a workflow with process and workflow calls.
+
+### Pipe `|`
+
+The `|` *pipe* operator can be used to chain processes, operators, and workflows:
+
+```nextflow
+process greet {
+    input:
+    val data
+
+    output:
+    val result
+
+    exec:
+    result = "$data world"
+}
+
+workflow {
+    channel.of('Hello','Hola','Ciao')
+        | greet
+        | map { v -> v.toUpperCase() }
+        | view
+}
+```
+
+The above snippet defines a process named `greet` and invokes it with the input channel. The result is then piped to the [map][operator-map] operator, which converts each string to uppercase, and finally to the [view operator][operator-view] operator which prints it.
+
+The same code can also be written as:
+
+```nextflow
+workflow {
+    ch1 = channel.of('Hello','Hola','Ciao')
+    ch2 = greet( ch1 )
+    ch2.map { v -> v.toUpperCase() }.view()
+}
+```
+
+### And `&`
+
+The `&` *and* operator can be used to call multiple processes in parallel with the same channel(s):
+
+```nextflow
+process greet {
+    input:
+    val data
+
+    output:
+    val result
+
+    exec:
+    result = "$data world"
+}
+
+process to_upper {
+    input:
+    val data
+
+    output:
+    val result
+
+    exec:
+    result = data.toUpperCase()
+}
+
+workflow {
+    channel.of('Hello')
+        | map { v -> v.reverse() }
+        | (greet & to_upper)
+        | mix
+        | view
+}
+```
+
+In the above snippet, the initial channel is piped to the [map][operator-map] operator, which reverses the string value. Then, the result is passed to the processes `greet` and `to_upper`, which are executed in parallel. Each process outputs a channel, and the two channels are combined using the [mix][operator-mix] operator. Finally, the result is printed using the [view][operator-view] operator.
+
+The same code can also be written as:
+
+```nextflow
+workflow {
+    ch = channel.of('Hello').map { v -> v.reverse() }
+    ch_greet = greet(ch)
+    ch_upper = to_upper(ch)
+    ch_greet.mix(ch_upper).view()
+}
+```
+
+## Process and workflow recursion
+
+<AddedInVersion version="21.11.0-edge" />
+
+:::note
+This feature requires the `nextflow.preview.recursion` feature flag to be enabled.
+:::
+
+Processes can be invoked recursively using the `recurse` method.
+
+```nextflow file=./snippets/recurse-process.nf
+```
+
+```nextflow file=./snippets/recurse-process.out
+```
+
+In the above example, the `count_down` process is first invoked with the value `params.start`. On each subsequent iteration, the process is invoked again using the output from the previous iteration. The recursion continues until the specified condition is satisfied, as defined by the `until` method, which terminates the recursion.
+
+The recursive output can also be limited using the `times` method:
+
+```groovy
+count_down
+    .recurse(params.start)
+    .times(3)
+    .view { v -> "${v}..." }
+```
+
+Workflows can also be invoked recursively:
+
+```nextflow file=./snippets/recurse-workflow.nf
+```
+
+```console file=./snippets/recurse-workflow.out
+```
+
+**Limitations**
+
+- A recursive process or workflow must have matching inputs and outputs, such that the outputs for each iteration can be supplied as the inputs for the next iteration.
+
+- Recursive workflows cannot use *reduction* operators such as `collect`, `reduce`, and `toList`, because these operators cause the recursion to hang indefinitely after the initial iteration.
+
+## Workflow outputs
+
+<AddedInVersion version="24.04.0">
+This feature is available as a preview in Nextflow [24.04][workflow-outputs-first-preview], [24.10][workflow-outputs-second-preview], and [25.04][workflow-outputs-third-preview].
+</AddedInVersion>
+
+A script can define an *output block* which declares the top-level outputs of the workflow. Each output should be assigned in the `publish` section of the entry workflow. Any channel in the workflow can be assigned to an output, including process and subworkflow outputs. This approach is intended to replace the [publishDir][process-publishdir] directive.
+
+Here is a basic example:
+
+```nextflow
+process fetch {
+    // ...
+
+    output:
+    path 'sample.txt'
+
+    // ...
+}
+
+workflow {
+    main:
+    ch_samples = fetch(params.input)
+
+    publish:
+    samples = ch_samples
+}
+
+output {
+    samples {
+        path '.'
+    }
+}
+```
+
+In the above example, the output of process `fetch` is assigned to the `samples` workflow output. How this output is published to a directory structure is described in the next section.
+
+### Publishing files
+
+The top-level output directory of a workflow run can be set using the `-output-dir` command-line option or the `outputDir` config option:
+
+```bash
+nextflow run main.nf -output-dir 'my-results'
+```
+
+```groovy
+// nextflow.config
+outputDir = 'my-results'
+```
+
+The default output directory is `results` in the launch directory.
+
+By default, all output files are published to the output directory. Each output in the output block can define where files are published using the `path` directive. For example:
+
+```nextflow
+workflow {
+    main:
+    ch_step1 = step1()
+    ch_step2 = step2(ch_step1)
+
+    publish:
+    step1 = ch_step1
+    step2 = ch_step2
+}
+
+output {
+    step1 {
+        path 'step1'
+    }
+    step2 {
+        path 'step2'
+    }
+}
+```
+
+The following directory structure will be created:
+
+```
+results/
+└── step1/
+    └── ...
+└── step2/
+    └── ...
+```
+
+All files received by an output will be published into the specified directory. Lists and maps are recursively scanned for nested files. For example:
+
+```nextflow
+workflow {
+    main:
+    ch_samples = channel.of(
+        [ [id: 'SAMP1'], [ file('1.txt'), file('2.txt') ] ]
+    )
+
+    publish:
+    samples = ch_samples // 1.txt and 2.txt will be published
+}
+```
+
+The `path` directive can also be a closure which defines a custom publish path for each channel value:
+
+```nextflow
+workflow {
+    main:
+    ch_samples = channel.of(
+        [id: 'SAMP1', fastq_1: file('1.fastq'), fastq_2: file('2.fastq')]
+    )
+
+    publish:
+    samples = ch_samples
+}
+
+output {
+    samples {
+        path { sample -> "fastq/${sample.id}/" }
+    }
+}
+```
+
+The above example will publish each channel value to a different subdirectory. In this case, each pair of FASTQ files will be published to a subdirectory based on the sample ID.
+
+The closure can even define a different path for each individual file using the `>>` operator:
+
+```nextflow
+output {
+    samples {
+        path { sample ->
+            sample.fastq_1 >> "fastq/${sample.id}/"
+            sample.fastq_2 >> "fastq/${sample.id}/"
+        }
+    }
+}
+```
+
+Each `>>` specifies a *source file* and *publish target*. The source file should be a file or collection of files, and the publish target should be a directory or file name. If the publish target ends with a slash, it is treated as the directory in which source files are published. Otherwise, it is treated as the target filename of a source file. Only files that are published with the `>>` operator are saved to the output directory.
+
+:::note
+Files that do not originate from the work directory are not published.
+:::
+
+### Index files
+
+Each output can create an index file of the values that were published. An index file preserves the structure of channel values, including metadata, which is simpler than encoding this information with directories and file names. The index file can be a CSV (`.csv`), JSON (`.json`), or YAML (`.yml`, `.yaml`) file. The channel values should be files, lists, or maps.
+
+For example:
+
+```nextflow
+workflow {
+    main:
+    ch_samples = channel.of(
+        [id: 1, name: 'sample 1', fastq_1: '1a.fastq', fastq_2: '1b.fastq'],
+        [id: 2, name: 'sample 2', fastq_1: '2a.fastq', fastq_2: '2b.fastq'],
+        [id: 3, name: 'sample 3', fastq_1: '3a.fastq', fastq_2: null]
+    )
+
+    publish:
+    samples = ch_samples
+}
+
+output {
+    samples {
+        path 'fastq'
+        index {
+            path 'samples.csv'
+        }
+    }
+}
+```
+
+The above example will write the following CSV file to `results/samples.csv`:
+
+```
+"1","sample 1","results/fastq/1a.fastq","results/fastq/1b.fastq"
+"2","sample 2","results/fastq/2a.fastq","results/fastq/2b.fastq"
+"3","sample 3","results/fastq/3a.fastq",""
+```
+
+You can customize the index file with additional directives, for example:
+
+```nextflow
+index {
+    path 'samples.csv'
+    header true
+    sep '|'
+}
+```
+
+This example will produce the following index file:
+
+```
+"id"|"name"|"fastq_1"|"fastq_2"
+"1"|"sample 1"|"results/fastq/1a.fastq"|"results/fastq/1b.fastq"
+"2"|"sample 2"|"results/fastq/2a.fastq"|"results/fastq/2b.fastq"
+"3"|"sample 3"|"results/fastq/3a.fastq"|""
+```
+
+:::note
+Files that do not originate from the work directory are not published, but are included in the index file.
+:::
+
+See [Output directives](#output-directives) for the list of available index directives.
+
+### Output directives
+
+The following directives are available for each output in the output block:
+
+##### `index`
+
+Create an index file which will contain a record of each published value.
+
+The following directives are available in an index definition:
+
+######
+
+`header`
+
+When `true`, the keys of the first record are used as the column names (default: `false`). Can also be a list of column names. Only used for CSV files.
+
+######
+
+`path`
+
+The name of the index file relative to the base output directory (required). Can be a CSV, JSON, or YAML file.
+
+##### `sep`
+
+The character used to separate values (default: `','`). Only used for CSV files.
+
+##### `label`
+
+Specify a label to be applied to every published file. Can be specified multiple times.
+
+##### `path`
+
+Specify the publish path relative to the output directory (default: `'.'`). Can be a path, a closure that defines a custom directory for each published value, or a closure that publishes individual files using the `>>` operator.
+
+#
+
+Additionally, the following options from the [workflow][config-workflow] config scope can be specified as directives:
+
+- `contentType`
+- `enabled`
+- `ignoreErrors`
+- `mode`
+- `overwrite`
+- `storageClass`
+- `tags`
+
+For example:
+
+```nextflow
+output {
+    samples {
+        mode 'copy'
+    }
+}
+```
+
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[config-workflow]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#workflow
+[dsl1-page]: /nextflow_docs/nextflow_repo/docs/migrations/dsl1.mdx
+[module-aliases]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-aliases
+[process-naming-outputs]: /nextflow_docs/nextflow_repo/docs/process.mdx#naming-outputs
+[operator-map]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#map
+[operator-mix]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#mix
+[operator-view]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#view
+[process-publishdir]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#publishdir
+[stdlib-types-boolean]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#boolean
+[stdlib-types-float]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#float
+[stdlib-types-integer]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#integer
+[stdlib-types-path]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#path
+[stdlib-types-string]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#string
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[workflow-outputs-first-preview]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx#workflow
+[workflow-outputs-second-preview]: /nextflow_docs/nextflow_repo/docs/migrations/24-10.mdx#workflow-outputs-second-preview
+[workflow-outputs-third-preview]: /nextflow_docs/nextflow_repo/docs/migrations/25-04.mdx#workflow-outputs-third-preview
diff --git a/docs/working-with-files.md b/docs/working-with-files.mdx
similarity index 92%
rename from docs/working-with-files.md
rename to docs/working-with-files.mdx
index 28cc987206..3ce81d4bb2 100644
--- a/docs/working-with-files.md
+++ b/docs/working-with-files.mdx
@@ -1,5 +1,3 @@
-(working-with-files)=
-
 # Working with files
 
 ## Opening files
@@ -18,11 +16,11 @@ When using the wildcard characters `*`, `?`, `[]` and `{}`, the argument is inte
 listOfFiles = file('some/path/*.fa')
 ```
 
-:::{note}
+:::note
 The `file()` method does not return a list if only one file is matched. Use the `files()` method to always return a list.
 :::
 
-:::{note}
+:::note
 A double asterisk (`**`) in a glob pattern works like `*` but also searches through subdirectories.
 :::
 
@@ -32,7 +30,7 @@ By default, wildcard characters do not match directories or hidden files. For ex
 listWithHidden = file('some/path/*.fa', hidden: true)
 ```
 
-:::{note}
+:::note
 To compose paths, instead of string interpolation, use the `resolve()` method or the `/` operator:
 
 ```nextflow
@@ -57,11 +55,11 @@ assert path.name == 'file.txt'
 assert path.parent == '/some/path'
 ```
 
-:::{tip}
+:::tip
 When calling an object method, any method that looks like `get*()` can also be accessed as a field. For example, `path.getName()` is equivalent to `path.name`, `path.getBaseName()` is equivalent to `path.baseName`, and so on.
 :::
 
-See the {ref}`stdlib-types-path` reference for the list of available methods.
+See the [Path][stdlib-types-path] reference for the list of available methods.
 
 ## Reading and writing
 
@@ -91,11 +89,11 @@ Or you can save a byte array to a file:
 myFile.bytes = binaryContent
 ```
 
-:::{note}
+:::note
 The above assignment overwrites any existing file contents, and implicitly creates the file if it doesn't exist.
 :::
 
-:::{warning}
+:::warning
 The above methods read and write the **entire** file contents at once, in a single variable or buffer. For this reason, when dealing with large files it is recommended that you use a more memory efficient approach, such as reading/writing a file line by line or using a fixed size buffer.
 :::
 
@@ -133,7 +131,7 @@ file('some/my_file.txt')
     .each { println it }
 ```
 
-:::{warning}
+:::warning
 The method `readLines()` reads the **entire** file at once and returns a list containing all the lines. For this reason, do not use it to read big files.
 :::
 
@@ -174,7 +172,7 @@ myFile.withReader {
 
 The methods `newInputStream()` and `withInputStream()` work similarly. The main difference is that they create an [InputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/InputStream.html) object useful for writing binary data.
 
-See the {ref}`stdlib-types-path` reference for the list of available methods.
+See the [Path][stdlib-types-path] reference for the list of available methods.
 
 ### Advanced file writing
 
@@ -193,11 +191,11 @@ sourceFile.withReader { source ->
 }
 ```
 
-See the {ref}`stdlib-types-path` reference for the list of available methods.
+See the [Path][stdlib-types-path] reference for the list of available methods.
 
 ## Filesystem operations
 
-Methods for performing filesystem operations such as copying, deleting, and directory listing are documented in the {ref}`stdlib-types-path` reference.
+Methods for performing filesystem operations such as copying, deleting, and directory listing are documented in the [Path][stdlib-types-path] reference.
 
 ### Listing directories
 
@@ -226,8 +224,6 @@ myDir.eachFile { item ->
 
 In general, you should not need to manually copy files, because Nextflow will automatically stage files in and out of the task environment based on the definition of process inputs and outputs. Ideally, any operation which transforms files should be encapsulated in a process, in order to leverage Nextflow's staging capabilities as much as possible.
 
-(remote-files)=
-
 ## Remote files
 
 Nextflow works with many types of remote files and objects using the same interface as for local files. The following protocols are supported:
@@ -249,11 +245,11 @@ It can then be used in the same way as a local file:
 println pdb.text
 ```
 
-:::{note}
+:::note
 Not all operations are supported for all protocols. For example, writing and directory listing is not supported for HTTP(S) and FTP paths.
 :::
 
-:::{note}
+:::note
 Additional configuration may be necessary for cloud object storage, such as authenticating with a private bucket. See the documentation for each cloud storage provider for further details.
 :::
 
@@ -263,10 +259,13 @@ When a process input file resides on a different file system than the work direc
 
 Remote files are staged in a subdirectory of the work directory with the form `stage-<session-id>/<hash>/<filename>`, where `<hash>` is determined by the remote file path. If multiple tasks request the same remote file, the file will be downloaded once and reused by each task. These files can be reused by resumed runs with the same session ID.
 
-:::{note}
+:::note
 Remote file staging can be a bottleneck during large-scale runs, particularly when input files are stored in object storage but need to be staged in a shared filesystem work directory. This bottleneck occurs because Nextflow handles all of these file transfers.
 
 To mitigate this, you can implement a custom process to download the required files, allowing you to stage multiple files efficiently through parallel jobs. Files should be given as a `val` input instead of a `path` input to bypass Nextflow's built-in remote file staging.
 
-Alternatively, use {ref}`fusion-page` with the work directory set to object storage. In this case, tasks can access remote files directly without any prior staging, eliminating the bottleneck.
+Alternatively, use [Fusion][fusion-page] with the work directory set to object storage. In this case, tasks can access remote files directly without any prior staging, eliminating the bottleneck.
 :::
+
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[stdlib-types-path]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#path
diff --git a/docs/your-first-script.md b/docs/your-first-script.mdx
similarity index 84%
rename from docs/your-first-script.md
rename to docs/your-first-script.mdx
index 8c86fb93e2..15ce849187 100644
--- a/docs/your-first-script.md
+++ b/docs/your-first-script.mdx
@@ -1,5 +1,3 @@
-(your-first-script)=
-
 # Your first script
 
 This guide details fundamental skills to run a basic Nextflow pipeline. It includes:
@@ -8,28 +6,27 @@ This guide details fundamental skills to run a basic Nextflow pipeline. It inclu
 - Modifying and resuming a pipeline
 - Configuring a pipeline parameter
 
-<h3>Prerequisites</h3>
-
+:::info[**Prerequisites**]
 You will need the following to get started:
 
-- Nextflow: See {ref}`install-page` for installation instructions.
+- Nextflow installed locally
+:::
 
 ## Run a pipeline
 
 You will run a basic Nextflow pipeline that splits a string of text into two files and then converts lowercase letters to uppercase letters. You can see the pipeline here:
 
-```{code-block} groovy
-:class: copyable
+```groovy
 // Default parameter input
 params.str = "Hello world!"
 
 // split process
 process split {
     publishDir "results/lower"
-    
+
     input:
     val x
-    
+
     output:
     path 'chunk_*'
 
@@ -66,8 +63,8 @@ workflow {
 
 This script defines two processes:
 
-- `split`: takes a string input, splits it into 6-character chunks, and writes the chunks to files with the prefix `chunk_`
-- `convert_to_upper`: takes files as input, transforms their contents to uppercase letters, and writes the uppercase strings to files with the prefix `upper_`
+- `split`: takes a string input, splits it into 6-character chunks, and writes the chunks to files with the prefix `chunk_`.
+- `convert_to_upper`: takes files as input, transforms their contents to uppercase letters, and writes the uppercase strings to files with the prefix `upper_`.
 
 The `split` output is emitted as a single element. The `flatten` operator splits this combined element so that each file is treated as a sole element.
 
@@ -75,19 +72,18 @@ The outputs from both processes are published in subdirectories (`lower` and `up
 
 To run your pipeline:
 
-1. Create a new file named `main.nf` in your current directory
-2. Copy and save the above pipeline to your new file
+1. Create a new file named `main.nf` in your current directory.
+2. Copy and save the above pipeline to your new file.
 3. Run your pipeline using the following command:
 
-    ```{code-block}
-    :class: copyable
+    ```bash
     nextflow run main.nf
     ```
 
 You will see output similar to the following:
 
 ```console
- N E X T F L O W   ~  version 24.10.3
+N E X T F L O W   ~  version 24.10.3
 
 Launching `main.nf` [big_wegener] DSL2 - revision: 13a41a8946
 
@@ -98,11 +94,10 @@ executor >  local (3)
 
 Nextflow creates a `work` directory to store files used during a pipeline run. Each execution of a process is run as a separate task. The `split` process is run as one task and the `convert_to_upper` process is run as two tasks. The hexadecimal string, for example, `82/457482`, is the beginning of a unique hash. It is a prefix used to identify the task directory where the script was executed.
 
-:::{tip}
+:::tip
 Run your pipeline with `-ansi-log false` to see each task printed on a separate line:
 
-```{code-block} bash
-:class: copyable
+```bash
 nextflow run main.nf -ansi-log false
 ```
 
@@ -116,9 +111,7 @@ Launching `main.nf` [peaceful_watson] DSL2 - revision: 13a41a8946
 [30/ba7de0] Submitted process > convert_to_upper (chunk_aa)
 ```
 
-::: 
-
-(getstarted-resume)=
+:::
 
 ## Modify and resume
 
@@ -126,11 +119,10 @@ Nextflow tracks task executions in a task cache, a key-value store of previously
 
 You can enable resumability using the `-resume` flag when running a pipeline. To modify and resume your pipeline:
 
-1. Open `main.nf`
+1. Open `main.nf`.
 2. Replace the `convert_to_upper` process with the following:
 
-    ```{code-block} groovy
-    :class: copyable
+    ```groovy
     process convert_to_upper {
         publishDir "results/upper"
         tag "$y"
@@ -148,11 +140,10 @@ You can enable resumability using the `-resume` flag when running a pipeline. To
     }
     ```
 
-3. Save your changes
+3. Save your changes.
 4. Run your updated pipeline using the following command:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     nextflow run main.nf -resume
     ```
 
@@ -170,9 +161,7 @@ executor >  local (2)
 
 Nextflow skips the execution of the `split` process and retrieves the results from the cache. The `convert_to_upper` process is executed twice.
 
-See {ref}`cache-resume-page` for more information about Nextflow cache and resume functionality. 
-
-(getstarted-params)=
+See [Caching and resuming][cache-resume-page] for more information about Nextflow cache and resume functionality.
 
 ## Pipeline parameters
 
@@ -182,8 +171,7 @@ You can configure the `str` parameter in your pipeline. To modify your `str` par
 
 1. Run your pipeline using the following command:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     nextflow run main.nf --str 'Bonjour le monde'
     ```
 
@@ -195,14 +183,18 @@ You will see output similar to the following:
 Launching `main.nf` [distracted_kalam] DSL2 - revision: 082867d4d6
 
 executor >  local (4)
-[55/a3a700] process > split (1)                   [100%] 1 of 1 ✔
+[55/a3a700] process > split (1)           [100%] 1 of 1 ✔
 [f4/af5ddd] process > convert_to_upper (chunk_ac) [100%] 3 of 3 ✔
 ```
 
 The input string is now longer and the `split` process splits it into three chunks. The `convert_to_upper` process is run three times.
 
-See {ref}`cli-params` for more information about modifying pipeline parameters.
+See [Pipeline parameters][cli-params] for more information about modifying pipeline parameters.
 
-<h2>Next steps</h2>
+## Next steps
 
 Your first script is a brief introduction to running pipelines, modifying and resuming pipelines, and pipeline parameters. See [training.nextflow.io](https://training.nextflow.io/) for further Nextflow training modules.
+
+[cache-resume-page]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[install-page]: /nextflow_docs/nextflow_repo/docs/install.mdx
diff --git a/new-docs/.gitignore b/new-docs/.gitignore
new file mode 100644
index 0000000000..b2d6de3062
--- /dev/null
+++ b/new-docs/.gitignore
@@ -0,0 +1,20 @@
+# Dependencies
+/node_modules
+
+# Production
+/build
+
+# Generated files
+.docusaurus
+.cache-loader
+
+# Misc
+.DS_Store
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
diff --git a/new-docs/README.md b/new-docs/README.md
new file mode 100644
index 0000000000..b28211a9bb
--- /dev/null
+++ b/new-docs/README.md
@@ -0,0 +1,41 @@
+# Website
+
+This website is built using [Docusaurus](https://docusaurus.io/), a modern static website generator.
+
+## Installation
+
+```bash
+yarn
+```
+
+## Local Development
+
+```bash
+yarn start
+```
+
+This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
+
+## Build
+
+```bash
+yarn build
+```
+
+This command generates static content into the `build` directory and can be served using any static contents hosting service.
+
+## Deployment
+
+Using SSH:
+
+```bash
+USE_SSH=true yarn deploy
+```
+
+Not using SSH:
+
+```bash
+GIT_USER=<Your GitHub username> yarn deploy
+```
+
+If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the `gh-pages` branch.
diff --git a/new-docs/blog/2019-05-28-first-blog-post.md b/new-docs/blog/2019-05-28-first-blog-post.md
new file mode 100644
index 0000000000..d3032efb35
--- /dev/null
+++ b/new-docs/blog/2019-05-28-first-blog-post.md
@@ -0,0 +1,12 @@
+---
+slug: first-blog-post
+title: First Blog Post
+authors: [slorber, yangshun]
+tags: [hola, docusaurus]
+---
+
+Lorem ipsum dolor sit amet...
+
+<!-- truncate -->
+
+...consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
diff --git a/new-docs/blog/2019-05-29-long-blog-post.md b/new-docs/blog/2019-05-29-long-blog-post.md
new file mode 100644
index 0000000000..eb4435de59
--- /dev/null
+++ b/new-docs/blog/2019-05-29-long-blog-post.md
@@ -0,0 +1,44 @@
+---
+slug: long-blog-post
+title: Long Blog Post
+authors: yangshun
+tags: [hello, docusaurus]
+---
+
+This is the summary of a very long blog post,
+
+Use a `<!--` `truncate` `-->` comment to limit blog post size in the list view.
+
+<!-- truncate -->
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
diff --git a/new-docs/blog/2021-08-01-mdx-blog-post.mdx b/new-docs/blog/2021-08-01-mdx-blog-post.mdx
new file mode 100644
index 0000000000..0c4b4a48b9
--- /dev/null
+++ b/new-docs/blog/2021-08-01-mdx-blog-post.mdx
@@ -0,0 +1,24 @@
+---
+slug: mdx-blog-post
+title: MDX Blog Post
+authors: [slorber]
+tags: [docusaurus]
+---
+
+Blog posts support [Docusaurus Markdown features](https://docusaurus.io/docs/markdown-features), such as [MDX](https://mdxjs.com/).
+
+:::tip
+
+Use the power of React to create interactive blog posts.
+
+:::
+
+{/* truncate */}
+
+For example, use JSX to create an interactive button:
+
+```js
+<button onClick={() => alert('button clicked!')}>Click me!</button>
+```
+
+<button onClick={() => alert('button clicked!')}>Click me!</button>
diff --git a/new-docs/blog/2021-08-26-welcome/docusaurus-plushie-banner.jpeg b/new-docs/blog/2021-08-26-welcome/docusaurus-plushie-banner.jpeg
new file mode 100644
index 0000000000..11bda09284
Binary files /dev/null and b/new-docs/blog/2021-08-26-welcome/docusaurus-plushie-banner.jpeg differ
diff --git a/new-docs/blog/2021-08-26-welcome/index.md b/new-docs/blog/2021-08-26-welcome/index.md
new file mode 100644
index 0000000000..349ea075f5
--- /dev/null
+++ b/new-docs/blog/2021-08-26-welcome/index.md
@@ -0,0 +1,29 @@
+---
+slug: welcome
+title: Welcome
+authors: [slorber, yangshun]
+tags: [facebook, hello, docusaurus]
+---
+
+[Docusaurus blogging features](https://docusaurus.io/docs/blog) are powered by the [blog plugin](https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog).
+
+Here are a few tips you might find useful.
+
+<!-- truncate -->
+
+Simply add Markdown files (or folders) to the `blog` directory.
+
+Regular blog authors can be added to `authors.yml`.
+
+The blog post date can be extracted from filenames, such as:
+
+- `2019-05-30-welcome.md`
+- `2019-05-30-welcome/index.md`
+
+A blog post folder can be convenient to co-locate blog post images:
+
+![Docusaurus Plushie](./docusaurus-plushie-banner.jpeg)
+
+The blog supports tags as well!
+
+**And if you don't want a blog**: just delete this directory, and use `blog: false` in your Docusaurus config.
diff --git a/new-docs/blog/authors.yml b/new-docs/blog/authors.yml
new file mode 100644
index 0000000000..0fd398733b
--- /dev/null
+++ b/new-docs/blog/authors.yml
@@ -0,0 +1,25 @@
+yangshun:
+  name: Yangshun Tay
+  title: Ex-Meta Staff Engineer, Co-founder GreatFrontEnd
+  url: https://linkedin.com/in/yangshun
+  image_url: https://github.com/yangshun.png
+  page: true
+  socials:
+    x: yangshunz
+    linkedin: yangshun
+    github: yangshun
+    newsletter: https://www.greatfrontend.com
+
+slorber:
+  name: Sébastien Lorber
+  title: Docusaurus maintainer
+  url: https://sebastienlorber.com
+  image_url: https://github.com/slorber.png
+  page:
+    # customize the url of the author page at /blog/authors/<permalink>
+    permalink: '/all-sebastien-lorber-articles'
+  socials:
+    x: sebastienlorber
+    linkedin: sebastienlorber
+    github: slorber
+    newsletter: https://thisweekinreact.com
diff --git a/new-docs/blog/tags.yml b/new-docs/blog/tags.yml
new file mode 100644
index 0000000000..bfaa778fbd
--- /dev/null
+++ b/new-docs/blog/tags.yml
@@ -0,0 +1,19 @@
+facebook:
+  label: Facebook
+  permalink: /facebook
+  description: Facebook tag description
+
+hello:
+  label: Hello
+  permalink: /hello
+  description: Hello tag description
+
+docusaurus:
+  label: Docusaurus
+  permalink: /docusaurus
+  description: Docusaurus tag description
+
+hola:
+  label: Hola
+  permalink: /hola
+  description: Hola tag description
diff --git a/new-docs/docusaurus.config.ts b/new-docs/docusaurus.config.ts
new file mode 100644
index 0000000000..396b152140
--- /dev/null
+++ b/new-docs/docusaurus.config.ts
@@ -0,0 +1,28 @@
+import type { Config } from "@docusaurus/types";
+import { 
+  createSeqeraConfig, 
+  getSeqeraThemeConfig,
+  getSeqeraPresetOptions 
+} from "@seqera/docusaurus-preset-seqera";
+
+export default async function createConfigAsync(): Promise<Config> {
+  return createSeqeraConfig({
+    plugins: [],
+    presets: [
+      [
+        "@seqera/docusaurus-preset-seqera",
+        getSeqeraPresetOptions({
+        docs: {
+          path: 'nextflow-docs',  // Path to YOUR docs folder
+          routeBasePath: '/',  // or '/nextflow' if you want
+          sidebarPath: './sidebars.ts',
+        },
+      }),
+      ],
+    ],
+
+    themeConfig: getSeqeraThemeConfig({
+ 
+    }),
+  }) satisfies Config;
+}
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/Dockerfile b/new-docs/nextflow-docs/Dockerfile
new file mode 100644
index 0000000000..a961249faf
--- /dev/null
+++ b/new-docs/nextflow-docs/Dockerfile
@@ -0,0 +1,14 @@
+FROM mambaorg/micromamba:1.5.8
+
+RUN micromamba install --yes --name base --channel conda-forge \
+      make=4.3 \
+      python=3.7 \
+      conda-forge:git=2.45.0 \
+      && \
+    micromamba clean --all --yes
+
+COPY requirements.txt .
+
+RUN eval "$(micromamba shell hook --shell=bash)" && \
+    micromamba activate && \
+    pip install -r requirements.txt
diff --git a/new-docs/nextflow-docs/LICENCE.txt b/new-docs/nextflow-docs/LICENCE.txt
new file mode 100644
index 0000000000..fe8dbc50fc
--- /dev/null
+++ b/new-docs/nextflow-docs/LICENCE.txt
@@ -0,0 +1,428 @@
+Attribution-ShareAlike 4.0 International
+
+=======================================================================
+
+Creative Commons Corporation ("Creative Commons") is not a law firm and
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+
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+
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+For the avoidance of doubt, this Section 4 supplements and does not
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+
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+
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+Section 6 -- Term and Termination.
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+
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diff --git a/new-docs/nextflow-docs/Makefile b/new-docs/nextflow-docs/Makefile
new file mode 100644
index 0000000000..8817d40c01
--- /dev/null
+++ b/new-docs/nextflow-docs/Makefile
@@ -0,0 +1,153 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Blow.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Blow.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/Blow"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Blow"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/new-docs/nextflow-docs/README.md b/new-docs/nextflow-docs/README.md
new file mode 100644
index 0000000000..f0b98c510d
--- /dev/null
+++ b/new-docs/nextflow-docs/README.md
@@ -0,0 +1,47 @@
+# Nextflow Documentation
+
+Nextflow documentation is written using [Sphinx](http://www.sphinx-doc.org/), [MyST](https://myst-parser.readthedocs.io/en/latest/) which is an extended version of Markdown for Sphinx, and the [Read The Docs theme for Sphinx](https://github.com/readthedocs/sphinx_rtd_theme).
+
+
+## Dependencies
+
+The most convenient approach is to create a Conda environment with Python 3.7 (other versions may work but haven't been tested).
+
+The build dependencies can be installed with `pip`:
+
+```bash
+cd docs
+pip install -r requirements.txt
+```
+
+Alternatively, you can use the Dockerfile to build the docs in a container (see below).
+
+
+## Contributing
+
+To edit and contribute to the documentation, you only need a text editor to change the appropriate `.md` files in this directory.
+
+Once you have made your changes, run the following command to build the HTML files:
+
+```bash
+make clean html
+```
+
+Alternatively, you can use the Dockerfile to build the docs in a container:
+
+```bash
+docker build -t nextflow/sphinx:5.3.0 .
+docker run -v $(pwd):/tmp nextflow/sphinx:5.3.0 -- make html
+```
+
+Then start up a local http server and open `localhost:8080` in your browser to verify the changes:
+
+```bash
+python -m http.server 8080 --directory _build/html/
+```
+
+
+## License
+
+Nextflow documentation is distributed under
+[Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license](https://creativecommons.org/licenses/by-sa/4.0/).
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+    v1 --> v2
+    v2 --> v4
+    v3 --> v5
+    v4 --> v5
+    v7 --> v8
+    v5 --> v8
+    v8 --> v9
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diff --git a/new-docs/nextflow-docs/_static/theme.css b/new-docs/nextflow-docs/_static/theme.css
new file mode 100644
index 0000000000..a7efb16ab4
--- /dev/null
+++ b/new-docs/nextflow-docs/_static/theme.css
@@ -0,0 +1,246 @@
+/* Inter font */
+@import url('https://fonts.googleapis.com/css2?family=Inter:wght@400;700&display=swap');
+
+/* Degular font */
+@font-face {
+    font-family: "Degular";
+    src: url('degular/Degular-Regular.woff2');
+    src: url('degular/Degular-Regular.woff2') format('woff2'),
+         url('degular/Degular-Regular.woff') format('woff');
+    font-weight: normal;
+    font-style: normal;
+}
+@font-face {
+    font-family: "Degular";
+    src: url('degular/Degular-Italic.woff2');
+    src: url('degular/Degular-Italic.woff2') format('woff2'),
+         url('degular/Degular-Italic.woff') format('woff');
+    font-weight: normal;
+    font-style: italic;
+}
+@font-face {
+    font-family: "Degular";
+    src: url('degular/Degular-Bold.woff2');
+    src: url('degular/Degular-Bold.woff2') format('woff2'),
+         url('degular/Degular-Bold.woff') format('woff');
+    font-weight: bold;
+    font-style: normal;
+}
+@font-face {
+    font-family: "Degular";
+    src: url('degular/Degular-BoldItalic.woff2');
+    src: url('degular/Degular-BoldItalic.woff2') format('woff2'),
+         url('degular/Degular-BoldItalic.woff') format('woff');
+    font-weight: bold;
+    font-style: italic;
+}
+
+/* fonts */
+body {
+    font-family: 'Inter', sans-serif;
+}
+
+.btn {
+    font-family: 'Inter', sans-serif;
+}
+
+.rst-content .toctree-wrapper>p.caption,
+h1,
+h2,
+h3,
+h4,
+h5,
+h6,
+legend {
+    font-family: 'Degular', sans-serif;
+}
+
+/* colors */
+.rst-content .danger {
+    background: #FEEDEC;
+}
+
+.rst-content .danger .admonition-title {
+    background: #C3514D;
+}
+
+.rst-content .warning {
+    background: #FDF0E9;
+}
+
+.rst-content .warning .admonition-title {
+    background: #BC6437;
+}
+
+.rst-content .note {
+    background: #E8F2FF;
+}
+
+.rst-content .note .admonition-title {
+    background: #3787E5;
+}
+
+.rst-content .tip {
+    background: #E2F7F3;
+}
+
+.rst-content .tip .admonition-title {
+    background: #0CAE8E;
+}
+
+a, a:visited {
+    color: #3787E5;
+}
+
+a:hover {
+    color: #77B5FE;
+}
+
+.rst-content code,
+.rst-content tt,
+code {
+    color: #C3514D;
+}
+
+.wy-menu-vertical header,
+.wy-menu-vertical p.caption {
+    color: #0DC09D;
+}
+
+.wy-menu-vertical a {
+    color: #EAEBEB;
+}
+
+.wy-menu-vertical a:hover {
+    background-color: #7B7B7B;
+}
+
+.wy-menu-vertical a:active {
+    background-color: #0DC09D;
+}
+
+.wy-side-nav-search {
+    background-color: #0DC09D;
+}
+
+.wy-side-nav-search input[type=text] {
+    border-color: #0DC09D;
+}
+
+.wy-side-nav-search img {
+    background-color: #0DC09D;
+}
+
+.wy-nav-side {
+    background: #160F26;
+}
+
+.wy-nav-top {
+    background: #0DC09D;
+}
+
+.wy-nav-top a {
+    color: #fff;
+}
+
+.wy-nav-top img {
+    width: auto;
+    background-color: inherit;
+    border-radius: unset;
+}
+
+footer {
+    color: #7B7B7B;
+}
+
+#search-results .context {
+    color: #7B7B7B;
+}
+
+.rst-content code.literal,
+.rst-content tt.literal {
+    color: #C3514D;
+}
+
+/* Custom footer with logo */
+.nav-footer-logo {
+    width: 300px;
+    margin-top: 2rem;
+    border-top: 1px solid #7B7B7B;
+    text-align: center;
+    font-size: 80%;
+}
+
+.nav-footer-logo a {
+    display: block;
+    padding: 2rem 0 0.5rem;
+    color: #7B7B7B;
+}
+
+.nav-footer-logo a img {
+    margin-top: 0.5rem;
+    width: 60%;
+}
+
+/* Version change admonitions */
+div.deprecated,
+div.versionadded,
+div.versionchanged {
+    border-left: 0.2rem solid;
+    border-radius: 0.25rem;
+    box-shadow: 0 0.2rem 0.5rem var(--pst-color-shadow),0 0 0.0625rem var(--pst-color-shadow)!important;
+    margin: 1rem auto;
+    overflow: hidden;
+    padding: 0.2rem 0.6rem;
+    page-break-inside: avoid;
+    position: relative;
+    transition: color .25s,background-color .25s,border-color .25s;
+    vertical-align: middle;
+}
+div.deprecated>p,
+div.versionadded>p,
+div.versionchanged>p {
+    margin-top: 0.5rem;
+    margin-bottom: 0.5rem;
+}
+div.deprecated>p:first-child::before,
+div.versionadded>p:first-child::before,
+div.versionchanged>p:first-child::before {
+    font-family: FontAwesome;
+    display: inline-block;
+    font-style: normal;
+    font-weight: 400;
+    line-height: 1;
+    text-decoration: inherit;
+    margin-right: 0.5rem;
+    content: "";
+    -webkit-font-smoothing: antialiased;
+    padding: 0.4rem 0.6rem;
+    margin: -0.2rem 0rem -0.2rem -0.6rem;
+}
+div.versionadded                         { border-color: #0CAE8E; background-color: #E2F7F3; }
+div.versionadded p:first-child::before   { color: #0CAE8E; }
+div.versionchanged                       { border-color: #BC6437; background-color: #FDF0E9; }
+div.versionchanged p:first-child::before { color: #BC6437; }
+div.deprecated                           { border-color: #C3514D; background-color: #FEEDEC; }
+div.deprecated p:first-child::before     { color: #C3514D; }
+
+/* Version in sidebar */
+.sidebar_version {
+    margin-top: 0.5rem;
+    font-size: 0.8rem;
+    color: #160F26;
+}
+.sidebar_version samp {
+    font-size: 0.6rem;
+}
+.sidebar_version select {
+    background-color: #0DC09D;
+    box-shadow: none;
+    color: #160F26;
+    border: 1px solid #160f26a3;
+    border-radius: 1rem;
+    padding: 0.15rem 0.2rem;
+    font-size: 0.7rem;
+    margin-left: 0.5rem;
+}
diff --git a/new-docs/nextflow-docs/_static/timeline-min.png b/new-docs/nextflow-docs/_static/timeline-min.png
new file mode 100644
index 0000000000..347f5a8ceb
Binary files /dev/null and b/new-docs/nextflow-docs/_static/timeline-min.png differ
diff --git a/new-docs/nextflow-docs/_static/workflow-notification-min.png b/new-docs/nextflow-docs/_static/workflow-notification-min.png
new file mode 100644
index 0000000000..f200ed2460
Binary files /dev/null and b/new-docs/nextflow-docs/_static/workflow-notification-min.png differ
diff --git a/new-docs/nextflow-docs/_templates/layout.html b/new-docs/nextflow-docs/_templates/layout.html
new file mode 100644
index 0000000000..ad62698389
--- /dev/null
+++ b/new-docs/nextflow-docs/_templates/layout.html
@@ -0,0 +1,46 @@
+{% extends "!layout.html" %}
+
+{% block sidebartitle %}
+    {{ super() }}
+    {%- set version_selected = "stable" -%}
+    {%- if "edge" in release %}{%- set version_selected = "edge" -%}{%- endif %}
+    {%- if "dev" in release %}{%- set version_selected = "dev" -%}{%- endif %}
+    <div class="sidebar_version">
+        <span class="version">Version {{ release }} {{ release_checked_out }}</span>
+        <select onchange="window.location = this.value;">
+            <option value="/docs/stable/index.html" {% if version_selected == 'stable' %}selected{% endif %}>Stable</option>
+            <option value="/docs/edge/index.html" {% if version_selected == 'edge' %}selected{% endif %}>Edge</option>
+            <option value="/docs/latest/index.html" {% if version_selected == 'dev' %}selected{% endif %}>Latest</option>
+        </select>
+        </select>
+    </div>
+{% endblock %}
+
+{% block navigation %}
+    {{ super() }}
+    <div class="nav-footer-logo">
+        <a href="https://seqera.io/" target="_blank" title="Developed by Seqera Labs">
+            Nextflow is developed by:<br>
+            <img src="{{ pathto('_static/seqera-logo.svg', 1) }}" alt="Seqera Labs">
+        </a>
+    </div>
+{% endblock %}
+
+{% block extrahead %}
+    {{ super() }}
+    <!-- Google Tag Manager -->
+    <script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':
+    new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],
+    j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src=
+    'https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);
+    })(window,document,'script','dataLayer','GTM-TNCXSWG');</script>
+    <!-- End Google Tag Manager -->
+{% endblock %}
+
+{% block footer %}
+    {{ super() }}
+    <!-- Google Tag Manager (noscript) -->
+    <noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-TNCXSWG"
+    height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript>
+    <!-- End Google Tag Manager (noscript) -->
+{% endblock %}
diff --git a/new-docs/nextflow-docs/amazons3.mdx b/new-docs/nextflow-docs/amazons3.mdx
new file mode 100644
index 0000000000..611083c760
--- /dev/null
+++ b/new-docs/nextflow-docs/amazons3.mdx
@@ -0,0 +1,102 @@
+# Amazon S3
+
+Nextflow includes support for AWS S3 storage. Files stored in an S3 bucket can be accessed transparently in your pipeline script like any other file in the local file system.
+
+## S3 path
+
+In order to access an S3 file, you only need to prefix the file path with the `s3` schema and the `bucket` name where it is stored.
+
+For example, if you need to access the file `/data/sequences.fa` stored in a bucket named `my-bucket`, that file can be accessed using the following fully qualified path:
+
+```
+s3://my-bucket/data/sequences.fa
+```
+
+The usual file operations can be applied to a path handle with the above notation. For example, the content of an S3 file can be printed as follows:
+
+```nextflow
+println file('s3://my-bucket/data/sequences.fa').text
+```
+
+See [Working with files][working-with-files] and the [Path][stdlib-types-path] reference to learn more about available file operations.
+
+## Security credentials
+
+AWS access credentials can be provided in two ways:
+
+1. Using AWS access and secret keys in your pipeline configuration.
+2. Using IAM roles to grant access to S3 storage on AWS EC2 instances.
+
+### AWS access and secret keys
+
+The AWS access and secret keys can be specified by using the `aws` section in the `nextflow.config` configuration file as shown below:
+
+```groovy
+aws {
+    accessKey = '<Your AWS access key>'
+    secretKey = '<Your AWS secret key>'
+    region = '<AWS region identifier>'
+}
+```
+
+If the access credentials are not found in the above file, Nextflow looks for AWS credentials in the following order:
+
+1. The `nextflow.config` file in the pipeline execution directory
+2. The environment variables `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY`
+3. The environment variables `AWS_ACCESS_KEY` and `AWS_SECRET_KEY`
+4. The profile in the AWS credentials file located at `~/.aws/credentials`
+    - Uses the `default `profile or the environment variable `AWS_PROFILE` if set
+5. The profile in the AWS client configuration file located at `~/.aws/config`
+    - Uses the `default `profile or the environment variable `AWS_PROFILE` if set
+6. The temporary AWS credentials provided by an IAM instance role. See [IAM Roles](http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/iam-roles-for-amazon-ec2.html) documentation for details.
+
+More information regarding [AWS Security Credentials](http://docs.aws.amazon.com/general/latest/gr/aws-security-credentials.html) are available in the AWS documentation.
+
+### IAM roles with AWS EC2 instances
+
+When running your pipeline in an EC2 instance, IAM roles can be used to grant access to AWS resources.
+
+In this scenario, you only need to launch the EC2 instance with an IAM role which includes the `AmazonS3FullAccess` policy. Nextflow will detect and automatically acquire the permission to access S3 storage, without any further configuration.
+
+Learn more about [Using IAM Roles to Delegate Permissions to Applications that Run on AWS EC2](http://docs.aws.amazon.com/IAM/latest/UserGuide/roles-usingrole-ec2instance.html) in the AWS documentation.
+
+## China regions
+
+To use an AWS China region, make sure to specify the corresponding AWS API S3 endpoint in the Nextflow configuration file as shown below:
+
+```groovy
+aws { 
+    client {
+        endpoint = "https://s3.cn-north-1.amazonaws.com.cn"        
+    }
+}
+```
+
+Read more about AWS API endpoints in the [AWS documentation](https://docs.aws.amazon.com/general/latest/gr/s3.html)
+
+## S3-compatible storage
+
+To use S3-compatible object storage such as [Ceph](https://ceph.io) or [Minio](https://min.io) specify the endpoint of 
+your storage provider and enable the [S3 path style access](https://docs.aws.amazon.com/AmazonS3/latest/userguide/VirtualHosting.html#path-style-access) 
+in your Nextflow configuration as shown below:
+
+
+```groovy
+aws {
+    accessKey = '<Your access key>'
+    secretKey = '<Your secret key>'
+    client {
+        endpoint = '<Your storage endpoint URL>'
+        s3PathStyleAccess = true
+    }
+}
+```
+
+## Advanced configuration
+
+See [AWS configuration][config-aws] for more information about advanced S3 client configuration options.
+
+
+[config-aws]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#aws
+[stdlib-types-path]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#path
+[working-with-files]: /nextflow_docs/nextflow_repo/docs/working-with-files.mdx
\ No newline at end of file
diff --git a/docs/aws.md b/new-docs/nextflow-docs/aws.mdx
similarity index 88%
rename from docs/aws.md
rename to new-docs/nextflow-docs/aws.mdx
index cb1c2e4888..fba195e282 100644
--- a/docs/aws.md
+++ b/new-docs/nextflow-docs/aws.mdx
@@ -1,8 +1,8 @@
-(aws-page)=
+
 
 # Amazon Web Services
 
-:::{tip}
+:::tip
 This page describes how to manually set up and use Nextflow with AWS Cloud.
 You may be interested in using [Batch Forge](https://docs.seqera.io/platform/latest/compute-envs/aws-batch) in [Seqera Platform](https://seqera.io/platform/),
 which automatically creates the required AWS infrastructure for you with minimal intervention.
@@ -14,7 +14,7 @@ Nextflow uses the [AWS security credentials](https://docs.aws.amazon.com/general
 
 The AWS credentials are selected from the following sources, in order of descending priority:
 
-1. Nextflow configuration file - `aws.accessKey` and `aws.secretKey`. See {ref}`AWS configuration<config-aws>` for more details.
+1. Nextflow configuration file - `aws.accessKey` and `aws.secretKey`. See [aws][config-aws] for more details.
 
 2. A custom profile in `$HOME/.aws/credentials` and/or `$HOME/.aws/config`. The profile can be supplied from the `aws.profile` config option, or the `AWS_PROFILE` or `AWS_DEFAULT_PROFILE` environmental variables.
 
@@ -24,8 +24,8 @@ The AWS credentials are selected from the following sources, in order of descend
 
 5. Single Sign-On (SSO) credentials. See the [AWS documentation](https://docs.aws.amazon.com/cli/latest/userguide/sso-configure-profile-token.html) for more details.
 
-   :::{versionadded} 23.07.0-edge
-   :::
+
+    <AddedInVersion version="23.07.0-edge" />
 
 6. EC2 instance profile credentials. See the [AWS documentation](http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/iam-roles-for-amazon-ec2.html) and [this blog post](https://aws.amazon.com/blogs/security/granting-permission-to-launch-ec2-instances-with-iam-roles-passrole-permission/) for more details.
 
@@ -88,7 +88,7 @@ Minimal permissions policies to be attached to the AWS account used by Nextflow
 
   Alternatively, you can use AWS provided `AmazonEC2ContainerRegistryReadOnly` managed policy.
 
-:::{note}
+:::note
 If you are running Fargate or Fargate Spot, you may need the following policies in addition to the listed above:
   ```json
   "ec2:DescribeSubnets"
@@ -150,28 +150,24 @@ Depending on the pipeline configuration, the above actions can be done all in a
 
 See the [bucket policy documentation](https://docs.aws.amazon.com/config/latest/developerguide/s3-bucket-policy.html) for additional details.
 
-(aws-batch)=
-
 ## AWS Batch
 
 [AWS Batch](https://aws.amazon.com/batch/) is a managed computing service that allows the execution of containerised workloads in the AWS cloud infrastructure. It dynamically provisions the optimal quantity and type of compute resources (e.g., CPU or memory optimized compute resources) based on the volume and specific resource requirements of the jobs submitted.
 
 Nextflow provides built-in support for AWS Batch, allowing the seamless deployment of Nextflow pipelines in the cloud, in which tasks are offloaded as Batch jobs.
 
-Read the {ref}`AWS Batch executor <awsbatch-executor>` section to learn more about the `awsbatch` executor in Nextflow.
-
-(aws-batch-cli)=
+See [AWS Batch][awsbatch-executor] to learn more about the `awsbatch` executor in Nextflow.
 
 ### AWS CLI
 
-:::{tip}
+:::tip
 The need for the AWS CLI is considered a legacy requirement for the deployment of Nextflow pipelines with AWS Batch.
-Instead, consider using {ref}`wave-page` and {ref}`fusion-page` to facilitate access to S3 without using the AWS CLI.
+Instead, consider using [Wave][wave-page] and [Fusion][fusion-page] to facilitate access to S3 without using the AWS CLI.
 :::
 
 Nextflow uses the [AWS command line tool](https://aws.amazon.com/cli/) (`aws`) to stage input files and output files between S3 and the task containers.
 
-The `aws` command can be made available by either (1) installing it in the container image(s) or (2) installing it in a {ref}`custom AMI <aws-custom-ami>` to be used instead of the default AMI when configuring AWS Batch.
+The `aws` command can be made available by either (1) installing it in the container image(s) or (2) installing it in a [custom AMI][aws-custom-ami]` to be used instead of the default AMI when configuring AWS Batch.
 
 ### Get started
 
@@ -186,7 +182,7 @@ The `aws` command can be made available by either (1) installing it in the conta
 
 3. In the AWS Console, create an S3 bucket for the work directory (see below). You can also create separate buckets for input data and results, as needed.
 
-4. Make sure that every process in your pipeline specifies a Docker container with the {ref}`process-container` directive.
+4. Make sure that every process in your pipeline specifies a Docker container with the [container][process-container] directive.
 
 5. Make sure that all of your container images are published in a Docker registry that can be reached by AWS Batch, such as [Docker Hub](https://hub.docker.com/), [Quay](https://quay.io/), or [Elastic Container Registry](https://aws.amazon.com/ecr/).
 
@@ -194,9 +190,9 @@ The `aws` command can be made available by either (1) installing it in the conta
 
 To configure your pipeline for AWS Batch:
 
-1. Specify the AWS Batch {ref}`executor <awsbatch-executor>`
-2. Specify the AWS Batch queue with the {ref}`process-queue` directive
-3. Specify any Batch job container options with the {ref}`process-containerOptions` directive.
+1. Specify the AWS Batch [executor][awsbatch-executor]
+2. Specify the AWS Batch queue with the [queue][process-queue] directive
+3. Specify any Batch job container options with the [containerOptions][process-containerOptions] directive.
 
 An example `nextflow.config` file is shown below:
 
@@ -217,16 +213,15 @@ aws {
 }
 ```
 
-:::{tip}
-Each process can be configured with its own queue by using the {ref}`process-queue` directive in the process definition or via {ref}`config-process-selectors` in your Nextflow configuration.
+:::tip
+Each process can be configured with its own queue by using the [queue][process-queue] directive in the process definition or via [Process selectors][config-process-selectors] in your Nextflow configuration.
 :::
 
 ## Container Options
 
-:::{versionadded} 21.12.1-edge
-:::
+<AddedInVersion version="21.12.1-edge" />
 
-The {ref}`process-containerOptions` directive can be used to control the properties of the container execution associated with each Batch job.
+The [containerOptions][process-containerOptions] directive can be used to control the properties of the container execution associated with each Batch job.
 
 The following container options are currently supported:
 
@@ -267,8 +262,6 @@ containerOptions '--ulimit nofile=1280:2560 --ulimit nproc=16:32 --privileged'
 
 Check the [AWS documentation](https://docs.aws.amazon.com/batch/latest/APIReference/API_ContainerProperties.html) for further details.
 
-(aws-custom-ami)=
-
 ## Custom AMI
 
 There are several reasons why you might need to create your own [AMI (Amazon Machine Image)](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AMIs.html) to use in your Compute Environments:
@@ -283,7 +276,7 @@ There are several reasons why you might need to create your own [AMI (Amazon Mac
 From the EC2 Dashboard, select **Launch Instance**, then select **Browse more AMIs**. In the new page, select
 **AWS Marketplace AMIs**, and then search for `Amazon ECS-Optimized Amazon Linux 2 (AL2) x86_64 AMI`. Select the AMI and continue as usual to configure and launch the instance.
 
-:::{note}
+:::note
 The selected instance has a root volume of 30GB. Make sure to increase its size or add a second EBS volume with enough storage for real genomic workloads.
 :::
 
@@ -293,17 +286,16 @@ Finally, select **Create Image** from the EC2 Dashboard to create a new AMI from
 
 The new AMI ID needs to be specified when creating the Batch Compute Environment.
 
-:::{warning}
+:::warning
 Any additional software must be installed on the EC2 instance *before* creating the AMI.
 :::
 
-(id2)=
 
 ### AWS CLI installation
 
-:::{tip}
+:::tip
 The need for the AWS CLI is considered a legacy requirement for the deployment of Nextflow pipelines with AWS Batch.
-Instead, consider using {ref}`wave-page` and {ref}`fusion-page` to facilitate access to S3 without using the AWS CLI.
+Instead, consider using [Wave][wave-page] and [Fusion][fusion-page] to facilitate access to S3 without using the AWS CLI.
 :::
 
 The [AWS CLI](https://aws.amazon.com/cli) should be installed in your custom AMI using a self-contained package manager such as [Conda](https://conda.io). That way, you can control which version of Python is used by the AWS CLI (which is written in Python).
@@ -328,7 +320,7 @@ $ ./miniconda/bin/aws --version
 aws-cli/1.29.20 Python/3.11.4 Linux/4.14.318-241.531.amzn2.x86_64 botocore/1.31.20
 ```
 
-:::{note}
+:::note
 The `aws` tool will be placed in a directory named `bin` in the main installation folder. Modifying this directory structure after the tool is installed will cause it to not work properly.
 :::
 
@@ -340,11 +332,7 @@ aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 
 Replace the path above with the one matching the location where the `aws` tool is installed in your AMI.
 
-:::{versionchanged} 19.07.0
-The `executor.awscli` config option was replaced by `aws.batch.cliPath`.
-:::
-
-:::{warning}
+:::warning
 The grandparent directory of the `aws` tool will be mounted into the container at the same path as the host, e.g. `/home/ec2-user/miniconda`, which will shadow existing files in the container. Make sure you use a path that is not already present in the container.
 :::
 
@@ -389,11 +377,11 @@ To test the installation:
 curl -s http://localhost:51678/v1/metadata | python -mjson.tool
 ```
 
-:::{note}
+:::note
 The `AmazonEC2ContainerServiceforEC2Role` policy must be attached to the instance role in order to be able to connect the EC2 instance created by the Compute Environment to the ECS container.
 :::
 
-:::{note}
+:::note
 The `AmazonEC2ContainerRegistryReadOnly` policy should be attached to the instance role in order to get read-only access to Amazon EC2 Container Registry repositories.
 :::
 
@@ -405,7 +393,7 @@ Nextflow automatically creates the Batch [Job definitions](http://docs.aws.amazo
 
 However, sometimes you may still need to specify a custom **Job Definition** to fine tune the configuration of a specific job, for example to define custom mount paths.
 
-To do that, first create a **Job Definition** in the AWS Console (or by other means). Note the name of the Job definition you created. You can then associate a process execution with this Job definition by using the {ref}`process-container` directive and specifying, in place of the container image name, the Job definition name prefixed by `job-definition://`, as shown below:
+To do that, first create a **Job Definition** in the AWS Console (or by other means). Note the name of the Job definition you created. You can then associate a process execution with this Job definition by using the [container][process-container] directive and specifying, in place of the container image name, the Job definition name prefixed by `job-definition://`, as shown below:
 
 ```groovy
 process.container = 'job-definition://your-job-definition-name'
@@ -415,7 +403,7 @@ process.container = 'job-definition://your-job-definition-name'
 
 Nextflow allows the use of multiple executors in the same workflow application. This feature enables the deployment of hybrid workloads in which some jobs are executed in the local computer or local computing cluster and some jobs are offloaded to AWS Batch.
 
-To enable this feature, use one or more {ref}`config-process-selectors` in your Nextflow configuration to apply the AWS Batch configuration to the subset of processes that you want to offload. For example:
+To enable this feature, use one or more [Process selectors][config-process-selectors] in your Nextflow configuration to apply the AWS Batch configuration to the subset of processes that you want to offload. For example:
 
 ```groovy
 process {
@@ -431,7 +419,7 @@ aws {
 }
 ```
 
-With the above configuration, processes with the `bigTask` {ref}`process-label` will run on AWS Batch, while the remaining processes will run in the local computer.
+With the above configuration, processes with the `bigTask` [label][process-label] will run on AWS Batch, while the remaining processes will run in the local computer.
 
 Then launch the pipeline with the -bucket-dir option to specify an AWS S3 path for the jobs computed with AWS Batch and, optionally, the -work-dir to specify the local storage for the jobs computed locally:
 
@@ -439,19 +427,16 @@ Then launch the pipeline with the -bucket-dir option to specify an AWS S3 path f
 nextflow run <script or project name> -bucket-dir s3://my-bucket/some/path
 ```
 
-:::{warning}
+:::warning
 The AWS S3 path needs to contain at least one sub-directory (e.g. `s3://my-bucket/work` rather than `s3://my-bucket`).
 :::
 
-:::{note}
+:::note
 Nextflow will automatically manage the transfer of input and output files between the local and cloud environments when using hybrid workloads.
 :::
 
 ### Volume mounts
 
-:::{versionadded} 19.07.0
-:::
-
 User provided container volume mounts can be provided as shown below:
 
 ```groovy
@@ -515,12 +500,9 @@ There are multiple reasons why this can happen. They are mainly related to the C
 
 This [AWS page](https://aws.amazon.com/premiumsupport/knowledge-center/batch-job-stuck-runnable-status/) provides several resolutions and tips to investigate and work around the issue.
 
-(aws-fargate)=
-
 ## AWS Fargate
 
-:::{versionadded} 23.12.0-edge
-:::
+<AddedInVersion version="23.12.0-edge" />
 
 Nextflow provides experimental support for the execution of [AWS Batch jobs with Fargate resources](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html).
 
@@ -542,11 +524,22 @@ wave.enabled = true
 See the AWS documentation for details how to create the required AWS Batch queue for Fargate, the Batch Job Role
 and the Batch Execution Role.
 
-:::{note}
+:::note
 Nextflow uses [s5cmd](https://github.com/peak/s5cmd) to download the task input data and upload the task outputs.
-To enable this capability, you need to enable the Wave service in the Nextflow configuration, as shown in the above example. See {ref}`Wave <wave-page>` documentation for more details.
+To enable this capability, you need to enable the Wave service in the Nextflow configuration, as shown in the above example. See [Wave][] for more details.
 :::
 
 ## Advanced configuration
 
-Read the {ref}`AWS configuration<config-aws>` section to learn more about advanced configuration options.
+See [aws][config-aws] to learn more about advanced configuration options.
+
+[awsbatch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#aws-batch
+[aws-custom-ami]: /nextflow_docs/nextflow_repo/docs/aws.mdx#custom-ami
+[config-aws]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#aws
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-containerOptions]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#containeroptions
+[process-label]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#label
+[process-queue]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#queue
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
diff --git a/docs/azure.md b/new-docs/nextflow-docs/azure.mdx
similarity index 96%
rename from docs/azure.md
rename to new-docs/nextflow-docs/azure.mdx
index 5cdc294487..433f0e1935 100644
--- a/docs/azure.md
+++ b/new-docs/nextflow-docs/azure.mdx
@@ -1,4 +1,4 @@
-(azure-page)=
+
 
 # Azure
 
@@ -9,7 +9,7 @@ Nextflow provides built-in support for Azure Cloud Services. It enables you to:
 - Store and access data using Azure Blob Storage and Azure file shares.
 - Execute workflows using Azure Batch.
 
-:::{tip}
+:::tip
 For automated Azure infrastructure setup, consider using [Batch Forge](https://docs.seqera.io/platform/latest/compute-envs/azure-batch#compute-environment) in [Seqera Platform](https://seqera.io/platform/).
 :::
 
@@ -37,7 +37,7 @@ To run pipelines with Azure Batch:
     nextflow run <PIPELINE_NAME>
     ```
 
-:::{tip}
+:::tip
 You can list Azure regions with:
 
 ```bash
@@ -70,12 +70,10 @@ For Azure Batch:
 
 To assign roles to a managed identity or service principal, see the [Azure documentation](https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current).
 
-(azure-managed-identities)=
-
 ### Managed identities
 
-:::{versionadded} 24.05.0-edge
-:::
+<AddedInVersion version="24.05.0-edge" />
+
 
 [Managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) is the recommended authentication method when running Nextflow within Azure. It automatically manages credentials without requiring you to store secrets.
 
@@ -117,8 +115,8 @@ Replace the following:
 - `BATCH_ACCOUNT_NAME`: your Azure Batch account name
 - `BATCH_ACCOUNT_LOCATION`: your Azure Batch account location
 
-:::{tip}
-Nextflow uses the `AZURE_MANAGED_IDENTITY_SYSTEM` environment variable if the managed identity is not set in the Nextflow configuration file. Set this to `true` to enable a system-assigned managed identity
+:::tip
+Nextflow uses the `AZURE_MANAGED_IDENTITY_SYSTEM` environment variable if the managed identity is not set in the Nextflow configuration file. Set this to `true` to enable a system-assigned managed identity.
 :::
 
 **User-assigned managed identity**
@@ -157,14 +155,13 @@ Replace the following:
 - `BATCH_ACCOUNT_NAME`: your Azure Batch account name
 - `BATCH_ACCOUNT_LOCATION`: your Azure Batch account location
 
-:::{tip}
+:::tip
 Nextflow uses the `AZURE_MANAGED_IDENTITY_USER` environment variable if the managed identity client ID is not provided in the Nextflow configuration file.
 :::
 
 ### Service principals
 
-:::{versionadded} 22.11.0-edge
-:::
+<AddedInVersion version="22.11.0-edge" />
 
 [Service principal](https://learn.microsoft.com/en-us/entra/identity-platform/app-objects-and-service-principals) credentials can be used to access Azure Batch and Storage accounts.
 
@@ -189,7 +186,7 @@ azure {
 }
 ```
 
-:::{tip}
+:::tip
 Nextflow uses the following environment variables if storage settings are not set in the Nextflow config file:
 
 - `AZURE_CLIENT_ID`: your Azure service principal application ID
@@ -228,11 +225,11 @@ You can also use a Shared Access Token (SAS) instead of an account key to provid
 azure.storage.sasToken = '<SAS_TOKEN>'
 ```
 
-:::{tip}
+:::tip
 When creating a SAS token, make sure to enable `Read`, `Write`, `Delete`, `List`, `Add`, `Create` permissions for the `Container` and `Object` resource types. The value of `sasToken` should be stripped of the leading `?` character.
 :::
 
-:::{tip}
+:::tip
 Nextflow uses the following environment variables if storage settings are not provided in the Nextflow configuration file:
 
 - `AZURE_STORAGE_ACCOUNT_NAME`: your Azure Storage account name
@@ -262,7 +259,7 @@ azure {
 }
 ```
 
-:::{tip}
+:::tip
 Nextflow uses the following environment variables if storage settings are not provided in the Nextflow configuration file:
 
 - `AZURE_STORAGE_ACCOUNT_NAME`: your Azure Storage account name
@@ -270,8 +267,6 @@ Nextflow uses the following environment variables if storage settings are not pr
 - `AZURE_STORAGE_SAS_TOKEN`: a shared access signature (SAS) token for Azure Storage access
 :::
 
-(azure-batch)=
-
 ## Azure Batch
 
 [Azure Batch](https://learn.microsoft.com/en-us/azure/batch/) is a managed computing service that enables large-scale parallel and high-performance computing (HPC) batch jobs in Azure. Nextflow provides a built-in executor for Azure Batch, allowing you to offload workflow tasks to the cloud.
@@ -317,7 +312,7 @@ azure {
 }
 ```
 
-:::{note}
+:::note
 The work directory must be a subdirectory, for example, `az://container/work`, not `az://container`.
 :::
 
@@ -343,7 +338,7 @@ You can increase your quota on the Azure Portal by opening your Batch account an
 
 Nextflow supports two approaches for managing Batch pools: auto pools and named pools. These approaches are described in the following sections.
 
-:::{warning}
+:::warning
 Clean up the Batch pools or use auto-scaling to avoid additional charges in the Batch account.
 :::
 
@@ -374,7 +369,7 @@ You can specify multiple machine families per process using glob patterns in the
 
 ```groovy
 // D or E v5 machines with data disk
-process.machineType = "Standard_D*d_v5,Standard_E*d_v5" 
+process.machineType = "Standard_D*d_v5,Standard_E*d_v5"
 ```
 
 For example, the following process creates a pool of *Standard_E8d_v5* machines when using `autoPoolMode`:
@@ -434,9 +429,9 @@ process {
 }
 ```
 
-The above example defines the configuration for two node pools, `small` and `large`. The `small` pool provisions 10 compute nodes of type *Standard_D2_v2*, and the `large` pool provisions 5 nodes of type *Standard_E2_v3*. See the {ref}`config-azure` configuration scope for the list of available configuration options.
+The above example defines the configuration for two node pools, `small` and `large`. The `small` pool provisions 10 compute nodes of type *Standard_D2_v2*, and the `large` pool provisions 5 nodes of type *Standard_E2_v3*. See the [azure][config-azure] configuration scope for the list of available configuration options.
 
-:::{warning}
+:::warning
 Pool names may contain alphanumeric characters, hyphens, and underscores. Hyphenated names must be quoted, e.g., `'pool-1'`.
 :::
 
@@ -494,11 +489,10 @@ The `azure.batch.pools.<POOL_NAME>.scaleFormula` setting can be used to specify
 
 By default, Nextflow creates SAS tokens for specific containers and passes them to tasks to enable file operations with Azure Storage. SAS tokens expire after a set period of time. The expiration time is 48 hours by default and can be configured using `azure.storage.tokenDuration` in your configuration.
 
-:::{versionadded} 25.05.0-edge
-:::
+<AddedInVersion version="25.05.0-edge" />
 
-:::{warning}
-Only available when using [Fusion filesystem](fusion.md)!
+:::warning
+Only available when using [Fusion filesystem](./fusion.mdx).
 :::
 
 You can also authenticate to Azure Storage using a managed identity when using Fusion.
@@ -531,7 +525,7 @@ For example, consider a *Standard_D4d_v5* machine with 4 vCPUs, 16 GB of memory,
 
 Resource overprovisioning can occur if tasks consume more than their allocated share of resources. For instance, the node described above may become overloaded and fail if a task with `cpus 2` uses more than 8 GB of memory or 75 GB of disk space. Make sure to accurately specify resource requirements to ensure optimal performance and prevent task failures.
 
-:::{warning}
+:::warning
 Azure virtual machines come with fixed storage disks that are not expandable. Tasks will fail if the tasks running concurrently on a node use more storage than the machine has available.
 :::
 
@@ -539,7 +533,7 @@ Azure virtual machines come with fixed storage disks that are not expandable. Ta
 
 Every process in your pipeline must specify a container in order to be executed on Azure Batch.
 
-Nextflow supports both public and private container images. You can pull public images from repositories such as <https://community.wave.seqera.io/>. You must authenticate for any private images that you use. Ensure the Batch pool has access when using a private registry like Azure Container Registry (ACR). Provide ACR credentials in the `azure.registry` configuration scope:
+Nextflow supports both public and private container images. You can pull public images from repositories such as [https://community.wave.seqera.io](https://community.wave.seqera.io). You must authenticate for any private images that you use. Ensure the Batch pool has access when using a private registry like Azure Container Registry (ACR). Provide ACR credentials in the `azure.registry` configuration scope:
 
 ```groovy
 azure {
@@ -551,7 +545,7 @@ azure {
 }
 ```
 
-:::{tip}
+:::tip
 Nextflow uses the following environment variables if the registry credentials are not provided in the Nextflow configuration file:
 
 - `AZURE_REGISTRY_USER_NAME`: the username for Azure Container Registry authentication
@@ -623,7 +617,7 @@ The subnet ID must be in the following format:
 
 Nextflow can submit tasks to existing pools that are already attached to a virtual network without requiring additional configuration.
 
-:::{warning}
+:::warning
 Virtual networks require Microsoft Entra authentication (service principal or managed identity).
 :::
 
@@ -667,7 +661,7 @@ azure {
 }
 ```
 
-:::{warning}
+:::warning
 File shares must be authenticated using a storage account key. Managed identity and service principal are not supported.
 :::
 
@@ -709,10 +703,12 @@ Launch the pipeline with the above configuration:
 nextflow run <PIPELINE_NAME>
 ```
 
-:::{note}
+:::note
 When using Fusion, `bucketDir` is not needed as all tasks will use the remote work directory. Specify `workDir` instead.
 :::
 
 ## Advanced configuration
 
-See the {ref}`config-azure` configuration scope for the list of available configuration options.
+See the [azure][config-azure] configuration scope for the list of available configuration options.
+
+[config-azure]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#azure
diff --git a/docs/cache-and-resume.md b/new-docs/nextflow-docs/cache-and-resume.mdx
similarity index 74%
rename from docs/cache-and-resume.md
rename to new-docs/nextflow-docs/cache-and-resume.mdx
index 2128663900..09e0a8ae67 100644
--- a/docs/cache-and-resume.md
+++ b/new-docs/nextflow-docs/cache-and-resume.mdx
@@ -1,4 +1,4 @@
-(cache-resume-page)=
+
 
 # Caching and resuming
 
@@ -10,42 +10,40 @@ You can enable resumability in Nextflow with the `-resume` flag when launching a
 
 All task executions are automatically saved to the task cache, regardless of the `-resume` option (so that you always have the option to resume later). The task cache is a key-value store, where each key-value pair corresponds to a previously-executed task.
 
-The task cache is used in conjunction with the [work directory](#work-directory) to recover cached tasks in a resumed run. It is also used by the {ref}`cli-log` sub-command to query task metadata.
-
-(cache-resume-task-hash)=
+The task cache is used in conjunction with the [work directory](#work-directory) to recover cached tasks in a resumed run. It is also used by the [`log`][cli-log] sub-command to query task metadata.
 
 ### Task hash
 
 The task hash is computed from the following metadata:
 
-- Session ID (see `workflow.sessionId` in the {ref}`stdlib-namespaces-workflow` namespace)
-- Task name (see `name` in {ref}`trace-report`)
+- Session ID (see `workflow.sessionId` in the [workflow][stdlib-namespaces-workflow] namespace)
+- Task name (see `name` in [Trace file][trace-report])
 - Task container image (if applicable)
-- Task {ref}`environment modules <process-module>` (if applicable)
-- Task {ref}`Conda environment <process-conda>` (if applicable)
-- Task {ref}`Spack environment <process-spack>` and {ref}`CPU architecture <process-arch>` (if applicable)
-- Task {ref}`inputs <process-input>`
-- Task {ref}`script <process-script>`
+- Task [environment modules][process-module] (if applicable)
+- Task [Conda environment][process-conda] (if applicable)
+- Task [Spack environment][process-spack] and [CPU architecture][process-arch>] (if applicable)
+- Task [inputs][process-input]
+- Task [script][process-script]
 - Any global variables referenced in the task script
-- Any task {ref}`process-ext` properties referenced in the task script
-- Any {ref}`bundled scripts <bundling-executables>` used in the task script
-- Whether the task is a {ref}`stub run <process-stub>`
+- Any task [`ext`][process-ext] properties referenced in the task script
+- Any [bundled scripts][bundling-executables] used in the task script
+- Whether the task is a [stub run][process-stub]
 
-:::{note}
+:::note
 Nextflow also includes an incrementing component in the hash generation process, which allows it to iterate through multiple hash values until it finds one that does not match an existing execution directory. This mechanism typically aligns with task retries (i.e., task attempts), however this is not guaranteed.
 :::
 
-:::{versionchanged} 23.09.2-edge
-The {ref}`process-ext` directive was added to the task hash.
-:::
+<ChangedInVersion version="23.09.2-edge">
+The [`ext`][process-ext] directive was added to the task hash.
+</ChangedInVersion>
 
 Nextflow computes this hash for every task when it is created but before it is executed. If resumability is enabled and there is an entry in the task cache with the same hash, Nextflow tries to recover the previous task execution. A cache hit does not guarantee that the task will be resumed, because it must also recover the task outputs from the [work directory](#work-directory).
 
-Files are hashed differently depending on the caching mode. See the {ref}`process-cache` directive for more details.
+Files are hashed differently depending on the caching mode. See the [`cache`][process-cache] directive for more details.
 
 ### Task entry
 
-The task entry is a serialized blob of the task metadata required to resume a task, including the fields used by the {ref}`trace-report` and the task input variables.
+The task entry is a serialized blob of the task metadata required to resume a task, including the fields used by the [Trace file][trace-report] and the task input variables.
 
 ### Cache stores
 
@@ -53,8 +51,7 @@ The default cache store uses the `.nextflow/cache` directory, relative to the la
 
 Due to the limitations of LevelDB, the database for a given session ID can only be accessed by one reader/writer at a time. This means, for example, that you cannot use `nextflow log` to query the task metadata for a pipeline run while it is still running.
 
-:::{versionadded} 23.07.0-edge
-:::
+<AddedInVersion version="23.07.0-edge" />
 
 The cloud cache is an alternative cache store that uses cloud storage instead of the local cache directory. You can use it by setting the `NXF_CLOUDCACHE_PATH` environment variable to the desired cache path (e.g. `s3://my-bucket/cache`) and providing the necessary credentials.
 
@@ -68,7 +65,7 @@ Each task uses a unique directory based on its hash. When a task is created, Nex
 
 When a previous task is retrieved from the task cache on a resumed run, Nextflow then checks the corresponding task directory in the work directory. If all the required outputs are present and the exit code is valid, then the task is successfully cached; otherwise, the task is re-executed.
 
-For this reason, it is important to preserve both the task cache (`.nextflow/cache`) and work directories in order to resume runs successfully. You can use the {ref}`cli-clean` command to delete specific runs from the cache.
+For this reason, it is important to preserve both the task cache (`.nextflow/cache`) and work directories in order to resume runs successfully. You can use the [`clean`][cli-clean] command to delete specific runs from the cache.
 
 ## Troubleshooting
 
@@ -98,7 +95,7 @@ process FOO {
 }
 ```
 
-Ensure that the `cache` directive has not been disabled. See {ref}`process-cache` for more information.
+Ensure that the `cache` directive has not been disabled. See [cache][process-cache]  for more information.
 
 ### Modified inputs
 
@@ -114,7 +111,7 @@ Modifying inputs that are used in the task hash invalidates the cache. Common ca
 
 Nextflow calculates a hash for an input file using its full path, last modified timestamp, and file size. If any of these attributes change, Nextflow re-executes the task.
 
-:::{warning}
+:::warning
 If a process modifies its input files, it cannot be resumed. Avoid processes that modify their own input files as this is considered an anti-pattern.
 :::
 
@@ -122,9 +119,7 @@ If a process modifies its input files, it cannot be resumed. Avoid processes tha
 
 Some shared file systems, such as NFS, may report inconsistent file timestamps, which can invalidate the cache when using the standard caching mode.
 
-To resolve this issue, use the `'lenient'` {ref}`caching mode <process-cache>` to ignore the last modified timestamp and use only the file path and size.
-
-(cache-global-var-race-condition)=
+To resolve this issue, use the `'lenient'` [caching mode][process-cache] to ignore the last modified timestamp and use only the file path and size.
 
 ### Race condition on a global variable
 
@@ -143,11 +138,9 @@ To resolve this issue, avoid declaring global variables in closures:
 channel.of(1,2,3).map { v -> def X=v; X+=2 }.view { v -> "ch1 = $v" }
 ```
 
-:::{versionadded} 25.04.0
-The {ref}`strict syntax <strict-syntax-page>` does not allow global variables to be declared in closures.
-:::
-
-(cache-nondeterministic-inputs)=
+<AddedInVersion version="25.04.0">
+The [strict syntax][strict-syntax-page] does not allow global variables to be declared in closures.
+</AddedInVersion>
 
 ### Non-deterministic process inputs
 
@@ -172,7 +165,7 @@ process check_bam_bai {
 }
 ```
 
-In the above example, the inputs will be merged without matching on `id`, in a similar manner as the {ref}`operator-merge` operator. As a result, the inputs are incorrect and non-deterministic.
+In the above example, the inputs will be merged without matching on `id`, in a similar manner as the [`merge`][operator-merge] operator. As a result, the inputs are incorrect and non-deterministic.
 
 To resolve this issue, use the `join` operator to join the channels into a single input channel before invoking the process:
 
@@ -204,9 +197,7 @@ Nextflow resumes from the previous run by default. If you want to resume from an
 nextflow run rnaseq-nf -resume 4dc656d2-c410-44c8-bc32-7dd0ea87bebf
 ```
 
-You can use the {ref}`cli-log` command to view all previous runs as well as the task executions for each run.
-
-(cache-compare-hashes)=
+You can use the [`log`][cli-log] command to view all previous runs as well as the task executions for each run.
 
 ### Comparing the hashes of two runs
 
@@ -219,8 +210,7 @@ One way to debug a resumed run is to compare the task hashes of each run using t
 
 While some manual effort is required, the final diff can often reveal the exact change that caused a task to be re-executed.
 
-:::{versionadded} 23.10.0
-:::
+<AddedInVersion version="23.10.0" />
 
 When using `-dump-hashes json`, the task hashes can be more easily extracted into a diff. Here is an example Bash script to perform two runs and produce a diff:
 
@@ -244,6 +234,25 @@ diff run_1.tasks.log run_2.tasks.log
 
 You can then view the `diff` output or use a graphical diff viewer to compare `run_1.tasks.log` and `run_2.tasks.log`.
 
-:::{versionadded} 25.04.0
-Nextflow now has a built-in way to compare two task runs. See the {ref}`data-lineage-page` guide for details.
-:::
+<AddedInVersion version="25.04.0">
+Nextflow now has a built-in way to compare two task runs. See the [Data lineage][data-lineage-page] guide for details.
+</AddedInVersion>
+
+[bundling-executables]: /nextflow_docs/nextflow_repo/docs/sharing.mdx#the-bin-directory
+[data-lineage-page]: /nextflow_docs/nextflow_repo/docs/tutorials/data-lineage.mdx
+[cli-clean]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#clean
+[cli-log]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#log
+[operator-join]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#join
+[process-arch]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#arch
+[process-cache]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cache
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
+[process-ext]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#ext
+[process-input]: /nextflow_docs/nextflow_repo/docs/process.mdx#inputs
+[operator-merge]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#merge
+[process-module]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#module
+[process-script]: /nextflow_docs/nextflow_repo/docs/process.mdx#script
+[process-spack]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#spack
+[process-stub]: /nextflow_docs/nextflow_repo/docs/process.mdx#stub
+[stdlib-namespaces-workflow]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-namespaces.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[trace-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
diff --git a/new-docs/nextflow-docs/channel.mdx b/new-docs/nextflow-docs/channel.mdx
new file mode 100644
index 0000000000..eeffd80636
--- /dev/null
+++ b/new-docs/nextflow-docs/channel.mdx
@@ -0,0 +1,88 @@
+# Dataflow
+
+Nextflow uses a **dataflow** programming model to define workflows declaratively. In this model, [processes][process-page] in a pipeline are connected to each other through *dataflow channels* and *dataflow values*.
+
+## Channels
+
+A *dataflow channel* (or simply *channel*) is an asynchronous sequence of values.
+
+The values in a channel cannot be accessed directly, but only through an operator or process. For example:
+
+```nextflow
+channel.of(1, 2, 3).view { v -> "channel emits ${v}" }
+```
+
+```console
+channel emits 1
+channel emits 2
+channel emits 3
+```
+
+### Factories
+
+A channel can be created by factories in the `channel` namespace. For example, the `channel.fromPath()` factory creates a channel from a file name or glob pattern, similar to the `files()` function:
+
+```nextflow
+channel.fromPath('input/*.txt').view()
+```
+
+See [Channel factories][channel-factory] for the full list of channel factories.
+
+### Operators
+
+Channel operators, or *operators* for short, are functions that consume and produce channels. Because channels are asynchronous, operators are necessary to manipulate the values in a channel. Operators are particularly useful for implementing glue logic between processes.
+
+Commonly used operators include:
+
+- [combine][operator-combine]: emit the combinations of two channels
+- [collect][operator-collect]: collect the values from a channel into a list
+- [filter][operator-filter]: select the values in a channel that satisfy a condition
+- [flatMap][operator-flatMap]: transform each value from a channel into a list and emit each list element separately
+- [groupTuple][operator-grouptuple]: group the values from a channel based on a grouping key
+- [join][operator-join]: join the values from two channels based on a matching key
+- [map][operator-map]: transform each value from a channel with a mapping function
+- [mix][operator-mix]: emit the values from multiple channels
+- [view][operator-view]: print each value in a channel to standard output
+
+See [Operators][operator-page] for the full list of operators.
+
+## Values
+
+A *dataflow value* is an asynchronous value.
+
+Dataflow values can be created using the [value][channel-value] factory, and they are created by processes (under [certain conditions][process-out-singleton]).
+
+A dataflow value cannot be accessed directly, but only through an operator or process. For example:
+
+```nextflow
+channel.value(1).view { v -> "dataflow value is ${v}" }
+```
+
+```console
+dataflow value is 1
+```
+
+See [Value][stdlib-types-value] for the set of available methods for dataflow values.
+
+[channel-of]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#of
+[channel-path]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#frompath
+[operator-map]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#map
+[operator-flatmap]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#flatmap
+[process-output]: /nextflow_docs/nextflow_repo/docs/process.mdx#outputs
+[channel-value]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#value
+[operator-first]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#first
+[operator-collect]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#collect
+[operator-reduce]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#reduce
+[process-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[process-out-singleton]: /nextflow_docs/nextflow_repo/docs/process.mdx#singleton-outputs
+[process-multiple-input-channels]: /nextflow_docs/nextflow_repo/docs/process.mdx#multiple-input-channels
+[channel-factory]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[operator-combine]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#combine
+[operator-filter]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#filter
+[operator-flatMap]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#flatmap
+[operator-grouptuple]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#grouptuple
+[operator-join]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#join
+[operator-mix]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#mix
+[operator-view]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#view
+[operator-page]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx
+[stdlib-types-value]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#valuev
diff --git a/new-docs/nextflow-docs/cli.mdx b/new-docs/nextflow-docs/cli.mdx
new file mode 100644
index 0000000000..7124767cb8
--- /dev/null
+++ b/new-docs/nextflow-docs/cli.mdx
@@ -0,0 +1,412 @@
+# Command line
+
+Nextflow provides a robust command line interface (CLI) for the management and execution of pipelines.
+
+Simply run `nextflow` with no options or `nextflow -h` to see the list of available top-level options and commands. See [CLI reference][cli-reference] for the full list of subcommands with examples.
+
+:::note
+Nextflow options use a single dash prefix, for example, `-resume`. Do not confuse with double dash notation, for example, `--resume`, which is instead used for [Pipeline parameters][cli-params].
+:::
+
+## Basic usage
+
+### Hard configuration override
+
+Use the specified configuration file(s) overriding any defaults.
+
+```bash
+nextflow -C my.config COMMAND [arg...]
+```
+
+The `-C` option is used to override *all* settings specified in the default config file. For soft override, please refer the `-c` option.
+
+- Override **any** default configuration with a custom configuration file:
+
+  ```bash
+  nextflow -C my.config run nextflow-io/hello
+  ```
+
+### JVM properties
+
+Set JVM properties.
+
+```bash
+nextflow -Dkey=value COMMAND [arg...]
+```
+
+This option allows the definition of custom Java system properties that can be used to properly configure or fine tuning the JVM instance used by the Nextflow runtime.
+
+For specifying other JVM level options, see the [Environment variables][config-env-vars] section.
+
+- Add JVM properties to the invoked pipeline:
+
+  ```bash
+  nextflow -Dfile.encoding=UTF-8 run nextflow-io/hello
+  ```
+
+### Execution as a background job
+
+Execute `nextflow` in the background.
+
+```bash
+nextflow -bg COMMAND [arg...]
+```
+
+The `-bg` option is used to invoke the nextflow execution in the background and allows the user to continue interacting with the terminal. This option is similar to `nohup` in behavior.
+
+- Invoke any execution as a background job:
+
+  ```bash
+  nextflow -bg run nextflow-io/hello
+  ```
+
+### Soft configuration override
+
+Add the specified file to configuration set.
+
+```bash
+nextflow -c nxf.config COMMAND [arg...]
+```
+
+The `-c` option is used to append a new configuration to the default configuration. The `-c` option allows us to update the config in an additive manner. For **hard override**, refer to the `-C` option.
+
+- Update *some* fields of the default config for any pipeline:
+
+  ```bash
+  nextflow -c nxf.config run nextflow-io/hello
+  ```
+
+### Help
+
+Print the help message.
+
+```bash
+nextflow -h
+```
+
+The `-h` option prints out the overview of the CLI interface and enumerates the top-level *options* and *commands*.
+
+### Execution logs
+
+Sets the path of the Nextflow log file.
+
+```bash
+nextflow -log custom.log COMMAND [arg...]
+```
+
+The `-log` option takes a path of the new log file which will be used instead of the default `.nextflow.log` or to save logs files to another directory.
+
+- Save all execution logs to the custom `/var/log/nextflow.log` file:
+
+  ```bash
+  nextflow -log /var/log/nextflow.log run nextflow-io/hello
+  ```
+
+### Quiet execution
+
+Disable the printing of information to the terminal.
+
+```bash
+nextflow -q COMMAND [arg...]
+```
+
+The `-q` option suppresses the banner and process-related info, and exits once the execution is completed. Please note that it does not affect any explicit print statement within a pipeline.
+
+- Invoke the pipeline execution without the banner and pipeline information:
+
+  ```bash
+  nextflow -q run nextflow-io/hello
+  ```
+
+### Logging to a syslog server
+
+Send logs to [Syslog](https://en.wikipedia.org/wiki/Syslog) server endpoint.
+
+```bash
+nextflow -syslog localhost:1234 COMMAND [arg...]
+```
+
+The `-syslog` option is used to send logs to a Syslog logging server at the specified endpoint.
+
+- Send the logs to a Syslog server at specific endpoint:
+
+  ```bash
+  nextflow -syslog localhost:1234 run nextflow-io/hello
+  ```
+
+### Version
+
+Print the Nextflow version information.
+
+```bash
+nextflow -v
+```
+
+The `-v` option prints out information about Nextflow, such as the version and build. The `-version` option, in addition, prints out the citation reference and official website.
+
+- The `-v` option prints out information about Nextflow, such as the version and build.:
+
+  ```bash
+  nextflow -v
+  ```
+
+  This prints an output similar to the following:
+
+  ```console
+  nextflow version 20.07.1.5412
+  ```
+
+- The `-version` option in addition prints out the citation reference and official website.:
+
+  ```bash
+  nextflow -version
+  ```
+
+  This prints an output similar to the following:
+
+  ```console
+  N E X T F L O W
+  version 20.07.1 build 5412
+  created 24-07-2020 15:18 UTC (20:48 IDT)
+  cite doi:10.1038/nbt.3820
+  http://nextflow.io
+  ```
+
+## Running pipelines
+
+The main purpose of the Nextflow CLI is to run Nextflow pipelines with the `run` command. Nextflow can execute a local script (e.g., `./main.nf`) or a remote project (e.g., `github.com/nextflow-io/hello`).
+
+### Launching a remote project
+
+To launch the execution of a pipeline project, hosted in a remote code repository, you simply need to specify its qualified name or the repository URL after the `run` command. The qualified name is formed by two parts: the `owner` name and the `repository` name separated by a `/` character.
+
+If a Nextflow project is hosted on GitHub, for example `http://github.com/nextflow-io/hello`, it can be executed by entering the following command in your shell terminal:
+
+```bash
+nextflow run nextflow-io/hello
+```
+
+or using the project URL:
+
+```bash
+nextflow run http://github.com/nextflow-io/hello
+```
+
+If the project is found, it will be automatically downloaded to the Nextflow home directory (`$HOME/.nextflow` by default) and cached for subsequent runs.
+
+:::note
+You must use the `-hub` option to specify the hosting service if your project is hosted on a service other than GitHub, e.g., `-hub bitbucket`. However, the `-hub` option is not required if you use the project URL.
+:::
+
+Try this feature by running the following command:
+
+```bash
+nextflow run nextflow-io/hello
+```
+
+It will download a trivial example from the repository published at [http://github.com/nextflow-io/hello](http://github.com/nextflow-io/hello) and execute it on your computer.
+
+If the `owner` is omitted, Nextflow will search your cached pipelines for a pipeline that matches the name specified. If no pipeline is found, Nextflow will try to download it using the `organization` name defined by the `NXF_ORG` environment variable (`nextflow-io` by default).
+
+:::note
+To access a private repository, specify the access credentials using the `-user` command line option. Then follow the interactive prompts to enter your password. Alternatively, define your private repository access credentials using Git. See [Git configuration][git-page] for more information.
+:::
+
+### Using a specific revision
+
+Any Git branch, tag, or commit of a project repository can be used when launching a pipeline by specifying the `-r` option:
+
+```bash
+nextflow run nextflow-io/hello -r mybranch
+```
+
+or
+
+```bash
+nextflow run nextflow-io/hello -r v1.1
+```
+
+These commands will execute two different project revisions based on the given Git branch/tag/commit.
+
+### Pipeline parameters
+
+Pipeline scripts can define *parameters* that can be overridden on the command line.
+
+Parameters can be declared in the main script:
+
+```nextflow
+params.alpha = 'default script value'
+
+workflow {
+  println "alpha = ${params.alpha}"
+}
+```
+
+Or in a config file:
+
+```groovy
+params {
+  alpha = 'default config value'
+}
+```
+
+The above parameter can be specified on the command line as `--alpha`:
+
+```bash
+nextflow run main.nf --alpha Hello
+```
+
+:::note
+Parameters that are specified on the command line without a value are set to `true`.
+:::
+
+:::note
+Parameters that are specified on the command line in kebab case (e.g., `--alpha-beta`) are automatically converted to camel case (e.g., `--alphaBeta`). Because of this, a parameter defined as `alphaBeta` in the pipeline script can be specified on the command line as `--alphaBeta` or `--alpha-beta`.
+:::
+
+:::note
+When a command line parameter includes one or more glob characters, i.e. wildcards like `*` or `?`, the parameter value must be enclosed in quotes to prevent Bash expansion and preserve the glob characters. For example:
+
+```bash
+nextflow run main.nf --files "*.fasta"
+```
+:::
+
+Parameters specified on the command line can be also specified in a params file using the `-params-file` option.
+
+```bash
+nextflow run main.nf -params-file pipeline_params.yml
+```
+
+The `-params-file` option loads parameters for your Nextflow pipeline from a JSON or YAML file. Parameters defined in the file are equivalent to specifying them directly on the command line. For example, instead of specifying parameters on the command line:
+
+```bash
+nextflow run main.nf --alpha 1 --beta two
+```
+
+Parameters can be represented in YAML format:
+
+```yaml
+alpha: 1
+beta: 'two'
+```
+
+Or in JSON format:
+
+```json
+{
+  "alpha": 1,
+  "beta": "two"
+}
+```
+
+:::note
+Parameter values in the params file can reference the following [built-in variables][config-constants]: `baseDir`, `projectDir`, `launchDir`.
+:::
+
+Parameters are applied in the following order (from lowest to highest priority):
+
+1. Parameters defined in pipeline scripts (e.g., `main.nf`)
+2. Parameters defined in [config files][config-params]
+3. Parameters specified in a params file (`-params-file`)
+4. Parameters specified on the command line (`--something value`)
+
+## Managing projects
+
+Nextflow seamlessly integrates with popular Git providers, including [BitBucket](http://bitbucket.org/), [GitHub](http://github.com), and [GitLab](http://gitlab.com) for managing Nextflow pipelines as version-controlled Git repositories.
+
+The following commands allow you to perform basic operations to manage your projects.
+
+### Listing available projects
+
+The `list` command allows you to list all the projects you have downloaded in your computer. For example:
+
+```bash
+nextflow list
+```
+
+This prints a list similar to the following:
+
+```console
+cbcrg/ampa-nf
+cbcrg/piper-nf
+nextflow-io/hello
+nextflow-io/examples
+```
+
+### Showing project information
+
+By using the `info` command you can show information from a downloaded project. For example:
+
+```bash
+nextflow info hello
+```
+
+This prints an output similar to the following:
+
+```console
+project name: nextflow-io/hello
+repository  : http://github.com/nextflow-io/hello
+local path  : $HOME/.nextflow/assets/nextflow-io/hello
+main script : main.nf
+revisions   :
+* master (default)
+  mybranch
+  v1.1 [t]
+  v1.2 [t]
+```
+
+Starting from the top it shows: the project name; the Git repository URL; the local directory where the project has been downloaded; the script that is executed when launched; the list of available revisions i.e. branches and tags. Tags are marked with a `[t]` on the right and the checked-out revision is marked with a `*` on the left.
+
+### Pulling or updating a project
+
+The `pull` command allows you to download a project from a GitHub repository or to update it if that repository has already been downloaded. For example:
+
+```bash
+nextflow pull nextflow-io/hello
+```
+
+Alternatively, you can use the repository URL as the name of the project to pull:
+
+```bash
+nextflow pull https://github.com/nextflow-io/hello
+```
+
+Downloaded pipeline projects are stored in your directory `$HOME/.nextflow/assets` directory.
+
+### Viewing the project code
+
+The `view` command shows the content of the pipeline script you have pulled. For example:
+
+```bash
+nextflow view nextflow-io/hello
+```
+
+By adding the `-l` option to the example above it will list the content of the repository.
+
+### Cloning a project into a directory
+
+The `clone` command allows you to copy a Nextflow pipeline project to a directory of your choice. For example:
+
+```bash
+nextflow clone nextflow-io/hello target-dir
+```
+
+If the destination directory is omitted the specified project is cloned to a directory with the same name as the pipeline base name (e.g., `hello`) in the current directory.
+
+The `clone` command can be used to inspect or modify the source code of a pipeline project. You can eventually commit and push back your changes by using the usual Git/GitHub workflow.
+
+### Deleting a project
+
+Downloaded pipelines can be deleted by using the `drop` command, as shown below:
+
+```bash
+nextflow drop nextflow-io/hello
+```
+
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[cli-reference]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx
+[config-constants]: /nextflow_docs/nextflow_repo/docs/config.mdx#constants
+[config-env-vars]: /nextflow_docs/nextflow_repo/docs/reference/env-vars.mdx
+[config-params]: /nextflow_docs/nextflow_repo/docs/config.mdx#parameters
+[git-page]: /nextflow_docs/nextflow_repo/docs/cli.mdx
diff --git a/docs/conda.md b/new-docs/nextflow-docs/conda.mdx
similarity index 68%
rename from docs/conda.md
rename to new-docs/nextflow-docs/conda.mdx
index 144ad8d864..6c41f777b3 100644
--- a/docs/conda.md
+++ b/new-docs/nextflow-docs/conda.mdx
@@ -1,39 +1,38 @@
-(conda-page)=
+
 
 # Conda environments
 
 [Conda](https://conda.io/) is an open source package and environment management system that simplifies the installation and the configuration of complex software packages in a platform agnostic manner.
 
-Nextflow has built-in support for Conda that allows the configuration of workflow dependencies using Conda recipes and environment files.
+Nextflow has built-in support for conda that allows the configuration of workflow dependencies using conda recipes and environment files.
 
 This allows Nextflow applications to use popular tool collections such as [Bioconda](https://bioconda.github.io) and the [Python Package index](https://pypi.org/), whilst taking advantage of the configuration flexibility provided by Nextflow.
 
 ## Prerequisites
 
-This feature requires the Conda or [Miniconda](https://conda.io/miniconda.html) package manager to be installed on your system.
+This feature requires the conda or [Miniconda](https://conda.io/miniconda.html) package manager to be installed on your system.
 
 ## How it works
 
-Nextflow automatically creates and activates the Conda environment(s) given the dependencies specified by each process.
+Nextflow automatically creates and activates the conda environment(s) given the dependencies specified by each process.
 
-Dependencies are specified by using the {ref}`process-conda` directive, providing either the names of the required Conda packages, the path of a Conda environment yaml file, or the path of an existing Conda environment directory.
+Dependencies are specified by using the [conda][process-conda] directive, providing either the names of the required conda packages, the path of a conda environment yaml file, or the path of an existing conda environment directory.
 
-:::{note}
-Conda environments are stored on the file system. By default, Nextflow instructs Conda to save the required environments in the pipeline work directory. The same environment may be created/saved multiple times across multiple executions when using different work directories.
+:::note
+Conda environments are stored on the file system. By default, Nextflow instructs conda to save the required environments in the pipeline work directory. The same environment may be created/saved multiple times across multiple executions when using different work directories.
 :::
 
-You can specify the directory where the Conda environments are stored using the `conda.cacheDir` configuration property. When using a computing cluster, make sure to use a shared file system path accessible from all compute nodes. See the {ref}`configuration page <config-conda>` for details about Conda configuration.
+You can specify the directory where the conda environments are stored using the `conda.cacheDir` configuration property. When using a computing cluster, make sure to use a shared file system path accessible from all compute nodes. See [Configuration][config-conda] for details about conda configuration.
 
-:::{warning}
-The Conda environment feature is not supported by executors that use remote object storage as a work directory. For example, AWS Batch.
+:::warning
+The conda environment feature is not supported by executors that use remote object storage as a work directory. For example, AWS Batch.
 :::
 
-### Enabling Conda environment
+### Enabling conda environment
 
-:::{versionadded} 22.08.0-edge
-:::
+<AddedInVersion version="22.08.0-edge" />
 
-The use of Conda recipes specified using the {ref}`process-conda` directive needs to be enabled explicitly in the pipeline configuration file (i.e. `nextflow.config`):
+The use of conda recipes specified using the [conda][process-conda] directive needs to be enabled explicitly in the pipeline configuration file (i.e., `nextflow.config`):
 
 ```groovy
 conda.enabled = true
@@ -41,7 +40,7 @@ conda.enabled = true
 
 Alternatively, it can be specified by setting the variable `NXF_CONDA_ENABLED=true` in your environment or by using the `-with-conda` command line option.
 
-### Use Conda package names
+### Use conda package names
 
 Conda package names can be specified using the `conda` directive. Multiple package names can be specified by separating them with a blank space. For example:
 
@@ -56,16 +55,15 @@ process hello {
 }
 ```
 
-Using the above definition, a Conda environment that includes BWA, Samtools and MultiQC tools is created and activated when the process is executed.
+Using the above definition, a conda environment that includes BWA, Samtools and MultiQC tools is created and activated when the process is executed.
 
-The usual Conda package syntax and naming conventions can be used. The version of a package can be specified after the package name as shown here `bwa=0.7.15`.
+The usual conda package syntax and naming conventions can be used. The version of a package can be specified after the package name as shown here `bwa=0.7.15`.
 
 The name of the channel where a package is located can be specified prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
 
-(conda-env-files)=
-### Use Conda environment files
+### Use conda environment files
 
-Conda environments can also be defined using one or more Conda environment files. This is a file that lists the required packages and channels structured using the YAML format. For example:
+Conda environments can also be defined using one or more conda environment files. This is a file that lists the required packages and channels structured using the YAML format. For example:
 
 ```yaml
 name: my-env
@@ -77,7 +75,7 @@ dependencies:
   - bwa=0.7.15
 ```
 
-Read the Conda documentation for more details about how to create [environment files](https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually).
+Read the conda documentation for more details about how to create [environment files](https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually).
 
 The path of an environment file can be specified using the `conda` directive:
 
@@ -92,11 +90,10 @@ process hello {
 }
 ```
 
-:::{warning}
+:::warning
 The environment file name **must** have a `.yml` or `.yaml` extension or else it won't be properly recognised.
 :::
 
-(conda-pypi)=
 ### Python Packages from PyPI
 
 Conda environment files can also be used to install Python packages from the [PyPI repository](https://pypi.org/), through the `pip` package manager (which must also be explicitly listed as a required package):
@@ -124,15 +121,15 @@ bioconda::bwa=0.7.15
 bioconda::multiqc=1.4
 ```
 
-:::{note}
+:::note
 Dependency files must be a text file with the `.txt` extension.
 :::
 
 ### Conda lock files
 
-The final method for providing packages to Conda is by using [Conda lock files](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#identical-conda-envs).
+The final method for providing packages to conda is by using [conda lock files](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#identical-conda-envs).
 
-To generate a lock file from an existing Conda environment, run the following command:
+To generate a lock file from an existing conda environment, run the following command:
 
 ```bash
 conda list --explicit > spec-file.txt
@@ -163,15 +160,15 @@ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.cond
 # .. and so on
 ```
 
-To use a Conda lock file with Nextflow, set the `conda` directive to the path of the lock file.
+To use a conda lock file with Nextflow, set the `conda` directive to the path of the lock file.
 
-:::{note}
+:::note
 Conda lock files must be a text file with the `.txt` extension.
 :::
 
-### Use existing Conda environments
+### Use existing conda environments
 
-If you already have a local Conda environment, you can use it in your workflow specifying the installation directory of such environment by using the `conda` directive:
+If you already have a local conda environment, you can use it in your workflow specifying the installation directory of such environment by using the `conda` directive:
 
 ```nextflow
 process hello {
@@ -186,16 +183,16 @@ process hello {
 
 ### Use Mamba to resolve packages
 
-:::{warning} *Experimental: may change in a future release.*
+:::warning{title="Experimental: may change in a future release."}
 :::
 
-It is also possible to use [mamba](https://github.com/mamba-org/mamba) to speed up the creation of conda environments. For more information on how to enable this feature please refer to {ref}`Conda <config-conda>`.
+It is also possible to use [mamba](https://github.com/mamba-org/mamba) to speed up the creation of conda environments. For more information on how to enable this feature please refer to [conda][config-conda].
 
 ## Best practices
 
-When a `conda` directive is used in any `process` definition within the workflow script, Conda tool is required for the workflow execution.
+When a `conda` directive is used in any `process` definition within the workflow script, conda tool is required for the workflow execution.
 
-Specifying the Conda environments in a separate configuration {ref}`profile <config-profiles>` is therefore recommended to allow the execution via a command line option and to enhance the workflow portability. For example:
+Specifying the conda environments in a separate configuration [profile][config-profiles] is therefore recommended to allow the execution via a command line option and to enhance the workflow portability. For example:
 
 ```groovy
 profiles {
@@ -210,8 +207,12 @@ profiles {
 }
 ```
 
-The above configuration snippet allows the execution either with Conda or Docker specifying `-profile conda` or `-profile docker` when running the workflow script.
+The above configuration snippet allows the execution either with conda or Docker specifying `-profile conda` or `-profile docker` when running the workflow script.
 
 ## Advanced settings
 
-Conda advanced configuration settings are described in the {ref}`Conda <config-conda>` section on the Nextflow configuration page.
+Conda advanced configuration settings are described in the [conda][config-conda] section on the Nextflow configuration page.
+
+[config-conda]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#conda
+[config-profiles]: /nextflow_docs/nextflow_repo/docs/config.mdx#config-profiles
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
diff --git a/new-docs/nextflow-docs/conf.py b/new-docs/nextflow-docs/conf.py
new file mode 100644
index 0000000000..19f6d82094
--- /dev/null
+++ b/new-docs/nextflow-docs/conf.py
@@ -0,0 +1,424 @@
+# -*- coding: utf-8 -*-
+#
+# Nextflow documentation build configuration file, created by
+# sphinx-quickstart on Sat May  5 16:57:28 2012.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+import sphinx_rtd_theme
+import datetime
+import subprocess
+import shlex
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = [
+  'sphinx.ext.mathjax',
+  'sphinxcontrib.mermaid',
+  'sphinxext.rediraffe',
+  'sphinx_rtd_theme',
+  'myst_parser',
+  'sphinx_tabs.tabs',
+  'sphinx_copybutton'
+]
+
+myst_enable_extensions = ['colon_fence', 'deflist', 'dollarmath']
+
+myst_heading_anchors = 3
+
+rediraffe_redirects = {
+    'getstarted.md': 'install.md',
+    'basic.md': 'overview.md',
+    'tracing.md': 'reports.md',
+    'mail.md': 'notifications.md',
+    'operator.md': 'reference/operator.md',
+    'dsl1.md': 'migrations/dsl1.md',
+    'updating-syntax.md': 'strict-syntax.md',
+    'updating-spot-retries.md': 'guides/updating-spot-retries.md',
+    'metrics.md': 'tutorials/metrics.md',
+    'data-lineage.md' : 'tutorials/data-lineage.md',
+    'workflow-outputs.md': 'tutorials/workflow-outputs.md',
+    'flux.md': 'tutorials/flux.md',
+    'developer/plugins.md': 'plugins/developing-plugins.md',
+    'plugins.md': 'plugins/plugins.md'
+}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.md'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Nextflow'
+copyright = str(datetime.date.today().year) + u', Seqera Labs, S.L'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+
+# AUTO-GENERATED BY GIT
+# Check if we are checked out at a specific version or not
+process = subprocess.Popen(shlex.split("git tag --points-at HEAD"), stdout=subprocess.PIPE)
+
+# The full version, including alpha/beta/rc tags.
+release = process.communicate()[0].decode("utf-8").strip()
+
+# The short X.Y version.
+version = release.replace("-edge", "")
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+html_title = f"Nextflow {release} documentation"
+
+# Get the current sha if not checked out at a specific version
+if len(release) == 0:
+    process = subprocess.Popen(shlex.split("git rev-parse --short HEAD"), stdout=subprocess.PIPE)
+    current_sha = process.communicate()[0].decode("utf-8").strip()
+    release = f"dev <samp>({current_sha})</samp>"
+    html_title = "Nextflow documentation"
+
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build', '**README.md']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'default'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# Add copyable selector
+copybutton_selector = ".copyable pre"
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {
+  'logo_only': True,
+  'display_version': False
+}
+
+html_context = {
+    "display_github": True,
+    "github_user": "nextflow-io",
+    "github_repo": "nextflow",
+    "github_version": "master",
+    "conf_py_path": "/docs/"
+}
+
+# Nextflow theme
+html_css_files = ['theme.css']
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = '_static/nextflow-logo.png'
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+html_favicon = '_static/favicon.ico'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+html_use_smartypants = False
+
+# Custom sidebar templates, maps document names to template names.
+html_sidebars = {
+    '**': ['globaltoc.html']
+}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+html_show_sourcelink = False
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Nextflowdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'Nextflow.tex', u'Nextflow Documentation',
+   u'Paolo Di Tommaso', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = '_static/nextflow-logo.png'
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'nextflow', u'Nextflow Documentation',
+     [u'Paolo Di Tommaso'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'Nextflow', u'Nextflow Documentation',
+   u'Paolo Di Tommaso', 'Nextflow', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+
+# -- Options for Epub output ---------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = u'Nextflow'
+epub_author = u'Paolo Di Tommaso'
+epub_publisher = u'Paolo Di Tommaso'
+epub_copyright = u'Copyright 2013-2024, Seqera Labs'
+
+# The language of the text. It defaults to the language option
+# or en if the language is not set.
+#epub_language = ''
+
+# The scheme of the identifier. Typical schemes are ISBN or URL.
+#epub_scheme = ''
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#epub_identifier = ''
+
+# A unique identification for the text.
+#epub_uid = ''
+
+# A tuple containing the cover image and cover page html template filenames.
+#epub_cover = ()
+
+# HTML files that should be inserted before the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_pre_files = []
+
+# HTML files that should be inserted after the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_post_files = []
+
+# A list of files that should not be packed into the epub file.
+#epub_exclude_files = []
+
+# The depth of the table of contents in toc.ncx.
+#epub_tocdepth = 3
+
+# Allow duplicate toc entries.
+#epub_tocdup = True
+
+# see also: https://github.com/pygments/pygments/blob/master/pygments/lexers/jvm.py
+from pygments.lexer import RegexLexer
+from sphinx.highlighting import lexers
+
+class NextflowLexer(RegexLexer):
+    """
+    For Nextflow source code.
+    """
+
+    import re
+    from pygments.lexer import bygroups, using, this, default
+    from pygments.token import Comment, Operator, Keyword, Name, String, Number, Whitespace
+    from pygments.util import shebang_matches
+
+    name = 'Nextflow'
+    url = 'https://nextflow.io/'
+    aliases = ['nextflow', 'nf']
+    filenames = ['*.nf']
+    mimetypes = ['text/x-nextflow']
+    # version_added = '1.5'
+
+    flags = re.MULTILINE | re.DOTALL
+
+    tokens = {
+        'root': [
+            # Nextflow allows a file to start with a shebang
+            (r'#!(.*?)$', Comment.Preproc, 'base'),
+            default('base'),
+        ],
+        'base': [
+            (r'[^\S\n]+', Whitespace),
+            (r'(//.*?)(\n)', bygroups(Comment.Single, Whitespace)),
+            (r'/\*.*?\*/', Comment.Multiline),
+            # keywords: go before method names to avoid lexing "throw new XYZ"
+            # as a method signature
+            (r'(assert|catch|else|'
+             r'if|instanceof|new|return|throw|try|in|as)\b',
+             Keyword),
+            # method names
+            (r'^(\s*(?:[a-zA-Z_][\w.\[\]]*\s+)+?)'  # return arguments
+             r'('
+             r'[a-zA-Z_]\w*'                        # method name
+             r'|"(?:\\\\|\\[^\\]|[^"\\])*"'         # or double-quoted method name
+             r"|'(?:\\\\|\\[^\\]|[^'\\])*'"         # or single-quoted method name
+             r')'
+             r'(\s*)(\()',                          # signature start
+             bygroups(using(this), Name.Function, Whitespace, Operator)),
+            (r'@[a-zA-Z_][\w.]*', Name.Decorator),
+            (r'(def|enum|include|from|output|process|workflow)\b', Keyword.Declaration),
+            (r'(boolean|byte|char|double|float|int|long|short|void)\b',
+             Keyword.Type),
+            (r'(true|false|null)\b', Keyword.Constant),
+            (r'""".*?"""', String.Double),
+            (r"'''.*?'''", String.Single),
+            (r'"(\\\\|\\[^\\]|[^"\\])*"', String.Double),
+            (r"'(\\\\|\\[^\\]|[^'\\])*'", String.Single),
+            (r'/(\\\\|\\[^\\]|[^/\\])*/', String),
+            (r"'\\.'|'[^\\]'|'\\u[0-9a-fA-F]{4}'", String.Char),
+            (r'(\.)([a-zA-Z_]\w*)', bygroups(Operator, Name.Attribute)),
+            (r'[a-zA-Z_]\w*:', Name.Label),
+            (r'[a-zA-Z_$]\w*', Name),
+            (r'[~^*!%&\[\](){}<>|+=:;,./?-]', Operator),
+            (r'[0-9][0-9]*\.[0-9]+([eE][0-9]+)?[fd]?', Number.Float),
+            (r'0x[0-9a-fA-F]+', Number.Hex),
+            (r'[0-9]+L?', Number.Integer),
+            (r'\n', Whitespace)
+        ],
+    }
+
+    def analyse_text(text):
+        return shebang_matches(text, r'nextflow')
+
+lexers['nextflow'] = NextflowLexer()
diff --git a/docs/config.md b/new-docs/nextflow-docs/config.mdx
similarity index 78%
rename from docs/config.md
rename to new-docs/nextflow-docs/config.mdx
index 65a15f9ce1..381e7899e8 100644
--- a/docs/config.md
+++ b/new-docs/nextflow-docs/config.mdx
@@ -1,4 +1,4 @@
-(config-page)=
+
 
 # Configuration
 
@@ -6,24 +6,22 @@
 
 When a pipeline script is launched, Nextflow looks for configuration files in multiple locations. Since each configuration file may contain conflicting settings, they are applied in the following order (from lowest to highest priority):
 
-1. The config file `$HOME/.nextflow/config` (or `$NXF_HOME/config` when {ref}`NXF_HOME <nxf-env-vars>` is set).
+1. The config file `$HOME/.nextflow/config` (or `$NXF_HOME/config` when [NXF_HOME][nxf-env-vars] is set).
 2. The config file `nextflow.config` in the project directory
 3. The config file `nextflow.config` in the launch directory
 4. Config files specified using the `-c <config-files>` option
 
-:::{tip}
+:::tip
 You can alternatively use the `-C <config-file>` option to specify a fixed set of configuration files and ignore all other files.
 :::
 
-(config-syntax)=
-
 ## Syntax
 
 The Nextflow configuration syntax is based on the Nextflow script syntax. It is designed for setting configuration options in a declarative manner while also allowing for dynamic expressions where appropriate.
 
 A Nextflow config file may consist of any number of *assignments*, *blocks*, and *includes*. Config files may also contain comments in the same manner as scripts.
 
-See {ref}`syntax-page` for more information about the Nextflow script syntax.
+See [syntax-page] for more information about the Nextflow script syntax.
 
 ### Assignments
 
@@ -35,7 +33,7 @@ docker.enabled = true
 process.maxErrors = 10
 ```
 
-A config option consists of an *option name* prefixed by any number of *scopes* separated by dots. Config scopes are used to group related config options. See {ref}`config-options` for the full set of config options.
+A config option consists of an *option name* prefixed by any number of *scopes* separated by dots. Config scopes are used to group related config options. See [Configuration options][config-options] for the full set of config options.
 
 The expression is typically a literal value such as a number, boolean, or string. However, any expression can be used:
 
@@ -70,7 +68,7 @@ executor {
 
 executor {
     retry {
-        maxAttempt = 5
+maxAttempt = 5
     }
 }
 ```
@@ -89,40 +87,43 @@ includeConfig 'path/extra.config'
 
 Relative paths are resolved against the location of the including file.
 
-:::{note}
+:::note
 Config includes can also be specified within config blocks. However, config files should only be included at the top level or in a [profile](#config-profiles) so that the included config file is valid on its own and in the context in which it is included.
 :::
 
-(config-constants)=
-
 ## Constants
 
 The following constants are globally available in a Nextflow configuration file:
 
-`baseDir: Path`
-: :::{deprecated} 20.04.0
-  :::
-: Alias for `projectDir`.
+##### `baseDir: Path`
+
+<DeprecatedInVersion version="20.04.0" />
+
+Alias for `projectDir`.
+
+##### `launchDir: Path`
+
+The directory where the workflow was launched.
+
+##### `projectDir: Path`
+
+The directory where the main script is located.
+
+##### `workDir: Path`
 
-`launchDir: Path`
-: The directory where the workflow was launched.
+The directory where the workflow work directory is located.
 
-`projectDir: Path`
-: The directory where the main script is located.
+##### `secrets: Map<String,String>`
 
-`secrets: Map<String,String>`
-: Map of pipeline secrets. See {ref}`secrets-page` for more information.
+Map of pipeline secrets. See [Secrets][secrets-page] for more information.
 
 ## Functions
 
 The following functions are globally available in a Nextflow configuration file:
 
-`env( name: String ) -> String`
-: :::{versionadded} 24.11.0-edge
-  :::
-: Get the value of the environment variable with the specified name in the Nextflow launch environment.
+##### `env( name: String ) -> String`
 
-(config-params)=
+Get the value of the environment variable with the specified name in the Nextflow launch environment.
 
 ## Parameters
 
@@ -138,17 +139,15 @@ params {
 }
 ```
 
-See {ref}`cli-params` for information about how to specify pipeline parameters.
+See [Pipeline parameters][cli-params] for information about how to specify pipeline parameters.
 
-:::{note}
+:::note
 When including a config file, the included config is evaluated with the parameters that are defined before the include. Parameters defined after the include are not visible to the included config.
 :::
 
-(config-process)=
-
 ## Process configuration
 
-The `process` scope allows you to specify {ref}`process directives <process-reference>` separately from the pipeline code.
+The `process` scope allows you to specify [process directives][process-reference] separately from the pipeline code.
 
 For example:
 
@@ -162,11 +161,9 @@ process {
 
 By using this configuration, all processes in your pipeline will be executed through the SGE cluster, with the specified settings.
 
-(config-process-selectors)=
-
 ### Process selectors
 
-The `withLabel` selectors allow the configuration of all processes annotated with a {ref}`process-label` directive as shown below:
+The `withLabel` selectors allow the configuration of all processes annotated with a [label][process-label] directive as shown below:
 
 ```groovy
 process {
@@ -185,9 +182,9 @@ In the same manner, the `withName` selector allows the configuration of a specif
 ```groovy
 process {
     withName: hello {
-        cpus = 4
-        memory = 8.GB
-        queue = 'short'
+cpus = 4
+memory = 8.GB
+queue = 'short'
     }
 }
 ```
@@ -196,12 +193,10 @@ The `withName` selector applies both to processes defined with the same name and
 
 Furthermore, selectors for the alias of an included process take priority over selectors for the original name of the process. For example, given a process defined as `hello` and included as `sayHello`, the selectors `withName: hello` and `withName: sayHello` will both be applied to the process, with the second selector taking priority over the first.
 
-:::{tip}
+:::tip
 Label and process names do not need to be enclosed with quotes, provided the name does not include special characters (`-`, `!`, etc) and is not a keyword or a built-in type identifier. When in doubt, you can enclose the label name or process name with single or double quotes.
 :::
 
-(config-selector-expressions)=
-
 ### Selector expressions
 
 Both label and process name selectors allow the use of a regular expression in order to apply the same configuration to all processes matching the specified pattern condition. For example:
@@ -229,8 +224,6 @@ process {
 
 The above configuration snippet sets 2 cpus for every process labeled as `hello` and 4 cpus to every process *not* labeled as `hello`. It also specifies the `long` queue for every process whose name does *not* start with `align`.
 
-(config-selector-priority)=
-
 ### Selector priority
 
 Process configuration settings are applied to a process in the following order (from lowest to highest priority):
@@ -254,13 +247,12 @@ process {
 ```
 
 With the above configuration:
+
 - All processes will use 4 cpus (unless otherwise specified in their process definition).
 - Processes annotated with the `hello` label will use 8 cpus.
 - Any process named `bye` (or imported as `bye`) will use 16 cpus.
 - Any process named `bye` (or imported as `bye`) invoked by a workflow named `aloha` will use 32 cpus.
 
-(config-profiles)=
-
 ## Config profiles
 
 Configuration files can define one or more *profiles*. A profile is a set of configuration settings that can be selected during pipeline execution using the `-profile` command line option.
@@ -292,16 +284,16 @@ The above configuration defines three profiles: `standard`, `cluster`, and `clou
 Configuration profiles can be specified at runtime as a comma-separated list:
 
 ```bash
-nextflow run <your script> -profile standard,cloud
+nextflow run main.nf -profile standard,cloud
 ```
 
 Config profiles are applied in the order in which they were defined in the config file, regardless of the order they are specified on the command line.
 
-:::{versionadded} 25.02.0-edge
-When using the {ref}`strict config syntax <updating-config-syntax>`, profiles are applied in the order in which they are specified on the command line.
-:::
+<AddedInVersion version="25.02.0-edge">
+When using the [strict config syntax][updating-config-syntax], profiles are applied in the order in which they are specified on the command line.
+</AddedInVersion>
 
-:::{danger}
+:::warning
 When defining a profile in the config file, avoid using both the dot and block syntax for the same scope. For example:
 
 ```groovy
@@ -324,16 +316,14 @@ process {
 }
 ```
 
-This limitation can be avoided by using the {ref}`strict config syntax <updating-config-syntax>`.
+This limitation can be avoided by using the [strict config syntax][updating-config-syntax].
 :::
 
-(config-workflow-handlers)=
-
 ## Workflow handlers
 
-:::{deprecated} 25.10.0
-Use a {ref}`trace observer <plugins-trace-observers>` in a plugin to add custom workflow handlers to a pipeline via configuration.
-:::
+<deprecatedInVersion version="25.10.0">
+Use a trace observer in a plugin to add custom workflow handlers to a pipeline via configuration.
+</deprecatedInVersion>
 
 You can define workflow event handlers in the config file:
 
@@ -349,4 +339,14 @@ workflow.onError = {
 }
 ```
 
-This approach is useful for handling workflow events without modifying the pipeline code. See {ref}`workflow-handlers` for more information.
+This approach is useful for handling workflow events without modifying the pipeline code. See [Workflow handlers][workflow-handlers] for more information.
+
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[config-options]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx
+[nxf-env-vars]: /nextflow_docs/nextflow_repo/docs/reference/env-vars.mdx#nextflow-settings
+[process-reference]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx
+[process-label]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#label
+[secrets-page]: /nextflow_docs/nextflow_repo/docs/secrets.mdx
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[updating-config-syntax]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx#configuration-syntax
+[workflow-handlers]: /nextflow_docs/nextflow_repo/docs/notifications.mdx#workflow-handlers
diff --git a/docs/container.md b/new-docs/nextflow-docs/container.mdx
similarity index 87%
rename from docs/container.md
rename to new-docs/nextflow-docs/container.mdx
index 58973e6a23..447a60beb1 100644
--- a/docs/container.md
+++ b/new-docs/nextflow-docs/container.mdx
@@ -1,19 +1,16 @@
-(container-page)=
+
 
 # Containers
 
 Nextflow supports a variety of container runtimes. Containerization allows you to write self-contained and truly reproducible computational pipelines, by packaging the binary dependencies of a script into a standard and portable format that can be executed on any platform that supports a container runtime. Furthermore, the same pipeline can be transparently executed with any of the supported container runtimes, depending on which runtimes are available in the target compute environment.
 
-:::{note}
-When creating a container image to use with Nextflow, make sure that Bash (3.x or later) and `ps` are installed in the image, along with other tools required for collecting metrics (See {ref}`this section <execution-report-tasks>`). Bash should be available on the path `/bin/bash` and it should be the container entrypoint.
+:::note
+When creating a container image to use with Nextflow, make sure that Bash (3.x or later) and `ps` are installed in the image, along with other tools required for collecting metrics (see [Tasks][execution-report-tasks] for more information). Bash should be available on the path `/bin/bash` and it should be the container entrypoint.
 :::
 
-(container-apptainer)=
-
 ## Apptainer
 
-:::{versionadded} 22.11.0-edge
-:::
+<AddedInVersion version="22.11.0-edge" />
 
 [Apptainer](https://apptainer.org) is an alternative container runtime to Docker and an open source fork of Singularity. The main advantages of Apptainer are that it can be used without root privileges and it doesn't require a separate daemon process. These, along with other features such as support for autofs mounts, makes Apptainer better suited to the requirements of HPC workloads. Apptainer is able to use existing Docker images and can pull from Docker registries.
 
@@ -27,7 +24,7 @@ Apptainer makes use of a container image file, which physically contains the con
 
 Apptainer allows paths that do not currently exist within the container to be created and mounted dynamically by specifying them on the command line. However this feature is only supported on hosts that support the [Overlay file system](https://en.wikipedia.org/wiki/OverlayFS) and is not enabled by default.
 
-:::{note}
+:::note
 Nextflow expects that data paths are defined system wide, and your Apptainer images need to be created having the mount paths defined in the container file system.
 :::
 
@@ -38,12 +35,12 @@ If your Apptainer installation support the "user bind control" feature, enable t
 The integration for Apptainer follows the same execution model implemented for Docker. You won't need to modify your Nextflow script in order to run it with Apptainer. Simply specify the Apptainer image file from where the containers are started by using the `-with-apptainer` command line option. For example:
 
 ```bash
-nextflow run <your script> -with-apptainer [apptainer image file]
+nextflow run main.nf -with-apptainer [apptainer image file]
 ```
 
 Every time your script launches a process execution, Nextflow will run it into an Apptainer container created by using the specified image. In practice Nextflow will automatically wrap your processes and launch them by running the `apptainer exec` command with the image you have provided.
 
-:::{note}
+:::note
 An Apptainer image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
 :::
 
@@ -56,19 +53,19 @@ apptainer.enabled = true
 
 In the above example replace `/path/to/apptainer.img` with any Apptainer image of your choice.
 
-Read the {ref}`config-page` page to learn more about the configuration file and how to use it to configure your pipeline execution.
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
 
-:::{note}
-Unlike Docker, Nextflow does not automatically mount host paths in the container when using Apptainer. It expects that the paths are configured and mounted system wide by the Apptainer runtime. If your Apptainer installation allows user defined bind points, read the {ref}`Apptainer configuration <config-apptainer>` section to learn how to enable Nextflow auto mounts.
+:::note
+Unlike Docker, Nextflow does not automatically mount host paths in the container when using Apptainer. It expects that the paths are configured and mounted system wide by the Apptainer runtime. If your Apptainer installation allows user defined bind points. See [Apptainer][config-apptainer] to learn how to enable Nextflow auto mounts.
 :::
 
-:::{warning}
+:::warning
 When a process input is a *symbolic link* file, make sure the linked file is stored in a host folder that is accessible from a bind path defined in your Apptainer installation. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
 :::
 
-:::{versionchanged} 23.07.0-edge
+<ChangedInVersion version="23.07.0-edge">
 Nextflow no longer mounts the home directory when launching an Apptainer container. To re-enable the old behavior, set the environment variable `NXF_APPTAINER_HOME_MOUNT` to `true`.
-:::
+</ChangedInVersion>
 
 ### Multiple containers
 
@@ -88,7 +85,7 @@ apptainer {
 }
 ```
 
-Read the {ref}`Process scope <config-process>` section to learn more about processes configuration.
+See [Process configuration][config-process] to learn more about processes configuration.
 
 ### Apptainer & Docker Hub
 
@@ -103,7 +100,7 @@ process.container = 'file:///path/to/apptainer.img'
 apptainer.enabled = true
 ```
 
-:::{warning}
+:::warning
 Use three `/` slashes to specify an **absolute** file path, otherwise the path will be interpreted as relative to the workflow launch directory.
 :::
 
@@ -116,7 +113,7 @@ apptainer.enabled = true
 
 You do not need to specify `docker://` to pull from a Docker repository. Nextflow will automatically prepend it to your image name when Apptainer is enabled. Additionally, the Docker engine will not work with containers specified as `docker://`.
 
-:::{note}
+:::note
 This feature requires the `apptainer` tool to be installed where the workflow execution is launched (as opposed to the compute nodes).
 :::
 
@@ -126,34 +123,31 @@ Nextflow uses the library directory to determine the location of Apptainer conta
 
 Nextflow first checks the library directory when searching for the image. If the image is not found it then checks the cache directory. The main difference between the library directory and the cache directory is that the first is assumed to be a read-only container repository, while the latter is expected to be writable path where container images can be added for caching purposes.
 
-:::{warning}
+:::warning
 When using a compute cluster, the Apptainer cache directory must reside in a shared filesystem accessible to all compute nodes.
 :::
 
-:::{danger}
-When pulling Docker images, Apptainer may be unable to determine the container size if the image was stored using an old Docker format, resulting in a pipeline execution error. See the Apptainer documentation for details.
+:::danger
+When pulling Docker images, Apptainer may be unable to determine the container size if the image was stored using an old Docker format, resulting in a pipeline execution error. See Apptainer documentation for details.
 :::
 
 ### Advanced settings
 
-Apptainer advanced configuration settings are described in {ref}`config-apptainer` section in the Nextflow configuration page.
-
-(container-charliecloud)=
+Apptainer advanced configuration settings are described in[Apptainer][config-apptainer] section in the Nextflow configuration page.
 
 ## Charliecloud
 
-:::{versionadded} 20.12.0-edge
-:::
+<AddedInVersion version="20.12.0-edge" />
 
-:::{versionchanged} 21.03.0-edge
+<ChangedInVersion version="21.03.0-edge">
 Requires Charliecloud 0.22 to 0.27.
-:::
+</ChangedInVersion>
 
-:::{versionchanged} 22.09.0-edge
+<ChangedInVersion version="22.09.0-edge">
 Requires Charliecloud 0.28 or later.
-:::
+</ChangedInVersion>
 
-:::{warning} *Experimental: not recommended for production environments.*
+:::warning{title="Experimental: not recommended for production environments."}
 :::
 
 [Charliecloud](https://hpc.github.io/charliecloud) is an alternative container runtime to Docker, that is better suited for use in HPC environments. Its main advantage is that it can be used without root privileges, making use of user namespaces in the Linux kernel. Charliecloud is able to pull from Docker registries.
@@ -167,12 +161,12 @@ You will need Charliecloud installed in your execution environment e.g. on your
 You won't need to modify your Nextflow script in order to run it with Charliecloud. Simply specify the docker image from where the containers are started by using the `-with-charliecloud` command line option. For example:
 
 ```bash
-nextflow run <your script> -with-charliecloud [container]
+nextflow run main.nf -with-charliecloud [container]
 ```
 
 Every time your script launches a process execution, Nextflow will run it into a charliecloud container created by using the specified container image. In practice Nextflow will automatically wrap your processes and run them by executing the `ch-run` command with the container you have provided.
 
-:::{note}
+:::note
 A container image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
 :::
 
@@ -183,13 +177,13 @@ process.container = '/path/to/container'
 charliecloud.enabled = true
 ```
 
-:::{warning}
-If an absolute path is provided, the container needs to be in the Charliecloud flat directory format. See the section below on compatibility with Docker registries.
+:::warning
+If an absolute path is provided, the container needs to be in the Charliecloud flat directory format. See below on compatibility with Docker registries.
 :::
 
-Read the {ref}`config-page` page to learn more about the configuration file and how to use it to configure your pipeline execution.
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
 
-:::{warning}
+:::warning
 Nextflow automatically manages the file system mounts whenever a container is launched depending on the process input files. However, when a process input is a *symbolic link*, the linked file **must** be stored in the same folder where the symlink is located, or a sub-folder of it. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
 :::
 
@@ -232,7 +226,7 @@ charliecloud {
 }
 ```
 
-Read the {ref}`Process scope <config-process>` section to learn more about processes configuration.
+See [Process configuration][config-process] to learn more about processes configuration.
 
 After running your pipeline, you can easily query the container image that each process used with the following command:
 
@@ -242,9 +236,7 @@ nextflow log last -f name,container
 
 ### Advanced settings
 
-Charliecloud advanced configuration settings are described in {ref}`config-charliecloud` section in the Nextflow configuration page.
-
-(container-docker)=
+Charliecloud advanced configuration settings are described in the [Charliecloud][config-charliecloud] section in the Nextflow configuration page.
 
 ## Docker
 
@@ -261,12 +253,12 @@ If you are running Docker on Mac OSX make sure you are mounting your local `/Use
 You won't need to modify your Nextflow script in order to run it with Docker. Simply specify the Docker image from where the containers are started by using the `-with-docker` command line option. For example:
 
 ```bash
-nextflow run <your script> -with-docker [docker image]
+nextflow run main.nf -with-docker [docker image]
 ```
 
 Every time your script launches a process execution, Nextflow will run it into a Docker container created by using the specified image. In practice Nextflow will automatically wrap your processes and run them by executing the `docker run` command with the image you have provided.
 
-:::{note}
+:::note
 A Docker image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
 :::
 
@@ -279,9 +271,9 @@ docker.enabled = true
 
 In the above example replace `nextflow/examples:latest` with any Docker image of your choice.
 
-Read the {ref}`config-page` page to learn more about the configuration file and how to use it to configure your pipeline execution.
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
 
-:::{warning}
+:::warning
 Nextflow automatically manages the file system mounts whenever a container is launched depending on the process input files. However, when a process input is a *symbolic link*, the linked file **must** be stored in the same folder where the symlink is located, or a sub-folder of it. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
 :::
 
@@ -326,18 +318,15 @@ docker {
 }
 ```
 
-Read the {ref}`Process scope <config-process>` section to learn more about processes configuration.
+See [Process configuration][config-process] to learn more.
 
 ### Advanced settings
 
-Docker advanced configuration settings are described in {ref}`config-docker` section in the Nextflow configuration page.
-
-(container-podman)=
+Docker advanced configuration settings are described in the [docker][config-docker] section in the Nextflow configuration page.
 
 ## Podman
 
-:::{versionadded} 20.01.0
-:::
+<AddedInVersion version="20.01.0" />
 
 [Podman](http://www.podman.io) is a drop-in replacement for Docker that can run containers with or without root privileges.
 
@@ -350,12 +339,12 @@ You will need Podman installed on your execution environment e.g. your computer
 You won't need to modify your Nextflow script in order to run it with Podman. Simply specify the Podman image from where the containers are started by using the `-with-podman` command line option. For example:
 
 ```bash
-nextflow run <your script> -with-podman [OCI container image]
+nextflow run main.nf -with-podman [OCI container image]
 ```
 
 Every time your script launches a process execution, Nextflow will run it into a Podman container created by using the specified image. In practice Nextflow will automatically wrap your processes and run them by executing the `podman run` command with the image you have provided.
 
-:::{note}
+:::note
 An OCI container image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
 :::
 
@@ -368,9 +357,9 @@ podman.enabled = true
 
 In the above example replace `nextflow/examples:latest` with any Podman image of your choice.
 
-Read the {ref}`config-page` page to learn more about the configuration file and how to use it to configure your pipeline execution.
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
 
-:::{warning}
+:::warning
 Nextflow automatically manages the file system mounts whenever a container is launched depending on the process input files. However, when a process input is a *symbolic link*, the linked file **must** be stored in the same folder where the symlink is located, or a sub-folder of it. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
 :::
 
@@ -415,19 +404,17 @@ podman {
 }
 ```
 
-Read the {ref}`Process scope <config-process>` section to learn more about processes configuration.
+See[Process configuration][config-process] to learn more about processes configuration.
 
 ### Advanced settings
 
-Podman advanced configuration settings are described in {ref}`config-podman` section in the Nextflow configuration page.
-
-(container-sarus)=
+Podman advanced configuration settings are described in the [podman][config-podman] section in the Nextflow configuration page.
 
 ## Sarus
 
-:::{versionadded} 22.12.0-edge
+<AddedInVersion version="22.12.0-edge">
 Requires Sarus 1.5.1 or later.
-:::
+</AddedInVersion>
 
 [Sarus](https://sarus.readthedocs.io) is an alternative container runtime to Docker. Sarus works by converting Docker images to a common format that can then be distributed and launched on HPC systems. The user interface to Sarus enables a user to select an image from [Docker Hub](https://hub.docker.com/) and then submit jobs which run entirely within the container.
 
@@ -450,7 +437,7 @@ sarus.enabled = true
 
 and it will always try to search the Docker Hub registry for the images.
 
-:::{note}
+:::note
 if you do not specify an image tag, the `latest` tag will be fetched by default.
 :::
 
@@ -473,16 +460,10 @@ sarus {
 }
 ```
 
-Read the {ref}`Process scope <config-process>` section to learn more about processes configuration.
-
-(container-shifter)=
+See [Process configuration][config-process] to learn more about processes configuration.
 
 ## Shifter
 
-:::{versionadded} 19.10.0
-Requires Shifter 18.03 or later.
-:::
-
 [Shifter](https://docs.nersc.gov/programming/shifter/overview/) is an alternative container runtime to Docker. Shifter works by converting Docker images to a common format that can then be distributed and launched on HPC systems. The user interface to Shifter enables a user to select an image from [Docker Hub](https://hub.docker.com/) and then submit jobs which run entirely within the container.
 
 ### Prerequisites
@@ -523,9 +504,7 @@ shifter {
 }
 ```
 
-Read the {ref}`Process scope <config-process>` section to learn more about processes configuration.
-
-(container-singularity)=
+See [Process configuration][config-process] to learn more about processes configuration.
 
 ## Singularity
 
@@ -541,7 +520,7 @@ Singularity makes use of a container image file, which physically contains the c
 
 Singularity allows paths that do not currently exist within the container to be created and mounted dynamically by specifying them on the command line. However this feature is only supported on hosts that support the [Overlay file system](https://en.wikipedia.org/wiki/OverlayFS) and is not enabled by default.
 
-:::{note}
+:::note
 Nextflow expects that data paths are defined system wide, and your Singularity images need to be created having the mount paths defined in the container file system.
 :::
 
@@ -552,12 +531,12 @@ If your Singularity installation support the "user bind control" feature, enable
 The integration for Singularity follows the same execution model implemented for Docker. You won't need to modify your Nextflow script in order to run it with Singularity. Simply specify the Singularity image file from where the containers are started by using the `-with-singularity` command line option. For example:
 
 ```bash
-nextflow run <your script> -with-singularity [singularity image file]
+nextflow run main.nf -with-singularity [singularity image file]
 ```
 
 Every time your script launches a process execution, Nextflow will run it into a Singularity container created by using the specified image. In practice Nextflow will automatically wrap your processes and launch them by running the `singularity exec` command with the image you have provided.
 
-:::{note}
+:::note
 A Singularity image can contain any tool or piece of software you may need to carry out a process execution. Moreover, the container is run in such a way that the process result files are created in the host file system, thus it behaves in a completely transparent manner without requiring extra steps or affecting the flow in your pipeline.
 :::
 
@@ -570,27 +549,27 @@ singularity.enabled = true
 
 In the above example replace `/path/to/singularity.img` with any Singularity image of your choice.
 
-Read the {ref}`config-page` page to learn more about the configuration file and how to use it to configure your pipeline execution.
+See [Configuration][config-page] to learn more about the configuration file and how to use it to configure your pipeline execution.
 
-:::{note}
-Unlike Docker, Nextflow does not automatically mount host paths in the container when using Singularity. It expects that the paths are configured and mounted system wide by the Singularity runtime. If your Singularity installation allows user defined bind points, read the {ref}`Singularity configuration <config-singularity>` section to learn how to enable Nextflow auto mounts.
+:::note
+Unlike Docker, Nextflow does not automatically mount host paths in the container when using Singularity. It expects that the paths are configured and mounted system wide by the Singularity runtime. If your Singularity installation allows user defined bind points, see [Singularity][config-singularity] to learn how to enable Nextflow auto mounts.
 :::
 
-:::{warning}
+:::warning
 When a process input is a *symbolic link* file, make sure the linked file is stored in a host folder that is accessible from a bind path defined in your Singularity installation. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
 :::
 
-:::{versionchanged} 23.07.0-edge
+<ChangedInVersion version="23.07.0-edge">
 Nextflow no longer mounts the home directory when launching a Singularity container. To re-enable the old behavior, set the environment variable `NXF_SINGULARITY_HOME_MOUNT` to `true`.
-:::
+</ChangedInVersion>
 
-:::{versionchanged} 23.09.0-edge
+<ChangedInVersion version="23.09.0-edge">
 Nextflow automatically mounts the required host paths in the container. To re-enable the old behavior, set the environment variable `NXF_SINGULARITY_AUTO_MOUNTS` to `false` or set `singularity.autoMounts=false` in the Nextflow configuration file.
-:::
+</ChangedInVersion>
 
-:::{versionchanged} 23.09.0-edge
+<ChangedInVersion version="23.09.0-edge">
 The execution command for Singularity/Apptainer containers can be set to `run` by means of the environment variable `NXF_SINGULARITY_RUN_COMMAND` (default command is `exec`).
-:::
+</ChangedInVersion>
 
 ### Multiple containers
 
@@ -611,7 +590,7 @@ singularity {
 }
 ```
 
-Read the {ref}`Process scope <config-process>` section to learn more about processes configuration.
+See [Process configuration][config-process] to learn more about processes configuration.
 
 ### Singularity & Docker Hub
 
@@ -628,7 +607,7 @@ process.container = 'file:///path/to/singularity.img'
 singularity.enabled = true
 ```
 
-:::{warning}
+:::warning
 Use three `/` slashes to specify an **absolute** file path, otherwise the path will be interpreted as relative to the workflow launch directory.
 :::
 
@@ -641,10 +620,6 @@ singularity.enabled = true
 
 You do not need to specify `docker://` to pull from a Docker repository. Nextflow will automatically prepend it to your image name when Singularity is enabled. Additionally, the Docker engine will not work with containers specified as `docker://`.
 
-:::{versionadded} 19.04.0
-Requires Singularity 3.0.3 or later.
-:::
-
 Nextflow supports the [Singularity Library](https://cloud.sylabs.io/library/) repository:
 
 ```groovy
@@ -659,14 +634,23 @@ Nextflow uses the library directory to determine the location of Singularity ima
 
 Nextflow first checks the library directory when searching for the image. If the image is not found it then checks the cache directory. The main difference between the library directory and the cache directory is that the first is assumed to be a read-only container repository, while the latter is expected to be writable path where container images can be added for caching purposes.
 
-:::{warning}
+:::warning
 When using a compute cluster, the Singularity cache directory must reside in a shared filesystem accessible to all compute nodes.
 :::
 
-:::{danger}
-When pulling Docker images, Singularity may be unable to determine the container size if the image was stored using an old Docker format, resulting in a pipeline execution error. See the Singularity documentation for details.
+:::danger
+When pulling Docker images, Singularity may be unable to determine the container size if the image was stored using an old Docker format, resulting in a pipeline execution error. See Singularity documentation for details.
 :::
 
 ### Advanced settings
 
-Singularity advanced configuration settings are described in {ref}`config-singularity` section in the Nextflow configuration page.
+Singularity advanced configuration settings are described in the [singularity][config-singularity] section in the Nextflow configuration page.
+
+[execution-report-tasks]: /nextflow_docs/nextflow_repo/docs/reports.mdx#tasks
+[config-page]: /nextflow_docs/nextflow_repo/docs/config.mdx
+[config-apptainer]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#apptainer
+[config-process]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-configuration
+[config-charliecloud]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#charliecloud
+[config-docker]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#docker
+[config-podman]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#podman
+[config-singularity]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#singularity
diff --git a/new-docs/nextflow-docs/developer-env.mdx b/new-docs/nextflow-docs/developer-env.mdx
new file mode 100644
index 0000000000..dfc765f5a8
--- /dev/null
+++ b/new-docs/nextflow-docs/developer-env.mdx
@@ -0,0 +1,305 @@
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+
+# Environment setup
+
+Setting up a Nextflow development environment is a prerequisite for creating, testing, and optimizing data analysis pipelines.
+
+<h3>Recommended tools</h3>
+
+- [VS Code][devenv-vscode]: A versatile code editor that enhances your Nextflow development with features like syntax highlighting and debugging.
+- [Extensions][devenv-extensions]: The VS Code marketplace offers a variety of extensions to enhance development. The [Nextflow extension][devenv-nextflow] is specifically designed to enhance Nextflow development with diagnostics, hover hints, code navigation, code completion, and more.
+- [Docker][devenv-docker]: A containerization platform that ensures your Nextflow workflows run consistently across different environments by packaging dependencies into isolated containers.
+- [Git][devenv-git]: A version control system that helps manage and track changes in your Nextflow projects, making collaboration, and code management more efficient.
+
+The sections below outline the steps for setting up these tools.
+
+:::note
+Nextflow must be installed separately. See [Installation][install-page] for Nextflow installation instructions.
+:::
+
+:::note
+If you are using a Windows computer, first install and configure the Windows Subsystem for Linux (WSL). See [Windows Subsystem for Linux][devenv-wsl] for installation instructions.
+:::
+
+## VS Code
+
+An Integrated Development Environment (IDE) provides a user-friendly interface for writing, editing, and managing code. Installing one is an essential step for setting up your environment. 
+
+Visual Studio Code (VS Code) is a popular lightweight IDE known for its versatility and extensibility. It offers features like syntax highlighting, intelligent code completion, and integrated debugging tools for various programming languages. VS Code supports Windows, macOS, and Linux, and is a good choice for both new and experienced Nextflow developers.
+
+<Tabs>
+<TabItem value="Windows" label="Windows" default>
+
+To install VS Code on Windows:
+
+1. Visit the [VS Code](https://code.visualstudio.com/download) website.
+1. Download VS Code for Windows.
+1. Double-click the installer executable (`.exe`) file and follow the setup steps.
+
+</TabItem>
+<TabItem value="macOS" label="macOS" default>
+
+To install VS Code on macOS:
+
+1. Visit the [VS Code](https://code.visualstudio.com/download) website.
+1. Download VS Code for macOS.
+1. Drag the `Visual Studio Code.app` application to the Applications folder to add it to the macOS Launchpad.
+
+</TabItem>
+<TabItem value="Linux" label="Linux" default>
+
+To install VS Code on Linux Debian/Ubuntu distributions:
+
+1. Visit the [VS Code](https://code.visualstudio.com/download) website.
+1. Download the VS Code Linux Debian/Ubuntu (`.deb`) distribution.
+1. Open a new terminal window.
+1. Navigate to the folder where you downloaded VS Code.
+1. Run `sudo apt install ./<file>.deb`, replacing `<file>` with the full file name.
+   
+   :::note
+   If you're using an older Linux distribution, run `sudo dpkg -i <file>.deb` to install VS Code and `sudo apt-get install -f` to install dependencies.
+   :::
+   
+See [Linux installation](https://code.visualstudio.com/docs/setup/linux#_installation) for information about installing VS Code on other distributions.
+
+</TabItem>
+</Tabs>
+
+## Extensions
+
+Extensions are a key feature of IDEs and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. Popular VS Code extensions for Nextflow developers are listed below:
+
+### Nextflow
+
+The VS Code [Nextflow extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) adds Nextflow language support to the editor. The Nextflow extension enhances development with:
+
+- Diagnostics
+- Hover hints
+- Code navigation
+- Code completion
+- Formatting
+- Renaming
+- Parameter schemas
+- DAG previews
+
+See [VS Code][vscode-page] for more information about the Nextflow extension features and how it enforces the Nextflow syntax.
+
+### nf-core
+
+[nf-core](https://nf-co.re/) is a community effort to collect a curated set of analysis pipelines built using Nextflow. The [nf-core extension pack](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) adds a selection of tools that support development. For example, it includes [Code Spell Checker](https://marketplace.visualstudio.com/items?itemName=streetsidesoftware.code-spell-checker), [Prettier](https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode), [Todo Tree](https://marketplace.visualstudio.com/items?itemName=Gruntfuggly.todo-tree), and [Markdown Extended](https://marketplace.visualstudio.com/items?itemName=jebbs.markdown-extended).
+
+See the [nf-core extension pack](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) for more information about the included tools.
+
+### Remote development
+
+The [Remote Development extension pack](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) enables you to run WSL, SSH, or a development container for editing and debugging with the full set of VS Code features.
+
+The pack includes the [Remote - SSH](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh), [Remote - Tunnels](https://marketplace.visualstudio.com/items?itemName=ms-vscode.remote-server), [Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers), and [WSL](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-wsl) extensions. See [Remote Development](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) for more information about the tools included in the remote development extension pack.
+
+:::note
+The Remote Development extension pack is required if you are developing using remote servers, Windows Subsystem for Linux, or Development Containers.
+:::
+
+Installing VS Code extensions requires just a few clicks in the Extensions Marketplace. 
+
+<Tabs>
+<TabItem value="Windows" label="Windows" default>
+
+To install a VS Code extension on Windows:
+
+1. Open VS Code.
+1. Open the **Extensions** view in the left-hand menu.
+1. Search for the extension.
+1. Select **Install**.
+
+</TabItem>
+<TabItem value="macOS" label="macOS" default>
+
+To install a VS Code extension on macOS:
+
+1. Open VS Code.
+1. Open the **Extensions** view in the left-hand menu.
+1. Search for the extension.
+1. Select **Install**.
+
+</TabItem>
+<TabItem value="Linux" label="Linux" default>
+
+To install a VS Code extension on Linux Debian/Ubuntu distributions:
+
+1. Open VS Code.
+1. Open the **Extensions** view in the left-hand menu.
+1. Search for the extension.
+1. Select **Install**.
+
+</TabItem>
+</Tabs>
+
+## Docker
+
+Docker is an open-source platform that simplifies application development, deployment, and execution by packaging applications and their dependencies into containers. Containerization enables the creation of self-contained and fully reproducible computational pipelines by bundling a script's binary dependencies into a standardized and portable format. Containers can be executed on any platform that supports a container runtime and ensures consistency across different environments.
+
+Docker Desktop provides a Graphical User Interface (GUI) for managing Docker containers. Installing Docker Desktop is a straightforward process that allows you to create, deploy, and manage applications within containers.
+
+<Tabs>
+<TabItem value="Windows" label="Windows" default>
+
+To install Docker Desktop on Windows:
+
+1. Go to [Install Docker Desktop on Windows](https://docs.docker.com/desktop/setup/install/windows-install/).
+1. Download the installer.
+1. Double-click Docker Desktop `Installer.exe` to run the installer. By default, Docker Desktop is installed at `C:\Program Files\Docker\Docker`.
+1. Depending on your choice of backend, select the **Use WSL 2 instead of Hyper-V** option on the Configuration page.
+
+    :::note
+    You won't be able to select which backend to use if your system only supports one of the two options.
+    :::
+
+1. Follow the instructions on the installation wizard to authorize the installer and proceed with the install.
+1. When the installation is complete, select **Close**.
+1. Start Docker Desktop.
+1. Review the Docker Subscription Service Agreement and select **Accept** to continue.
+
+    :::note
+    Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop.
+    :::
+
+1. Docker Desktop starts after you accept the terms.
+
+</TabItem>
+<TabItem value="macOS" label="macOS" default>
+
+To install Docker Desktop on macOS:
+
+1. Go to [Install Docker Desktop on Mac](https://docs.docker.com/desktop/install/mac-install/).
+1. Download the installer for your chip type.
+1. Double-click `Docker.dmg` to open the installer.
+1. Drag the Docker icon to the **Applications** folder to add it to the macOS Launchpad.
+1. Double-click **Docker.app** in the **Applications** folder to start Docker.
+1. Review the Docker Subscription Service Agreement and select **Accept** to continue.
+
+    :::note
+    Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop.
+    :::
+    
+1. From the installation window, select **Use recommended settings (Requires password)**.
+
+    :::note
+    The **recommended settings** allow Docker Desktop to automatically set the necessary configuration settings. Advanced settings allow you to set the location of the Docker CLI tools either in the system or user directory, enable the default Docker socket, and enable privileged port mapping. See [Settings](https://docs.docker.com/desktop/settings/#advanced), for more information and how to set the location of the Docker CLI tools.
+    :::
+
+1. Select **Finish**. If you have applied any of the previous configurations that require a password, enter your password to confirm your choice.
+
+</TabItem>
+<TabItem value="Linux" label="Linux" default>
+
+To install Docker Desktop on Linux Debian/Ubuntu distributions:
+
+1. Set up Docker's package repository. See step one of [Install using the `apt` repository](https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository).
+1. Download the latest Debian/Ubuntu (`.deb`) distribution.
+1. In your terminal, run `sudo apt-get install ./docker-desktop-amd64.deb`
+
+    :::note
+    By default, Docker Desktop is installed at `/opt/docker-desktop`.
+    :::
+
+1. Double-click **Docker Desktop** in your Applications menu to start Docker.
+1. Review the Docker Subscription Service Agreement and select **Accept** to continue.
+1. From the installation window, select **Use recommended settings (Requires password)**. Docker Desktop starts after you accept the terms.
+
+    :::note
+    Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop.
+    :::
+
+</TabItem>
+</Tabs>
+
+Nextflow supports multiple container technologies (e.g., Singularity and Podman) so you can choose the one that best fits your needs. See [Containers][containers-page] for more information about other supported container engines.
+
+## Git
+
+Git provides powerful version control that helps track code changes. Git operates locally, meaning you don't need an internet connection to track changes, but it can also be used with remote platforms like GitHub, GitLab, or Bitbucket for collaborative development.
+
+Nextflow seamlessly integrates with Git for source code management providers to manage pipelines as version-controlled Git repositories.
+
+<Tabs>
+<TabItem value="Windows" label="Windows" default>
+
+Git is already installed on most WSL distributions. You can check if it is already installed by running `git version`.
+
+To install the latest stable Git version on Linux Debian/Ubuntu distributions:
+
+1. Open a terminal window and run `sudo apt-get install git-all`.
+1. Once complete, run `git version` to verify Git was installed.
+
+See [git-scm documentation](https://git-scm.com/downloads/linux) for more information about installing Git on other Linux distributions.
+
+</TabItem>
+<TabItem value="macOS" label="macOS" default>
+
+To install Git on macOS with [Homebrew](https://docs.brew.sh/):
+
+1. Open a terminal window and run `brew install git`.
+
+    :::note
+    You must have Homebrew installed. See [Homebrew installation](https://docs.brew.sh/Installation) for instructions.
+    :::
+
+1. Once complete, run `git version` to verify Git was installed.
+
+To install Git on macOS with [Xcode](https://developer.apple.com/xcode/):
+
+1. Open the App Store on your Mac.
+1. Search for Xcode.
+1. Select **Install**.
+1. Once complete, open a new terminal window and run `git version` to verify Git was installed.
+
+</TabItem>
+<TabItem value="Linux" label="Linux" default>
+
+Git is already installed on most Linux Debian/Ubuntu distributions.
+
+To install the latest stable Git version on Linux Debian/Ubuntu distributions:
+
+1. Open a terminal window and run `sudo apt-get install git-all`.
+1. Once complete, run `git version` to verify Git was installed.
+
+See [git-scm documentation](https://git-scm.com/downloads/linux) for more information about installing Git on other Linux distributions.
+
+</TabItem>
+</Tabs>
+
+## Windows Subsystem for Linux
+
+Developers can access the power of both Windows and Linux on a Windows machine. The Windows Subsystem for Linux (WSL) lets developers install a Linux distribution and use Linux applications, utilities, and Bash command-line tools directly on Windows without the overhead of a virtual machine or dual-boot setup.
+
+WSL is an optional feature on Windows 10 version 2004 and higher (Build 19041 and higher) or Windows 11. You can enable it through PowerShell or Windows Command Prompt. The steps below outline the recommended setup.
+
+To enable WSL on Windows using Powershell or Windows Command Prompt:
+
+1. Right-click and select **Run as administrator** to use PowerShell or Windows Command Prompt in administrator mode.
+1. Run `wsl --install`.
+
+    :::note
+    This command will enable the features necessary to run WSL and install the Ubuntu distribution.
+    :::
+
+1. When prompted, restart Windows.
+1. After restarting Windows, open the Ubuntu distribution and create a new Linux **User Name** and **Password** when prompted.
+
+    :::note
+    The **User Name** and **Password** is specific to each Linux distribution that you install and has no bearing on your Windows user name.
+    :::
+
+See [Set up a WSL development environment](https://learn.microsoft.com/en-us/windows/wsl/setup/environment) for more about installing WSL.
+
+[containers-page]: /nextflow_docs/nextflow_repo/docs/container.mdx
+[devenv-docker]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#docker
+[devenv-extensions]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#extensions
+[devenv-git]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#git
+[devenv-nextflow]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#nextflow
+[devenv-vscode]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#vs-code
+[devenv-wsl]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#windows-subsystem-for-linux
+[install-page]: /nextflow_docs/nextflow_repo/docs/install.mdx
+[vscode-page]: /nextflow_docs/nextflow_repo/docs/vscode.mdx
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/developer/config-scopes.mdx b/new-docs/nextflow-docs/developer/config-scopes.mdx
new file mode 100644
index 0000000000..2db1354bf5
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/config-scopes.mdx
@@ -0,0 +1,176 @@
+# Configuration scopes
+
+This page provides guidance on defining configuration scopes in the Nextflow runtime.
+
+## Overview
+
+The Nextflow configuration is defined as a collection of *scope classes*. Each scope class defines the set of available options, including their name, type, and an optional description for a specific configuration scope.
+
+Scope classes are used to generate a configuration spec, which is in turn used for several purposes:
+
+- Validating config options at runtime (`nextflow run` and `nextflow config`)
+
+- Providing code intelligence in the language server (validation, hover hints, code completion)
+
+- Generating reference documentation (in progress)
+
+Scope classes are also used by the runtime itself as type-safe domain objects. This way, the construciton of domain objects from the configuration map is isolated from the rest of the runtime.
+
+## Definition
+
+### Config scopes
+
+A *config scope* is defined as a class that implements the `ConfigScope` interface. Top-level scope classes must have the `@ScopeName` annotation, which defines the name of the config scope.
+
+For example:
+
+```groovy
+package nextflow.hello
+
+import nextflow.config.spec.ConfigScope
+import nextflow.config.spec.ScopeName
+
+@ScopeName('hello')
+class HelloConfig implements ConfigScope {
+}
+```
+
+A scope class must provide a default constructor, so that it can be instantiated as an extension point. If no such constructor is defined, the config scope will not be detected by Nextflow. In the above example, this constructor is implicitly defined because no constructors were declared.
+
+The fully-qualified class name (in this case, `nextflow.hello.HelloConfig`) must be included in the list of extension points.
+
+### Config options
+
+A *config option* is defined as a field with the `@ConfigOption` annotation. The field name determines the name of the config option.
+
+For example:
+
+```groovy
+    @ConfigOption
+    String createMessage
+```
+
+The `@ConfigOption` annotation can specify an optional set of types that are valid in addition to the field type. For example, the `fusion.tags` option, which accepts either a String or Boolean, is declared as follows:
+
+```groovy
+    @ConfigOption(types=[Boolean])
+    String tags
+```
+
+The field type and any additional types are included in the config spec, allowing them to be used for validation.
+
+The field type can be any Java or Groovy class, but in practice it should be a class that can be constructed from primitive values (numbers, booleans, strings). For example, `Duration` and `MemoryUnit` are standard Nextflow types that can each be constructed from an integer or string.
+
+### Nested scopes
+
+A *nested scope* is defined as a field whose type is an implementation of `ConfigScope`. The field name determines the name of the nested scope.
+
+The scope class referenced by the field type defines config options and scopes in the same manner as top-level scope classes. Unlike top-level scopes, nested scope classes do not need to use the `@ScopeName` annotation or provide a default constructor.
+
+See `ExecutorConfig` and `ExecutorRetryConfig` for an example of how a nested scope is defined and constructed.
+
+### Placeholder scopes
+
+A *placeholder scope* is a config scope that applies to a collection of user-defined names.
+
+For example, the `azure.batch.pools` scope allows the user to define a set of named pools, where each pool is configured with a standard set of options such as `autoScale`, `lowPriority`, `maxVmCount`, etc. These options are defined in a placeholder scope with a placeholder name of `<name>`. Thus, the generic name for the `autoScale` option is `azure.batch.pools.<name>.autoScale`.
+
+A placeholder scope is defined as a field with type `Map<String, P>`, where `P` is a nested scope class which defines the scope options. The field should have the `@PlaceholderName` annotation which defines the placeholder name (e.g. `<name>`).
+
+See `AzBatchOpts` and `AzPoolOpts` for an example of how placeholder scopes are defined and constructed.
+
+### Descriptions
+
+Top-level scope classes and config options should use the `@Description` annotation to provide a description of the scope or option. This description is included in the config spec, which is in turn used by the language server to provide hover hints.
+
+For example:
+
+```groovy
+@ScopeName('hello')
+@Description('''
+    The `hello` scope controls the behavior of the `nf-hello` plugin.
+''')
+class HelloConfig implements ConfigScope {
+
+    @ConfigOption
+    @Description('''
+        Message to print to standard output when a run is initialized.
+    ''')
+    String createMessage
+}
+```
+
+Nested scopes and placeholder scopes may also use this annotation, but will inherit the description of the top-level scope by default.
+
+### Best practices
+
+The Nextflow runtime adheres the following best practices where appropriate:
+
+- Config options should be declared as public and final, so that the scope class can be used as an immutable domain object.
+
+- Scope classes should define a constructor that initializes each field from a map, casting each map property to the required type and providing default values as needed.
+
+- In cases where an option defaults to an environment variable, the environment map should be provided as an additional constructor argument rather than accessing the system environment directly.
+
+- In cases where an option with a primitive type (e.g., `int`, `float`, `boolean`) can be unspecified without a default value, it should be declared with the equivalent reference type (e.g. `Integer`, `Float`, `Boolean`), otherwise it should use the primitive type.
+
+- In cases where an option represents a path, it should be declared as a `String` and allow clients to construct paths as needed, since path construction may depend on plugins which aren't yet loaded.
+
+For example:
+
+```groovy
+import nextflow.config.spec.ConfigOption
+import nextflow.config.spec.ConfigScope
+import nextflow.config.spec.ScopeName
+
+@ScopeName('hello')
+class HelloConfig implements ConfigScope {
+
+    @ConfigOption
+    final String createMessage
+
+    @ConfigOption
+    final boolean verbose
+
+    HelloConfig() {}
+
+    HelloConfig(Map opts, Map env) {
+        this.createMessage = opts.createMessage ?: env.get('NXF_HELLO_CREATE_MESSAGE')
+        this.verbose = opts.verbose as boolean
+    }
+}
+```
+
+## Usage
+
+### Runtime
+
+Nextflow validates the config map after it is loaded. Top-level config scopes are loaded by the plugin system as extension points and converted into a config spec, which is used to validate the config map.
+
+Plugins are loaded after the config is loaded and before it is validated, since plugins can also define config scopes. If a third-party plugin declares a config scope, it must be explicitly enabled in order to validate config options from the plugin. Otherwise, Nextflow will report these options as unrecognized.
+
+Core plugins are loaded automatically based on other config options. Therefore, Nextflow only validates config from a core plugin when that plugin is loaded. Otherwise, any config options from the plugin are ignored -- they are neither validated nor reported as unrecognized.
+
+For example, when the `process.executor` config option is set to `'awsbatch'`, the `nf-amazon` is automatically loaded. In this case, all options in the `aws` config scope will be validated. If the executor is not set to `'awsbatch'`, all `aws` options will be ignored. This way, config files can be validated appropriately without loading additional core plugins that won't be used by the run.
+
+The scope classes themselves can be used to construct domain objects on-demand from the config map. For example, an `ExecutorConfig` can be constructed from the `executor` config scope as follows:
+
+```groovy
+new ExecutorConfig( Global.session.config.executor as Map ?: Collections.emptyMap() )
+```
+
+:::note
+In practice, it is better to avoid the use of `Global` and provide an instance of `Session` to the client class instead.
+:::
+
+### Config spec
+
+Config scope classes can be converted into a config spec with the `SpecNode` class, which uses reflection to extract metadata such as scope names, option names, types, and descriptions. This spec is rendered to JSON and used by the language server at build-time to provide code intelligence such as code completion and hover hints.
+
+### Documentation
+
+The config spec described above can be rendered to Markdown using the `MarkdownRenderer` class. It produces a Markdown document approximating the [Configuration options][config-options] page.
+
+This approach to docs generation is not yet complete, and has not been incorporated into the build process yet. However, it can be used to check for discrepancies between the source code and docs when making changes. The documentation should match the `@Description` annotations as closely as possible, but may contain additional details such as version notes and extra paragraphs.
+
+[config-options]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx
diff --git a/new-docs/nextflow-docs/developer/diagram.mdx b/new-docs/nextflow-docs/developer/diagram.mdx
new file mode 100644
index 0000000000..edf4a3a93e
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagram.mdx
@@ -0,0 +1,80 @@
+# Workflow diagram
+
+The following diagram is a high-level overview of the Nextflow source code in a similar style as the [workflow diagram][workflow-diagram] visualization for Nextflow pipelines. Each node and subgraph is a class. Arrows depict the flow of data and/or communication between classes.
+
+In general, nodes with sharp corners are "record" classes that simply hold information, while nodes with rounded edges are "function" classes that transform some input into an output. Subgraphs are either long-running classes, i.e. "places where things happen", or one of the other two types for which it was useful to expand and show internal details.
+
+```mermaid
+flowchart TB
+  subgraph Launcher
+    subgraph CmdRun
+      subgraph AssetManager
+        ScriptFile
+      end
+      subgraph ConfigBuilder
+        ConfigParser([ConfigParser])
+        ConfigBase([ConfigBase])
+      end
+      subgraph ScriptRunner
+        subgraph Session
+          ConfigMap
+          DAG
+          ExecutorFactory([ExecutorFactory])
+          subgraph TaskProcessor
+            TaskRun
+          end
+          subgraph Executor
+            subgraph TaskMonitor
+              TaskHandler
+            end
+            TaskBean
+            BashWrapperBuilder([BashWrapperBuilder])
+          end
+          TraceRecord
+          CacheFactory([CacheFactory])
+          CacheDB
+          TraceObserver([TraceObserver])
+        end
+        ScriptParser([ScriptParser])
+        BaseScript([BaseScript])
+        subgraph ScriptMeta
+          WorkflowDef([WorkflowDef])
+          ProcessDef([ProcessDef])
+          FunctionDef([FunctionDef])
+        end
+        IncludeDef([IncludeDef])
+        OpCall([OpCall])
+      end
+      ConfigParser --> ConfigBase
+      ConfigBase --> ConfigMap
+      ScriptFile --> ScriptParser
+      ScriptParser --> BaseScript
+      BaseScript --> WorkflowDef
+      BaseScript --> ProcessDef
+      BaseScript --> FunctionDef
+      BaseScript --> IncludeDef
+      IncludeDef --> ScriptParser
+      WorkflowDef --> OpCall
+      OpCall --> DAG
+      ProcessDef --> DAG
+      DAG --> TaskRun
+      TaskRun --> DAG
+      ExecutorFactory --> Executor
+      ConfigMap --> Executor
+      ProcessDef --> TaskProcessor
+      ConfigMap --> TaskProcessor
+      TaskRun --> TaskHandler
+      TaskRun --> TaskBean
+      TaskBean --> BashWrapperBuilder
+      BashWrapperBuilder --> TaskHandler
+      CacheFactory --> CacheDB
+      TaskHandler --> CacheDB
+      TaskHandler --> TraceRecord
+      TraceRecord --> CacheDB
+      TaskHandler --> TraceObserver
+    end
+  end
+```
+
+[nextflow-diagram]: /nextflow_docs/nextflow_repo/docs/reports.mdx#workflow-diagram
+```
diff --git a/new-docs/nextflow-docs/developer/diagrams/.gitignore b/new-docs/nextflow-docs/developer/diagrams/.gitignore
new file mode 100644
index 0000000000..657f47cd79
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/.gitignore
@@ -0,0 +1 @@
+nextflow-merged.mmd
diff --git a/new-docs/nextflow-docs/developer/diagrams/README.md b/new-docs/nextflow-docs/developer/diagrams/README.md
new file mode 100644
index 0000000000..392029fbe3
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/README.md
@@ -0,0 +1,17 @@
+# Class Diagrams
+
+This directory contains class diagrams of the Nextflow source code, abridged and annotated for relevance and ease of use.
+
+Each node is a class. Fields are selectively documented in order to show only core data structures and the classes that "own" them. Methods are not explicitly documented, but they are mentioned in certain links where appropriate.
+
+Links between classes denote one of the following relationships:
+
+- Inheritance (`A <|-- B`): `B` is a subclass of `A`
+- Composition (`A --* B`): `A` contains `B`
+- Instantiation (`A --> B : f`): `A` creates instance(s) of `B` at runtime via `A::f()`
+
+Some links are commented out or not included at all, in order to focus on the most important classes and relationships. You can view these "hidden" links by simply uncommenting them, but I have found that their significance is sufficiently clear from the description files.
+
+A separate diagram description is provided for each package. These files are interoperable, which means that you can combine any subset of files into a larger diagram description. The `merge-diagrams.sh` can create a merged file for you automatically, and it includes a sensible default set of packages.
+
+You can use the [Mermaid Live Editor](https://mermaid-js.github.io/mermaid-live-editor/edit) or the [Mermaid CLI](https://github.com/mermaid-js/mermaid-cli) to render the diagram in a variety of image formats.
diff --git a/new-docs/nextflow-docs/developer/diagrams/merge-diagrams.sh b/new-docs/nextflow-docs/developer/diagrams/merge-diagrams.sh
new file mode 100755
index 0000000000..087422500a
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/merge-diagrams.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+packages=()
+packages+=("nextflow")
+# packages+=("nextflow.ast")
+packages+=("nextflow.cache")
+packages+=("nextflow.cli")
+# packages+=("nextflow.cloud.aws")
+# packages+=("nextflow.cloud.aws.nio")
+# packages+=("nextflow.cloud.azure")
+# packages+=("nextflow.cloud.google")
+packages+=("nextflow.config")
+# packages+=("nextflow.container")
+packages+=("nextflow.dag")
+# packages+=("nextflow.executor")
+# packages+=("nextflow.extension")
+# packages+=("nextflow.ga4gh")
+# packages+=("nextflow.k8s")
+# packages+=("nextflow.plugin")
+packages+=("nextflow.processor")
+# packages+=("nextflow.scm")
+packages+=("nextflow.script")
+# packages+=("nextflow.secret")
+# packages+=("nextflow.trace")
+
+outfile="nextflow-merged.mmd"
+
+echo "classDiagram" > ${outfile}
+
+for package in "${packages[@]}"; do
+    echo "${package}"
+
+    tail -n +2 "${package}.mmd" >> ${outfile}
+    echo >> ${outfile}
+done
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.ast.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.ast.mmd
new file mode 100644
index 0000000000..fab36a2c21
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.ast.mmd
@@ -0,0 +1,7 @@
+classDiagram
+    %%
+    %% nextflow.ast
+    %%
+    ScriptParser --> NextflowDSLImpl : parse
+    ScriptParser --> NextflowXformImpl : parse
+    ScriptParser --> OpXformImpl : parse
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.cache.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.cache.mmd
new file mode 100644
index 0000000000..6b241d3ee0
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.cache.mmd
@@ -0,0 +1,22 @@
+classDiagram
+    %%
+    %% nextflow.cache
+    %%
+    Session --* CacheDB
+
+    CacheDB --* CacheStore
+
+    CacheStore <|-- DefaultCacheStore
+    CacheStore <|-- CloudCacheStore
+
+    class DefaultCacheStore {
+        uniqueId : UUID
+        runName : String
+        baseDir : Path
+    }
+
+    class CloudCacheStore {
+        uniqueId : UUID
+        runName : String
+        basePath : Path
+    }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.cli.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.cli.mmd
new file mode 100644
index 0000000000..228acacd37
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.cli.mmd
@@ -0,0 +1,29 @@
+classDiagram
+    %%
+    %% nextflow.cli
+    %%
+    class Launcher {
+        cliOptions : CliOptions
+        command : CmdBase
+    } 
+    Launcher --* CliOptions
+    Launcher --* CmdBase
+
+    %% CmdBase <|-- CmdClean
+    %% CmdBase <|-- CmdClone
+    %% CmdBase <|-- CmdConfig
+    CmdBase <|-- CmdConsole
+    %% CmdBase <|-- CmdDrop
+    %% CmdBase <|-- CmdFs
+    CmdBase <|-- CmdHelp
+    CmdBase <|-- CmdInfo
+    %% CmdBase <|-- CmdKubeRun
+    %% CmdBase <|-- CmdList
+    %% CmdBase <|-- CmdLog
+    %% CmdBase <|-- CmdNode
+    %% CmdBase <|-- CmdPlugin
+    %% CmdBase <|-- CmdPull
+    CmdBase <|-- CmdRun
+    %% CmdBase <|-- CmdSecret
+    %% CmdBase <|-- CmdSelfUpdate
+    %% CmdBase <|-- CmdView
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.aws.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.aws.mmd
new file mode 100644
index 0000000000..d3adbc00f4
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.aws.mmd
@@ -0,0 +1,21 @@
+classDiagram
+    %%
+    %% nextflow.cloud.aws
+    %%
+    Executor <|-- AwsBatchExecutor
+    TaskHandler <|-- AwsBatchTaskHandler
+    BashWrapperBuilder <|-- AwsBatchScriptLauncher
+
+    AwsBatchExecutor --* AwsOptions
+    AwsOptions --* AwsConfig
+    AwsConfig --* AwsBatchConfig
+    AwsConfig --* AwsS3Config
+
+    AwsBatchExecutor --> ParallelPollingMonitor : init
+    AwsBatchExecutor --> AwsBatchTaskHandler : submit
+    AwsBatchTaskHandler --> AwsBatchScriptLauncher : submit
+
+    %% TaskPollingMonitor <|-- ParallelPollingMonitor
+
+    SimpleFileCopyStrategy <|-- AwsBatchFileCopyStrategy
+    AwsBatchScriptLauncher --* AwsBatchFileCopyStrategy
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.aws.nio.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.aws.nio.mmd
new file mode 100644
index 0000000000..69242f88b2
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.aws.nio.mmd
@@ -0,0 +1,33 @@
+classDiagram
+    %%
+    %% nextflow.cloud.aws.nio
+    %%
+    FileSystemProvider <|-- S3FileSystemProvider
+
+    S3FileSystemProvider --> S3FileSystem : newFileSystem
+
+    class S3FileSystem {
+        client : S3Client
+        endpoint : String
+    }
+    S3FileSystem --* S3Client
+
+    class S3Client {
+        client : AmazonS3
+        cannedAcl : CannedAccessControlList
+        kmsKeyId : String
+        storageEncryption : SSEAlgorithm
+        transferManager : TransferManager
+        transferPool : ExecutorService
+        uploadChunkSize : Long
+        uploadMaxThreads : Integer
+    }
+
+    Path <|-- S3Path
+
+    class S3Path {
+        bucket : String
+        parts : List~String~
+        fileSystem : S3FileSystem
+    }
+    S3Path --* S3FileSystem
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.azure.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.azure.mmd
new file mode 100644
index 0000000000..6993609b33
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.azure.mmd
@@ -0,0 +1,17 @@
+classDiagram
+    %%
+    %% nextflow.cloud.azure
+    %%
+    Executor <|-- AzBatchExecutor
+    TaskHandler <|-- AzBatchTaskHandler
+    BashWrapperBuilder <|-- AzBatchScriptLauncher
+
+    AzBatchExecutor --* AzConfig
+    AzBatchExecutor --> AzBatchService : register
+
+    AzBatchExecutor --> TaskPollingMonitor : init
+    AzBatchExecutor --> AzBatchTaskHandler : submit
+    AzBatchTaskHandler --> AzBatchScriptLauncher : submit
+
+    SimpleFileCopyStrategy <|-- AzFileCopyStrategy
+    AzBatchScriptLauncher --* AzFileCopyStrategy
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.google.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.google.mmd
new file mode 100644
index 0000000000..bd428f7586
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.cloud.google.mmd
@@ -0,0 +1,13 @@
+classDiagram
+    %%
+    %% nextflow.cloud.google
+    %%
+    Executor <|-- GoogleBatchExecutor
+    TaskHandler <|-- GoogleBatchTaskHandler
+    BashWrapperBuilder <|-- GoogleBatchScriptLauncher
+
+    GoogleBatchExecutor --* BatchConfig
+
+    GoogleBatchExecutor --> TaskPollingMonitor : init
+    GoogleBatchExecutor --> GoogleBatchTaskHandler : submit
+    GoogleBatchTaskHandler --> GoogleBatchScriptLauncher : submit
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.config.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.config.mmd
new file mode 100644
index 0000000000..6962ab5b1b
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.config.mmd
@@ -0,0 +1,7 @@
+classDiagram
+    %%
+    %% nextflow.config
+    %%
+    Session --* ConfigMap
+    CmdRun --> ConfigBuilder : run
+    ConfigBuilder --> ConfigMap : build
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.container.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.container.mmd
new file mode 100644
index 0000000000..f2ce814750
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.container.mmd
@@ -0,0 +1,16 @@
+classDiagram
+    %%
+    %% nextflow.container
+    %%
+    direction LR
+
+    BashWrapperBuilder --> ContainerBuilder : build
+
+    ContainerBuilder <|-- CharliecloudBuilder
+    ContainerBuilder <|-- DockerBuilder
+    ContainerBuilder <|-- PodmanBuilder
+    ContainerBuilder <|-- ShifterBuilder
+    ContainerBuilder <|-- SingularityBuilder
+    ContainerBuilder <|-- UdockerBuilder
+
+    SingularityBuilder <|-- ApptainerBuilder
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.dag.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.dag.mmd
new file mode 100644
index 0000000000..6858074e33
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.dag.mmd
@@ -0,0 +1,33 @@
+classDiagram
+    %%
+    %% nextflow.dag
+    %%
+    Session --* DAG
+
+    class DAG {
+        vertices : List~Vertex~
+        edges : List~Edge~
+    }
+    DAG "1" --* "*" Vertex
+    DAG "1" --* "*" Edge
+
+    class Vertex {
+        label : String
+        type : Type
+        operators : List~DataflowProcessor~
+        process : TaskProcessor
+    }
+
+    class Edge {
+        channel : Object
+        from : Vertex
+        to : Vertex
+        label : String
+    }
+
+    %% DagRenderer <|-- CytoscapeHtmlRenderer
+    %% DagRenderer <|-- CytoscapeJsRenderer
+    %% DagRenderer <|-- DotRenderer
+    %% DagRenderer <|-- GexfRenderer
+    %% DagRenderer <|-- GraphvizRenderer
+    %% DagRenderer <|-- MermaidRenderer
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.executor.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.executor.mmd
new file mode 100644
index 0000000000..08c33527c2
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.executor.mmd
@@ -0,0 +1,66 @@
+classDiagram
+    %%
+    %% nextflow.executor
+    %%
+    ExecutorFactory --> Executor : getExecutor
+
+    class Executor {
+        name : String
+        monitor : TaskMonitor
+    }
+    Executor --* TaskMonitor
+    Executor --> TaskHandler : submit
+
+    TaskMonitor <|-- TaskPollingMonitor
+
+    class TaskPollingMonitor {
+        capacity : int
+        submitRateLimit : RateLimiter
+        pollIntervalMillis : long
+        dumpInterval : Duration
+    }
+
+    TaskPollingMonitor <|-- LocalPollingMonitor
+
+    class LocalPollingMonitor {
+        maxCpus : int
+        maxMemory : long
+    }
+
+    Executor <|-- AbstractGridExecutor
+    Executor <|-- LocalExecutor
+    %% Executor <|-- NopeExecutor
+    %% AbstractGridExecutor <|-- CondorExecutor
+    %% AbstractGridExecutor <|-- HyperQueueExecutor
+    %% AbstractGridExecutor <|-- LsfExecutor
+    %% AbstractGridExecutor <|-- MoabExecutor
+    %% AbstractGridExecutor <|-- NqsiiExecutor
+    %% AbstractGridExecutor <|-- OarExecutor
+    %% AbstractGridExecutor <|-- PbsExecutor
+    %% AbstractGridExecutor <|-- SgeExecutor
+    %% AbstractGridExecutor <|-- SlurmExecutor
+    %% PbsExecutor <|-- PbsProExecutor
+    %% SgeExecutor <|-- CrgExecutor
+
+    %% TaskHandler <|-- CachedTaskHandler
+    TaskHandler <|-- GridTaskHandler
+    TaskHandler <|-- LocalTaskHandler
+    TaskHandler <|-- NativeTaskHandler
+    %% TaskHandler <|-- NopeTaskHandler
+    %% TaskHandler <|-- StoredTaskHandler
+
+    class BashWrapperBuilder {
+        bean : TaskBean
+        copyStrategy : ScriptFileCopyStrategy
+    }
+    BashWrapperBuilder --* TaskBean
+    BashWrapperBuilder --* ScriptFileCopyStrategy
+
+    ScriptFileCopyStrategy <|-- SimpleFileCopyStrategy
+
+    class SimpleFileCopyStrategy {
+        stageinMode : String
+        stageoutMode : String
+        targetDir : Path
+        workDir : Path
+    }
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.extension.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.extension.mmd
new file mode 100644
index 0000000000..290246b883
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.extension.mmd
@@ -0,0 +1,30 @@
+classDiagram
+    %%
+    %% nextflow.extension
+    %%
+    direction LR
+
+    ChannelEx --> DumpOp : dump
+    Nextflow --> GroupKey : groupKey
+
+    OperatorImpl --> BranchOp : branch
+    OperatorImpl --> BufferOp : buffer
+    OperatorImpl --> CollectFileOp : collectFile
+    OperatorImpl --> CollectOp : collect
+    OperatorImpl --> CombineOp : combine
+    OperatorImpl --> ConcatOp : concat
+    OperatorImpl --> CrossOp : cross
+    OperatorImpl --> GroupTupleOp : groupTuple
+    OperatorImpl --> JoinOp : join
+    OperatorImpl --> MapOp : map
+    OperatorImpl --> MergeOp : merge
+    OperatorImpl --> MixOp : mix
+    OperatorImpl --> MultiMapOp : multiMap
+    OperatorImpl --> RandomSampleOp : randomSample
+    OperatorImpl --> SplitOp : splitCsv, splitFasta, splitFastq, splitText
+    OperatorImpl --> TakeOp : take
+    OperatorImpl --> ToListOp : toList, toSortedList
+    OperatorImpl --> TransposeOp : transpose
+    OperatorImpl --> UntilOp : until
+
+    WorkflowBinding --> OpCall : invokeMethod
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.ga4gh.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.ga4gh.mmd
new file mode 100644
index 0000000000..7f2c508b3d
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.ga4gh.mmd
@@ -0,0 +1,14 @@
+classDiagram
+    %%
+    %% nextflow.ga4gh
+    %%
+    Executor <|-- TesExecutor
+    %% TaskHandler <|-- TesTaskHandler
+    %% BashWrapperBuilder <|-- TesBashBuilder
+
+    TesExecutor --> TaskPollingMonitor : init
+    TesExecutor --> TesTaskHandler : submit
+    TesTaskHandler --> TesBashBuilder : submit
+
+    %% ScriptFileCopyStrategy <|-- TesFileCopyStrategy
+    TesBashBuilder --* TesFileCopyStrategy
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.k8s.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.k8s.mmd
new file mode 100644
index 0000000000..e329942fb3
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.k8s.mmd
@@ -0,0 +1,57 @@
+classDiagram
+    %%
+    %% nextflow.k8s
+    %%
+    Executor <|-- K8sExecutor
+    TaskHandler <|-- K8sTaskHandler
+    BashWrapperBuilder <|-- K8sWrapperBuilder
+
+    K8sExecutor --> TaskPollingMonitor : init
+    K8sExecutor --> K8sTaskHandler : submit
+    K8sExecutor --* K8sClient
+    K8sTaskHandler --> K8sWrapperBuilder : submit
+
+    CmdKubeRun --> K8sDriverLauncher : run
+
+    class K8sDriverLauncher {
+        args : List~String~
+        cmd : CmdKubeRun
+        config : ConfigObject
+        configMapName : String
+        headCpus : int
+        headImage : String
+        headMemory : String
+        headPreScript : String
+        paramsFile : String
+        pipelineName : String
+        runName : String
+    }
+    K8sDriverLauncher --* K8sClient
+    K8sDriverLauncher --* K8sConfig
+
+    K8sClient --* ClientConfig
+    %% ConfigDiscovery --> ClientConfig : discover
+
+    class K8sConfig {
+        target : Map
+        podOptions : PodOptions
+    }
+    K8sConfig --* PodOptions
+
+    class PodOptions {
+        affinity : Map
+        annotations : Map
+        automountServiceAccountToken : boolean
+        configMaps : Collection~PodMountConfig~
+        envVars : Collection~PodEnv~
+        imagePullPolicy : String
+        imagePullSecret : String
+        labels : Map
+        nodeSelector : PodNodeSelector
+        priorityClassName : String
+        privileged : Boolean
+        secrets : Collection~PodMountSecret~
+        securityContext : PodSecurityContext
+        tolerations : List~Map~
+        volumeClaims : Collection~PodVolumeClaim~
+    }
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.mmd
new file mode 100644
index 0000000000..c683746488
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.mmd
@@ -0,0 +1,21 @@
+classDiagram
+    %%
+    %% nextflow
+    %%
+    class Nextflow
+    class Channel
+    class Session {
+        baseDir : Path
+        binding : ScriptBinding
+        cache : CacheDB
+        commandLine : String
+        commitId : String
+        config : Map
+        configFiles : List~Path~
+        dag : DAG
+        profile : String
+        runName : String
+        script : BaseScript
+        uniqueId : UUID
+        workDir : Path
+    }
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.plugin.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.plugin.mmd
new file mode 100644
index 0000000000..2d576aaad8
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.plugin.mmd
@@ -0,0 +1,14 @@
+classDiagram
+    %%
+    %% nextflow.plugin
+    %%
+    CmdRun --> Plugins : run
+
+    Plugins --> PluginsFacade : init
+
+    PluginsFacade "1" --> "*" PluginRef : load
+
+    class PluginRef {
+        id : String
+        version : String
+    }
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.processor.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.processor.mmd
new file mode 100644
index 0000000000..196433ff69
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.processor.mmd
@@ -0,0 +1,44 @@
+classDiagram
+    %%
+    %% nextflow.processor
+    %%
+    %% ProcessDef --> TaskProcessor : run
+
+    class TaskProcessor {
+        config : ProcessConfig
+        executor : Executor
+        id : int
+        name : String
+        operator : DataflowProcessor
+        taskBody : BodyDef
+    }
+    TaskProcessor --> TaskRun : invokeTask
+    TaskProcessor --> PublishDir : finalizeTask
+
+    class TaskRun {
+        config : TaskConfig
+        context : TaskContext
+        hash : HashCode
+        id : TaskId
+        index : int
+        inputs : Map
+        name : String
+        outputs : Map
+        runType : RunType
+        type : ScriptType
+        workDir : Path
+    }
+    TaskRun --* TaskConfig
+    TaskRun --* TaskContext
+    TaskRun --> TaskBean : toTaskBean
+
+    class TaskConfig {
+        target : Map
+        binding : Map
+    }
+
+    class TaskContext {
+        holder : Map
+        script : Script
+        name : String
+    }
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.scm.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.scm.mmd
new file mode 100644
index 0000000000..1c52075372
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.scm.mmd
@@ -0,0 +1,26 @@
+classDiagram
+    %%
+    %% nextflow.scm
+    %%
+    direction LR
+
+    CmdRun --> AssetManager : run
+
+    class AssetManager {
+        project : String
+        localPath : File
+        mainScript : String
+        repositoryProvider : RepositoryProvider
+        hub : String
+        providerConfigs : List~ProviderConfig~
+    }
+    AssetManager --* RepositoryProvider
+    AssetManager "1" --* "*" ProviderConfig
+
+    RepositoryProvider <|-- AzureRepositoryProvider
+    RepositoryProvider <|-- BitbucketRepositoryProvider
+    RepositoryProvider <|-- BitbucketServerRepositoryProvider
+    RepositoryProvider <|-- GiteaRepositoryProvider
+    RepositoryProvider <|-- GithubRepositoryProvider
+    RepositoryProvider <|-- GitlabRepositoryProvider
+    RepositoryProvider <|-- LocalRepositoryProvider
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.script.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.script.mmd
new file mode 100644
index 0000000000..4b22d49cf7
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.script.mmd
@@ -0,0 +1,130 @@
+classDiagram
+    %%
+    %% nextflow.script
+    %%
+    CmdRun --> ScriptRunner : run
+
+    class ScriptRunner {
+        scriptFile : ScriptFile
+        session : Session
+    }
+    ScriptRunner --* ScriptFile
+    ScriptRunner --> ScriptParser : execute
+    ScriptParser --> BaseScript : parse
+
+    class ScriptFile {
+        source : Path
+        main : Path
+        repository : String
+        revisionInfo : AssetManager.RevisionInfo
+        localPath : Path
+        projectName : String
+    }
+
+    class BaseScript {
+        meta : ScriptMeta
+        entryFlow : WorkflowDef
+    }
+    BaseScript --* ScriptBinding
+    BaseScript --* ScriptMeta
+    BaseScript --> IncludeDef : include
+
+    IncludeDef --> ScriptParser : load0
+
+    class ScriptBinding {
+        scriptPath : Path
+        args : List~String~
+        params : ParamsMap
+        configEnv : Map
+        entryName : String
+    }
+
+    class ScriptMeta {
+        scriptPath : Path
+        definitions : Map
+        imports : Map
+        module : boolean
+    }
+    ScriptMeta "1" --* "*" ComponentDef : definitions
+    ScriptMeta "1" --* "*" ComponentDef : imports
+
+    ComponentDef <|-- FunctionDef
+    ComponentDef <|-- ProcessDef
+    ComponentDef <|-- WorkflowDef
+
+    class FunctionDef {
+        target : Object
+        name : String
+        alias : String
+    }
+
+    class ProcessDef {
+        processName : String
+        simpleName : String
+        baseName : String
+        rawBody : Closure~BodyDef~
+    }
+    ProcessDef --* ProcessConfig
+    ProcessDef --* BodyDef
+    ProcessDef --* ChannelOut
+
+    class WorkflowDef {
+        name : String
+        body : BodyDef
+        declaredInputs : List~String~
+        declaredOutputs : List~String~
+        variableNames : Set~String~
+    }
+    WorkflowDef --* BodyDef
+    WorkflowDef --* WorkflowBinding
+    WorkflowDef --* ChannelOut
+
+    class ProcessConfig {
+        configProperties : Map
+        inputs : InputsList
+        outputs : OutputsList
+    }
+    ProcessConfig --* InputsList
+    ProcessConfig --* OutputsList
+
+    class BodyDef {
+        closure : Closure
+        source : String
+        type : ScriptType
+        isShell : boolean
+    }
+
+    class ChannelOut {
+        target : List~DataflowWriteChannel~
+        channels : Map
+    }
+
+    class WorkflowBinding {
+        vars : Map
+    }
+
+    class InputsList {
+        target : List~InParam~
+    }
+    InputsList "1" --* "*" InParam
+
+    class OutputsList {
+        target : List~OutParam~
+    }
+    OutputsList "1" --* "*" OutParam
+
+    %% InParam <|-- BaseInParam
+    %% BaseInParam <|-- EachInParam
+    %% BaseInParam <|-- EnvInParam
+    %% BaseInParam <|-- FileInParam
+    %% BaseInParam <|-- StdInParam
+    %% BaseInParam <|-- TupleInParam
+    %% BaseInParam <|-- ValueInParam
+
+    %% OutParam <|-- BaseOutParam
+    %% BaseOutParam <|-- EachOutParam
+    %% BaseOutParam <|-- EnvOutParam
+    %% BaseOutParam <|-- FileOutParam
+    %% BaseOutParam <|-- StdOutParam
+    %% BaseOutParam <|-- TupleOutParam
+    %% BaseOutParam <|-- ValueOutParam
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.secret.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.secret.mmd
new file mode 100644
index 0000000000..1ee67a0363
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.secret.mmd
@@ -0,0 +1,12 @@
+classDiagram
+    %%
+    %% nextflow.secret
+    %%
+    ConfigBuilder --> SecretsLoader : build
+    BaseScript --> SecretsLoader : run
+    BashWrapperBuilder --> SecretsLoader : build
+
+    SecretsLoader --> SecretsProvider : load
+    SecretsProvider --> Secret : getSecret
+    SecretsProvider <|-- LocalSecretsProvider
+    Secret <|-- SecretImpl
diff --git a/new-docs/nextflow-docs/developer/diagrams/nextflow.trace.mmd b/new-docs/nextflow-docs/developer/diagrams/nextflow.trace.mmd
new file mode 100644
index 0000000000..9498988d4c
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/nextflow.trace.mmd
@@ -0,0 +1,13 @@
+classDiagram
+    %%
+    %% nextflow.trace
+    %%
+    Session --> TraceObserverFactory : init
+
+    TraceObserverFactory "1" --> "*" TraceObserver : create
+    TraceObserver <|-- AnsiLogObserver
+    TraceObserver <|-- GraphObserver
+    TraceObserver <|-- ReportObserver
+    TraceObserver <|-- TimelineObserver
+    TraceObserver <|-- TraceFileObserver
+    TraceObserver <|-- WorkflowStatsObserver
diff --git a/new-docs/nextflow-docs/developer/diagrams/overview.mmd b/new-docs/nextflow-docs/developer/diagrams/overview.mmd
new file mode 100644
index 0000000000..a59e924c47
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/diagrams/overview.mmd
@@ -0,0 +1,69 @@
+flowchart TB
+  subgraph Launcher
+    subgraph CmdRun
+      subgraph AssetManager
+        ScriptFile
+      end
+      subgraph ConfigBuilder
+        ConfigParser([ConfigParser])
+        ConfigBase([ConfigBase])
+      end
+      subgraph ScriptRunner
+        subgraph Session
+          ConfigMap
+          DAG
+          ExecutorFactory([ExecutorFactory])
+          subgraph TaskProcessor
+            TaskRun
+          end
+          subgraph Executor
+            subgraph TaskMonitor
+              TaskHandler
+            end
+            TaskBean
+            BashWrapperBuilder([BashWrapperBuilder])
+          end
+          TraceRecord
+          CacheFactory([CacheFactory])
+          CacheDB
+          TraceObserver([TraceObserver])
+        end
+        ScriptParser([ScriptParser])
+        BaseScript([BaseScript])
+        subgraph ScriptMeta
+          WorkflowDef([WorkflowDef])
+          ProcessDef([ProcessDef])
+          FunctionDef([FunctionDef])
+        end
+        IncludeDef([IncludeDef])
+        OpCall([OpCall])
+      end
+      ConfigParser --> ConfigBase
+      ConfigBase --> ConfigMap
+      ScriptFile --> ScriptParser
+      ScriptParser --> BaseScript
+      BaseScript --> WorkflowDef
+      BaseScript --> ProcessDef
+      BaseScript --> FunctionDef
+      BaseScript --> IncludeDef
+      IncludeDef --> ScriptParser
+      WorkflowDef --> OpCall
+      OpCall --> DAG
+      ProcessDef --> DAG
+      DAG --> TaskRun
+      TaskRun --> DAG
+      ExecutorFactory --> Executor
+      ConfigMap --> Executor
+      ProcessDef --> TaskProcessor
+      ConfigMap --> TaskProcessor
+      TaskRun --> TaskHandler
+      TaskRun --> TaskBean
+      TaskBean --> BashWrapperBuilder
+      BashWrapperBuilder --> TaskHandler
+      CacheFactory --> CacheDB
+      TaskHandler --> CacheDB
+      TaskHandler --> TraceRecord
+      TraceRecord --> CacheDB
+      TaskHandler --> TraceObserver
+    end
+  end
\ No newline at end of file
diff --git a/docs/developer/index.md b/new-docs/nextflow-docs/developer/index.mdx
similarity index 96%
rename from docs/developer/index.md
rename to new-docs/nextflow-docs/developer/index.mdx
index 8922757f1e..55e62bed2d 100644
--- a/docs/developer/index.md
+++ b/new-docs/nextflow-docs/developer/index.mdx
@@ -1,4 +1,4 @@
-(contributing-page)=
+
 
 # Overview
 
@@ -80,9 +80,9 @@ Links between classes denote one of the following relationships:
 - Composition (`A --* B`): `A` contains `B`
 - Instantiation (`A --> B : f`): `A` creates instance(s) of `B` at runtime via `A::f()`
 
-See {ref}`packages-page` for the list of Nextflow packages.
+See [packages-page][packages-page] for the list of Nextflow packages.
 
-```{warning}
+```warning
 Class diagrams are manually curated, so they might not always reflect the latest version of the source code.
 ```
 
@@ -157,16 +157,15 @@ Refer to the [build.yml](https://github.com/nextflow-io/nextflow/tree/master/.gi
 
 ### Groovy REPL
 
-The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java on the {ref}`Installation <install-requirements>` page.
+The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java on the [Installation][install-requirements] page.
 
-:::{note}
+:::note
 If you are using WSL, you must also install an X server for Windows, such as [VcXsrv](https://sourceforge.net/projects/vcxsrv/) or [Xming](http://www.straightrunning.com/XmingNotes/), in order to use these commands.
 :::
 
 ### IntelliJ IDEA
 
-:::{versionadded} 23.09.0-edge
-:::
+<AddedInVersion version="23.09.0-edge" />
 
 You can perform limited breakpoint debugging on a Nextflow script using IntelliJ IDEA.
 
@@ -179,3 +178,6 @@ You can perform limited breakpoint debugging on a Nextflow script using IntelliJ
 4. Select the green bug icon to begin the remote debug session. The Debug window will appear and allow you to step through and inspect your script as it runs.
 
 Note that this approach can only be used to debug the *script* execution, which does not include the *pipeline* execution.
+
+[install-requirements]: /nextflow_docs/nextflow_repo/docs/install.mdx#requirements
+[packages-page]: /nextflow_docs/nextflow_repo/docs/developer/packages.mdx
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/developer/nextflow.ast.mdx b/new-docs/nextflow-docs/developer/nextflow.ast.mdx
new file mode 100644
index 0000000000..b6d65dd338
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.ast.mdx
@@ -0,0 +1,179 @@
+
+# `nextflow.ast`
+
+The `nextflow.ast` package implements the Nextflow language extensions as AST transforms.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.ast
+    %%
+    ScriptParser --> NextflowDSLImpl : parse
+    ScriptParser --> NextflowXformImpl : parse
+    ScriptParser --> OpXformImpl : parse
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The Nextflow scripting language is essentially Groovy with some extensions, implemented as transformations to the abstract syntax tree (AST). Every Nextflow script is syntactically (but not semantically) valid Groovy.
+
+You can see the effect of Nextflow's AST transforms by using the Nextflow console:
+
+1. Run `nextflow console` to open the console
+2. Enter a Nextflow script
+3. Execute the script
+4. Go to **Script** > **Inspect AST**
+
+Here is an example:
+
+```nextflow
+params.str = 'Hello world!'
+
+process split_letters {
+  output:
+    path 'chunk_*'
+
+  script:
+  """
+  printf '${params.str}' | split -b 6 - chunk_
+  """
+}
+
+process convert_to_upper {
+  input:
+    path x
+  output:
+    stdout
+
+  script:
+  """
+  cat $x | tr '[a-z]' '[A-Z]'
+  """
+}
+
+workflow {
+  split_letters | flatten | convert_to_upper | view { it.trim() }
+}
+```
+
+Here it is after being parsed and de-sugared by Groovy:
+
+```groovy
+params.str = 'Hello world!'
+
+process( split_letters( {
+  output:
+    path('chunk_*')
+
+  script:
+  """
+  printf '${params.str}' | split -b 6 - chunk_
+  """
+} ))
+
+process( convert_to_upper( {
+  input:
+    path(x)
+  output:
+    stdout
+
+  script:
+  """
+  cat $x | tr '[a-z]' '[A-Z]'
+  """
+} ))
+
+workflow({
+  split_letters | flatten | convert_to_upper | view { it.trim() }
+})
+```
+
+Here it is after being transformed by Nextflow (whitespace edited for readability):
+
+```groovy
+import static nextflow.Nextflow.*
+
+import org.apache.commons.lang.StringUtils as StringUtils
+import groovy.transform.Field as Field
+import java.nio.file.Path as Path
+import nextflow.Channel as Channel
+import nextflow.util.Duration as Duration
+import nextflow.util.MemoryUnit as MemoryUnit
+import nextflow.io.ValueObject as ValueObject
+import nextflow.Channel as channel
+
+@groovy.transform.BaseScript
+public class script1677225313239 extends nextflow.script.BaseScript { 
+
+    public script1677225313239() {
+        nextflow.script.ScriptMeta.get(this).setDsl1ProcessNames(['split_letters', 'convert_to_upper'])
+    }
+
+    public script1677225313239(final groovy.lang.Binding context) {
+        super.setBinding(context)
+        nextflow.script.ScriptMeta.get(this).setDsl1ProcessNames(['split_letters', 'convert_to_upper'])
+    }
+
+    public static void main(final java.lang.String[] args) {
+        org.codehaus.groovy.runtime.InvokerHelper.runScript(script1677225313239, args)
+    }
+
+    @groovy.transform.Generated
+    protected java.lang.Object runScript() {
+        params.str = 'Hello world!'
+
+        this.process('split_letters', { 
+            this._out_path('chunk_*')
+            new nextflow.script.BodyDef(
+                {
+                    "printf '$params.str' | split -b 6 - chunk_"
+                },
+                '"""\n  printf \'${params.str}\' | split -b 6 - chunk_\n  """\n',
+                'script',
+                [
+                    new nextflow.script.TokenValRef('params.str', 8, 13)
+                ]
+            )
+        })
+
+        this.process('convert_to_upper', { 
+            this._in_path(new nextflow.script.TokenVar('x'))
+            this._out_stdout()
+            new nextflow.script.BodyDef(
+                { 
+                    "cat $x | tr '[a-z]' '[A-Z]'"
+                },
+                '"""\n  cat $x | tr \'[a-z]\' \'[A-Z]\'\n  """\n',
+                'script',
+                [
+                    new nextflow.script.TokenValRef('x', 19, 8)
+                ]
+            )
+        })
+
+        this.workflow({ 
+            new nextflow.script.BodyDef(
+                {
+                    split_letters | flatten | convert_to_upper | this.view({ 
+                        it.trim()
+                    })
+                },
+                '  split_letters | flatten | convert_to_upper | view { it.trim() }\n',
+                'workflow',
+                [
+                    new nextflow.script.TokenValRef('flatten', 24, 18),
+                    new nextflow.script.TokenValRef('split_letters', 24, 3),
+                    new nextflow.script.TokenValRef('convert_to_upper', 24, 28)
+                ]
+            )
+        })
+    }
+
+}
+```
diff --git a/new-docs/nextflow-docs/developer/nextflow.cache.mdx b/new-docs/nextflow-docs/developer/nextflow.cache.mdx
new file mode 100644
index 0000000000..48ac59c33c
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.cache.mdx
@@ -0,0 +1,43 @@
+
+# `nextflow.cache`
+
+The `nextflow.cache` package implements the cache database of previously executed tasks.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cache
+    %%
+    Session --* CacheDB
+
+    CacheDB --* CacheStore
+
+    CacheStore <|-- DefaultCacheStore
+    CacheStore <|-- CloudCacheStore
+
+    class DefaultCacheStore {
+        uniqueId : UUID
+        runName : String
+        baseDir : Path
+    }
+
+    class CloudCacheStore {
+        uniqueId : UUID
+        runName : String
+        basePath : Path
+    }
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The cache database uses [Kryo](https://github.com/EsotericSoftware/kryo) to serialize and deserialize task data. Each key-value pair in the cache database corresponds to a task. The key is the task hash, and the value consists of (1) the task `TraceRecord`, (2) the `TaskContext`, and (3) the task reference count.
+
+The default cache store is backed by [LevelDB](https://mvnrepository.com/artifact/org.iq80.leveldb/leveldb) and is stored in `.nextflow/cache/<session-id>` relative to the launch directory.
+
+The cloud cache store is backed by remote object storage such as Amazon S3, Azure Blob Storage, and Google Cloud Storage. It stores each task entry as a separate object.
diff --git a/new-docs/nextflow-docs/developer/nextflow.cli.mdx b/new-docs/nextflow-docs/developer/nextflow.cli.mdx
new file mode 100644
index 0000000000..e3ac6387df
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.cli.mdx
@@ -0,0 +1,46 @@
+
+# `nextflow.cli`
+
+The `nextflow.cli` package implements the command line interface.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cli
+    %%
+    class Launcher {
+        cliOptions : CliOptions
+        command : CmdBase
+    } 
+    Launcher --* CliOptions
+    Launcher --* CmdBase
+
+    %% CmdBase <|-- CmdClean
+    %% CmdBase <|-- CmdClone
+    %% CmdBase <|-- CmdConfig
+    CmdBase <|-- CmdConsole
+    %% CmdBase <|-- CmdDrop
+    %% CmdBase <|-- CmdFs
+    CmdBase <|-- CmdHelp
+    CmdBase <|-- CmdInfo
+    %% CmdBase <|-- CmdKubeRun
+    %% CmdBase <|-- CmdList
+    %% CmdBase <|-- CmdLog
+    %% CmdBase <|-- CmdNode
+    %% CmdBase <|-- CmdPlugin
+    %% CmdBase <|-- CmdPull
+    CmdBase <|-- CmdRun
+    %% CmdBase <|-- CmdSecret
+    %% CmdBase <|-- CmdSelfUpdate
+    %% CmdBase <|-- CmdView
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The `Launcher` class is the entrypoint for Nextflow. It uses [JCommander](https://jcommander.org/) to parse the command-line arguments. Additionally, there is a class for each subcommand which implements the application logic of that command. By far the most complex command is `CmdRun`.
diff --git a/new-docs/nextflow-docs/developer/nextflow.cloud.aws.mdx b/new-docs/nextflow-docs/developer/nextflow.cloud.aws.mdx
new file mode 100644
index 0000000000..89ef9cd43b
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.cloud.aws.mdx
@@ -0,0 +1,35 @@
+
+# `nextflow.cloud.aws`
+
+The `nextflow.cloud.aws` package implements the AWS Batch executor.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cloud.aws
+    %%
+    Executor <|-- AwsBatchExecutor
+    TaskHandler <|-- AwsBatchTaskHandler
+    BashWrapperBuilder <|-- AwsBatchScriptLauncher
+
+    AwsBatchExecutor --* AwsOptions
+    AwsOptions --* AwsConfig
+    AwsConfig --* AwsBatchConfig
+    AwsConfig --* AwsS3Config
+
+    AwsBatchExecutor --> ParallelPollingMonitor : init
+    AwsBatchExecutor --> AwsBatchTaskHandler : submit
+    AwsBatchTaskHandler --> AwsBatchScriptLauncher : submit
+
+    %% TaskPollingMonitor <|-- ParallelPollingMonitor
+
+    SimpleFileCopyStrategy <|-- AwsBatchFileCopyStrategy
+    AwsBatchScriptLauncher --* AwsBatchFileCopyStrategy
+
+```
+
+:::note
+Some classes may be excluded from the above diagrams for brevity.
+:::
diff --git a/new-docs/nextflow-docs/developer/nextflow.cloud.aws.nio.mdx b/new-docs/nextflow-docs/developer/nextflow.cloud.aws.nio.mdx
new file mode 100644
index 0000000000..a33d4f22c5
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.cloud.aws.nio.mdx
@@ -0,0 +1,51 @@
+
+# `nextflow.cloud.aws.nio`
+
+The `nextflow.cloud.aws.nio` package implements the S3 filesystem.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cloud.aws.nio
+    %%
+    FileSystemProvider <|-- S3FileSystemProvider
+
+    S3FileSystemProvider --> S3FileSystem : newFileSystem
+
+    class S3FileSystem {
+        client : S3Client
+        endpoint : String
+    }
+    S3FileSystem --* S3Client
+
+    class S3Client {
+        client : AmazonS3
+        cannedAcl : CannedAccessControlList
+        kmsKeyId : String
+        storageEncryption : SSEAlgorithm
+        transferManager : TransferManager
+        transferPool : ExecutorService
+        uploadChunkSize : Long
+        uploadMaxThreads : Integer
+    }
+
+    Path <|-- S3Path
+
+    class S3Path {
+        bucket : String
+        parts : List~String~
+        fileSystem : S3FileSystem
+    }
+    S3Path --* S3FileSystem
+
+```
+
+:::note
+Some classes may be excluded from the above diagrams for brevity.
+:::
+
+## Notes
+
+The S3 filesystem translates Java Path API calls into S3 API calls, which allows Nextflow to interact with S3 objects through the same interface for local files.
diff --git a/new-docs/nextflow-docs/developer/nextflow.cloud.azure.mdx b/new-docs/nextflow-docs/developer/nextflow.cloud.azure.mdx
new file mode 100644
index 0000000000..4e21dec1cc
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.cloud.azure.mdx
@@ -0,0 +1,31 @@
+
+# `nextflow.cloud.azure`
+
+The `nextflow.cloud.azure` package implements the Azure Batch executor.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cloud.azure
+    %%
+    Executor <|-- AzBatchExecutor
+    TaskHandler <|-- AzBatchTaskHandler
+    BashWrapperBuilder <|-- AzBatchScriptLauncher
+
+    AzBatchExecutor --* AzConfig
+    AzBatchExecutor --> AzBatchService : register
+
+    AzBatchExecutor --> TaskPollingMonitor : init
+    AzBatchExecutor --> AzBatchTaskHandler : submit
+    AzBatchTaskHandler --> AzBatchScriptLauncher : submit
+
+    SimpleFileCopyStrategy <|-- AzFileCopyStrategy
+    AzBatchScriptLauncher --* AzFileCopyStrategy
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
diff --git a/new-docs/nextflow-docs/developer/nextflow.cloud.google.mdx b/new-docs/nextflow-docs/developer/nextflow.cloud.google.mdx
new file mode 100644
index 0000000000..305b261320
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.cloud.google.mdx
@@ -0,0 +1,27 @@
+
+# `nextflow.cloud.google`
+
+The `nextflow.cloud.google` package implements the Google Batch executor.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.cloud.google
+    %%
+    Executor <|-- GoogleBatchExecutor
+    TaskHandler <|-- GoogleBatchTaskHandler
+    BashWrapperBuilder <|-- GoogleBatchScriptLauncher
+
+    GoogleBatchExecutor --* BatchConfig
+
+    GoogleBatchExecutor --> TaskPollingMonitor : init
+    GoogleBatchExecutor --> GoogleBatchTaskHandler : submit
+    GoogleBatchTaskHandler --> GoogleBatchScriptLauncher : submit
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
diff --git a/new-docs/nextflow-docs/developer/nextflow.config.mdx b/new-docs/nextflow-docs/developer/nextflow.config.mdx
new file mode 100644
index 0000000000..a43f475381
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.config.mdx
@@ -0,0 +1,27 @@
+
+# `nextflow.config`
+
+The `nextflow.config` package contains the implementation of the Nextflow configuration.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.config
+    %%
+    Session --* ConfigMap
+    CmdRun --> ConfigBuilder : run
+    ConfigBuilder --> ConfigMap : build
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+Any command that parses Nextflow config files (`config`, `run`, etc) uses the `ConfigBuilder` to build a `ConfigMap` from a set of config files. The `ConfigBuilder` itself uses a `ConfigParser` to parse the config files.
+
+The Nextflow configuration language is essentially Groovy with some extensions. These extensions are implemented in `ConfigBase` and `ConfigTransformImpl`.
diff --git a/new-docs/nextflow-docs/developer/nextflow.container.mdx b/new-docs/nextflow-docs/developer/nextflow.container.mdx
new file mode 100644
index 0000000000..a406a62bcc
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.container.mdx
@@ -0,0 +1,36 @@
+
+# `nextflow.container`
+
+The `nextflow.container` package implements the integration with container runtimes.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.container
+    %%
+    direction LR
+
+    BashWrapperBuilder --> ContainerBuilder : build
+
+    ContainerBuilder <|-- CharliecloudBuilder
+    ContainerBuilder <|-- DockerBuilder
+    ContainerBuilder <|-- PodmanBuilder
+    ContainerBuilder <|-- ShifterBuilder
+    ContainerBuilder <|-- SingularityBuilder
+    ContainerBuilder <|-- UdockerBuilder
+
+    SingularityBuilder <|-- ApptainerBuilder
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The `ContainerBuilder` class is the base class for all container runtimes supported by Nextflow. It produces the container wrapper command for a given task run.
+
+Executors that support containerized tasks insert this wrapper command into the task wrapper script (`.command.run`). Executors that are *container-native*, i.e. that launch the task wrapper itself inside a container, don't need to generate a container wrapper command.
diff --git a/new-docs/nextflow-docs/developer/nextflow.dag.mdx b/new-docs/nextflow-docs/developer/nextflow.dag.mdx
new file mode 100644
index 0000000000..16c09b70d0
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.dag.mdx
@@ -0,0 +1,55 @@
+
+# `nextflow.dag`
+
+The `nextflow.dag` package implements the workflow DAG and renderers for several diagram formats.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.dag
+    %%
+    Session --* DAG
+
+    class DAG {
+        vertices : List~Vertex~
+        edges : List~Edge~
+    }
+    DAG "1" --* "*" Vertex
+    DAG "1" --* "*" Edge
+
+    class Vertex {
+        label : String
+        type : Type
+        operators : List~DataflowProcessor~
+        process : TaskProcessor
+    }
+
+    class Edge {
+        channel : Object
+        from : Vertex
+        to : Vertex
+        label : String
+    }
+
+    %% DagRenderer <|-- CytoscapeHtmlRenderer
+    %% DagRenderer <|-- CytoscapeJsRenderer
+    %% DagRenderer <|-- DotRenderer
+    %% DagRenderer <|-- GexfRenderer
+    %% DagRenderer <|-- GraphvizRenderer
+    %% DagRenderer <|-- MermaidRenderer
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The workflow DAG defines the network of processes, channels, and operators that comprise a workflow. It is produced by the execution of the Nextflow script. See [nextflow.script][nextflow-script] for more details.
+
+Implementations of the `DagRenderer` interface define how to render the workflow DAG to a particular diagram format. See [Workflow diagram][workflow-diagram] for more details.
+
+[nextflow-script]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.script.mdx
+[workflow-diagram]: /nextflow_docs/nextflow_repo/docs/reports.mdx#workflow-diagram
diff --git a/new-docs/nextflow-docs/developer/nextflow.executor.mdx b/new-docs/nextflow-docs/developer/nextflow.executor.mdx
new file mode 100644
index 0000000000..daf0e63085
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.executor.mdx
@@ -0,0 +1,90 @@
+
+# `nextflow.executor`
+
+The `nextflow.executor` package defines the executor interface and implements several built-in executors.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.executor
+    %%
+    ExecutorFactory --> Executor : getExecutor
+
+    class Executor {
+        name : String
+        monitor : TaskMonitor
+    }
+    Executor --* TaskMonitor
+    Executor --> TaskHandler : submit
+
+    TaskMonitor <|-- TaskPollingMonitor
+
+    class TaskPollingMonitor {
+        capacity : int
+        submitRateLimit : RateLimiter
+        pollIntervalMillis : long
+        dumpInterval : Duration
+    }
+
+    TaskPollingMonitor <|-- LocalPollingMonitor
+
+    class LocalPollingMonitor {
+        maxCpus : int
+        maxMemory : long
+    }
+
+    Executor <|-- AbstractGridExecutor
+    Executor <|-- LocalExecutor
+    %% Executor <|-- NopeExecutor
+    %% AbstractGridExecutor <|-- CondorExecutor
+    %% AbstractGridExecutor <|-- HyperQueueExecutor
+    %% AbstractGridExecutor <|-- LsfExecutor
+    %% AbstractGridExecutor <|-- MoabExecutor
+    %% AbstractGridExecutor <|-- NqsiiExecutor
+    %% AbstractGridExecutor <|-- OarExecutor
+    %% AbstractGridExecutor <|-- PbsExecutor
+    %% AbstractGridExecutor <|-- SgeExecutor
+    %% AbstractGridExecutor <|-- SlurmExecutor
+    %% PbsExecutor <|-- PbsProExecutor
+    %% SgeExecutor <|-- CrgExecutor
+
+    %% TaskHandler <|-- CachedTaskHandler
+    TaskHandler <|-- GridTaskHandler
+    TaskHandler <|-- LocalTaskHandler
+    TaskHandler <|-- NativeTaskHandler
+    %% TaskHandler <|-- NopeTaskHandler
+    %% TaskHandler <|-- StoredTaskHandler
+
+    class BashWrapperBuilder {
+        bean : TaskBean
+        copyStrategy : ScriptFileCopyStrategy
+    }
+    BashWrapperBuilder --* TaskBean
+    BashWrapperBuilder --* ScriptFileCopyStrategy
+
+    ScriptFileCopyStrategy <|-- SimpleFileCopyStrategy
+
+    class SimpleFileCopyStrategy {
+        stageinMode : String
+        stageoutMode : String
+        targetDir : Path
+        workDir : Path
+    }
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The `Executor` class is the base class for all Nextflow executors. The main purpose of an `Executor` is to submit tasks to an underlying compute environment, such as an HPC scheduler or cloud batch executor. It uses a `TaskMonitor` to manage the lifecycle of all tasks and a `TaskHandler` to manage each individual task. Most executors use the same polling monitor, but each executor implements its own task handler to customize it for a particular compute environment.
+See [nextflow.processor][nextflow.processor] for more details about these classes.
+
+The built-in executors include the local executor (`LocalExecutor`) and the various grid executors (SLURM, PBS, LSF, etc), all of which extend `AbstractGridExecutor`. The `LocalExecutor` implements both "script" tasks (processes with a `script` or `shell` block) and "native" tasks (processes with an `exec` block).
+
+The `BashWrapperBuilder` is used by executors to generate the wrapper script (`.command.run`) for a task, from a template script called `command-run.txt`, as well as the task configuration and the execution environment.
+
+[nextflow.processor]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.processor.mdx
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/developer/nextflow.extension.mdx b/new-docs/nextflow-docs/developer/nextflow.extension.mdx
new file mode 100644
index 0000000000..6c3eef9837
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.extension.mdx
@@ -0,0 +1,52 @@
+
+# `nextflow.extension`
+
+The `nextflow.extension` package implements the channel operators and other extension methods.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.extension
+    %%
+    direction LR
+
+    ChannelEx --> DumpOp : dump
+    Nextflow --> GroupKey : groupKey
+
+    OperatorImpl --> BranchOp : branch
+    OperatorImpl --> BufferOp : buffer
+    OperatorImpl --> CollectFileOp : collectFile
+    OperatorImpl --> CollectOp : collect
+    OperatorImpl --> CombineOp : combine
+    OperatorImpl --> ConcatOp : concat
+    OperatorImpl --> CrossOp : cross
+    OperatorImpl --> GroupTupleOp : groupTuple
+    OperatorImpl --> JoinOp : join
+    OperatorImpl --> MapOp : map
+    OperatorImpl --> MergeOp : merge
+    OperatorImpl --> MixOp : mix
+    OperatorImpl --> MultiMapOp : multiMap
+    OperatorImpl --> RandomSampleOp : randomSample
+    OperatorImpl --> SplitOp : splitCsv, splitFasta, splitFastq, splitText
+    OperatorImpl --> TakeOp : take
+    OperatorImpl --> ToListOp : toList, toSortedList
+    OperatorImpl --> TransposeOp : transpose
+    OperatorImpl --> UntilOp : until
+
+    WorkflowBinding --> OpCall : invokeMethod
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+Operators are implemented using the [GPars](http://gpars.org/1.2.1/guide/guide/dataflow.html) dataflow library. In general, an operator consumes one or more `DataflowReadChannel`s and produces one or more `DataflowWriteChannel`s. See [Operators][operator-page] for details about each operator.
+
+Other notable classes include `Bolts` and `FilesEx`, which implement various extension methods used throughout the Nextflow codebase. If you see a method that doesn't appear to be implemented by the calling object, it may be implemented in one of these extension classes.
+
+[operator-page]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/developer/nextflow.k8s.mdx b/new-docs/nextflow-docs/developer/nextflow.k8s.mdx
new file mode 100644
index 0000000000..fd7532e5f9
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.k8s.mdx
@@ -0,0 +1,74 @@
+
+# `nextflow.k8s`
+
+The `nextflow.k8s` package implements the Kubernetes executor and the `kuberun` command.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.k8s
+    %%
+    Executor <|-- K8sExecutor
+    TaskHandler <|-- K8sTaskHandler
+    BashWrapperBuilder <|-- K8sWrapperBuilder
+
+    K8sExecutor --> TaskPollingMonitor : init
+    K8sExecutor --> K8sTaskHandler : submit
+    K8sExecutor --* K8sClient
+    K8sTaskHandler --> K8sWrapperBuilder : submit
+
+    CmdKubeRun --> K8sDriverLauncher : run
+
+    class K8sDriverLauncher {
+        args : List~String~
+        cmd : CmdKubeRun
+        config : ConfigObject
+        configMapName : String
+        headCpus : int
+        headImage : String
+        headMemory : String
+        headPreScript : String
+        paramsFile : String
+        pipelineName : String
+        runName : String
+    }
+    K8sDriverLauncher --* K8sClient
+    K8sDriverLauncher --* K8sConfig
+
+    K8sClient --* ClientConfig
+    %% ConfigDiscovery --> ClientConfig : discover
+
+    class K8sConfig {
+        target : Map
+        podOptions : PodOptions
+    }
+    K8sConfig --* PodOptions
+
+    class PodOptions {
+        affinity : Map
+        annotations : Map
+        automountServiceAccountToken : boolean
+        configMaps : Collection~PodMountConfig~
+        envVars : Collection~PodEnv~
+        imagePullPolicy : String
+        imagePullSecret : String
+        labels : Map
+        nodeSelector : PodNodeSelector
+        priorityClassName : String
+        privileged : Boolean
+        secrets : Collection~PodMountSecret~
+        securityContext : PodSecurityContext
+        tolerations : List~Map~
+        volumeClaims : Collection~PodVolumeClaim~
+    }
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The Kubernetes integration uses the K8s HTTP API to interact with K8s clusters, and relies on the `kubectl` command and `~/.kube/config` file for authentication.
diff --git a/new-docs/nextflow-docs/developer/nextflow.mdx b/new-docs/nextflow-docs/developer/nextflow.mdx
new file mode 100644
index 0000000000..d5351fcbd3
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.mdx
@@ -0,0 +1,47 @@
+
+# `nextflow`
+
+The `nextflow` package contains various top-level classes.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow
+    %%
+    class Nextflow
+    class Channel
+    class Session {
+        baseDir : Path
+        binding : ScriptBinding
+        cache : CacheDB
+        commandLine : String
+        commitId : String
+        config : Map
+        configFiles : List~Path~
+        dag : DAG
+        profile : String
+        runName : String
+        script : BaseScript
+        uniqueId : UUID
+        workDir : Path
+    }
+
+```
+
+```note
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The `Nextflow` class implements several methods that are exposed to Nextflow scripts. See [Global namespace][stdlib-namespaces-global] for details.
+
+The `Channel` class implements the channel factory methods, and it is exposed directly to Nextflow scripts. See [Dataflow][channel-page] for details.
+
+The `Session` class is the top-level representation of a Nextflow run, or "session". See [nextflow.script][nextflow-script] for more details about how a `Session` is created.
+
+[dataflow-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[nextflow-script]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.script.mdx
+[stdlib-namespaces-global]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-namespaces.mdx#global-namespace
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/developer/nextflow.plugin.mdx b/new-docs/nextflow-docs/developer/nextflow.plugin.mdx
new file mode 100644
index 0000000000..d5786c175c
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.plugin.mdx
@@ -0,0 +1,31 @@
+
+# `nextflow.plugin`
+
+The `nextflow.plugin` package implements the plugin manager.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.plugin
+    %%
+    CmdRun --> Plugins : run
+
+    Plugins --> PluginsFacade : init
+
+    PluginsFacade "1" --> "*" PluginSpec : load
+
+    class PluginSpec {
+        id : String
+        version : String
+    }
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The plugin system uses the [PF4J](https://pf4j.org/) library, which allows for extension classes to be loaded at runtime. Each plugin includes a manifest of extension classes, all of which extend or implement some base class in Nextflow. The `Plugins` class can be used to query the available extensions for a given base class. Extensions can be assigned a priority using the `@Priority` annotation, to ensure that certain extensions are used over others when available.
diff --git a/new-docs/nextflow-docs/developer/nextflow.processor.mdx b/new-docs/nextflow-docs/developer/nextflow.processor.mdx
new file mode 100644
index 0000000000..f718d1f591
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.processor.mdx
@@ -0,0 +1,69 @@
+
+# `nextflow.processor`
+
+The `nextflow.processor` package implements the execution and monitoring of tasks.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.processor
+    %%
+    %% ProcessDef --> TaskProcessor : run
+
+    class TaskProcessor {
+        config : ProcessConfig
+        executor : Executor
+        id : int
+        name : String
+        operator : DataflowProcessor
+        taskBody : BodyDef
+    }
+    TaskProcessor --> TaskRun : invokeTask
+    TaskProcessor --> PublishDir : finalizeTask
+
+    class TaskRun {
+        config : TaskConfig
+        context : TaskContext
+        hash : HashCode
+        id : TaskId
+        index : int
+        inputs : Map
+        name : String
+        outputs : Map
+        runType : RunType
+        type : ScriptType
+        workDir : Path
+    }
+    TaskRun --* TaskConfig
+    TaskRun --* TaskContext
+    TaskRun --> TaskBean : toTaskBean
+
+    class TaskConfig {
+        target : Map
+        binding : Map
+    }
+
+    class TaskContext {
+        holder : Map
+        script : Script
+        name : String
+    }
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+While the [`executor`][nextflow-executor] package defines how tasks are submitted to a particular execution backend (such as an HPC scheduler), the `processor` package defines how tasks are created and executed. As such, these packages work closely together, and in fact several components of the `Executor` interface, specifically the `TaskHandler` and `TaskMonitor`, are defined in this package.
+
+The `TaskProcessor` is by far the largest and most complex class in this package. It implements both the dataflow operator for a given process as well as the task execution logic. In other words, it defines the mapping from an abstract process definition with input and output channels into concrete task executions.
+
+A `TaskRun` represents a particular task execution. There is also `TaskBean`, which is a serializable representation of a task. Legends say that `TaskBean` was originally created to support a "daemon" mode in which Nextflow would run on both the head node and the worker nodes, so the Nextflow "head" would need to send tasks to the Nextflow "workers". This daemon mode was never completed, but echoes of it remain (see `CmdNode`, `DaemonLauncher`, and the `nf-ignite` plugin).
+
+When a `TaskProcessor` receives a set of input values, it creates a `TaskRun` and submits it to an `Executor`, which in turn submits the task to a underlying execution backend. The executor's `TaskMonitor` then monitors the status of the task, and when it is completed, returns it to the task processor for finalization. If the task completed successfully, the task processor collects the task outputs and emits them on the corresponding output channels. If the task failed, the task processor will retry it if possible, or else return a task error to the workflow run.
+
+[nextflow-executor]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.executor.mdx
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/developer/nextflow.scm.mdx b/new-docs/nextflow-docs/developer/nextflow.scm.mdx
new file mode 100644
index 0000000000..ea647d2e8f
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.scm.mdx
@@ -0,0 +1,43 @@
+
+# `nextflow.scm`
+
+The `nextflow.scm` package defines the Git provider interface and implements several built-in Git providers.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.scm
+    %%
+    direction LR
+
+    CmdRun --> AssetManager : run
+
+    class AssetManager {
+        project : String
+        localPath : File
+        mainScript : String
+        repositoryProvider : RepositoryProvider
+        hub : String
+        providerConfigs : List~ProviderConfig~
+    }
+    AssetManager --* RepositoryProvider
+    AssetManager "1" --* "*" ProviderConfig
+
+    RepositoryProvider <|-- AzureRepositoryProvider
+    RepositoryProvider <|-- BitbucketRepositoryProvider
+    RepositoryProvider <|-- BitbucketServerRepositoryProvider
+    RepositoryProvider <|-- GiteaRepositoryProvider
+    RepositoryProvider <|-- GithubRepositoryProvider
+    RepositoryProvider <|-- GitlabRepositoryProvider
+    RepositoryProvider <|-- LocalRepositoryProvider
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The `RepositoryProvider` class is the base class for all Git providers. It defines how to authenticate with the provider, clone a Git repository, inspect branches and tags, etc.
diff --git a/new-docs/nextflow-docs/developer/nextflow.script.mdx b/new-docs/nextflow-docs/developer/nextflow.script.mdx
new file mode 100644
index 0000000000..0cb9e3bced
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.script.mdx
@@ -0,0 +1,154 @@
+
+# `nextflow.script`
+
+The `nextflow.script` package implements the parsing and execution of Nextflow scripts.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.script
+    %%
+    CmdRun --> ScriptRunner : run
+
+    class ScriptRunner {
+        scriptFile : ScriptFile
+        session : Session
+    }
+    ScriptRunner --* ScriptFile
+    ScriptRunner --> ScriptParser : execute
+    ScriptParser --> BaseScript : parse
+
+    class ScriptFile {
+        source : Path
+        main : Path
+        repository : String
+        revisionInfo : AssetManager.RevisionInfo
+        localPath : Path
+        projectName : String
+    }
+
+    class BaseScript {
+        meta : ScriptMeta
+        entryFlow : WorkflowDef
+    }
+    BaseScript --* ScriptBinding
+    BaseScript --* ScriptMeta
+    BaseScript --> IncludeDef : include
+
+    IncludeDef --> ScriptParser : load0
+
+    class ScriptBinding {
+        scriptPath : Path
+        args : List~String~
+        params : ParamsMap
+        configEnv : Map
+        entryName : String
+    }
+
+    class ScriptMeta {
+        scriptPath : Path
+        definitions : Map
+        imports : Map
+        module : boolean
+    }
+    ScriptMeta "1" --* "*" ComponentDef : definitions
+    ScriptMeta "1" --* "*" ComponentDef : imports
+
+    ComponentDef <|-- FunctionDef
+    ComponentDef <|-- ProcessDef
+    ComponentDef <|-- WorkflowDef
+
+    class FunctionDef {
+        target : Object
+        name : String
+        alias : String
+    }
+
+    class ProcessDef {
+        processName : String
+        simpleName : String
+        baseName : String
+        rawBody : Closure~BodyDef~
+    }
+    ProcessDef --* ProcessConfig
+    ProcessDef --* BodyDef
+    ProcessDef --* ChannelOut
+
+    class WorkflowDef {
+        name : String
+        body : BodyDef
+        declaredInputs : List~String~
+        declaredOutputs : List~String~
+        variableNames : Set~String~
+    }
+    WorkflowDef --* BodyDef
+    WorkflowDef --* WorkflowBinding
+    WorkflowDef --* ChannelOut
+
+    class ProcessConfig {
+        configProperties : Map
+        inputs : InputsList
+        outputs : OutputsList
+    }
+    ProcessConfig --* InputsList
+    ProcessConfig --* OutputsList
+
+    class BodyDef {
+        closure : Closure
+        source : String
+        type : ScriptType
+        isShell : boolean
+    }
+
+    class ChannelOut {
+        target : List~DataflowWriteChannel~
+        channels : Map
+    }
+
+    class WorkflowBinding {
+        vars : Map
+    }
+
+    class InputsList {
+        target : List~InParam~
+    }
+    InputsList "1" --* "*" InParam
+
+    class OutputsList {
+        target : List~OutParam~
+    }
+    OutputsList "1" --* "*" OutParam
+
+    %% InParam <|-- BaseInParam
+    %% BaseInParam <|-- EachInParam
+    %% BaseInParam <|-- EnvInParam
+    %% BaseInParam <|-- FileInParam
+    %% BaseInParam <|-- StdInParam
+    %% BaseInParam <|-- TupleInParam
+    %% BaseInParam <|-- ValueInParam
+
+    %% OutParam <|-- BaseOutParam
+    %% BaseOutParam <|-- EachOutParam
+    %% BaseOutParam <|-- EnvOutParam
+    %% BaseOutParam <|-- FileOutParam
+    %% BaseOutParam <|-- StdOutParam
+    %% BaseOutParam <|-- TupleOutParam
+    %% BaseOutParam <|-- ValueOutParam
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The execution of a Nextflow pipeline occurs in two phases. In the first phase, Nextflow parses and runs the script (using the language extensions in [nextflow.ast][nextflow-ast] and [nextflow.extension][nextflow-extension]), which produces the workflow DAG. In the second phase, Nextflow executes the workflow.
+
+:::note
+In DSL1, there was no separation between workflow construction and execution -- dataflow operators were executed as soon as they were constructed. DSL2 introduced lazy execution in order to separate process definition from execution, and thereby facilitate subworkflows and modules.
+:::
+
+[nextflow-ast]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.ast.mdx
+[nextflow-extension]: /nextflow_docs/nextflow_repo/docs/developer/nextflow.extension.mdx
diff --git a/new-docs/nextflow-docs/developer/nextflow.secret.mdx b/new-docs/nextflow-docs/developer/nextflow.secret.mdx
new file mode 100644
index 0000000000..84f88682b3
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.secret.mdx
@@ -0,0 +1,30 @@
+
+# `nextflow.secret`
+
+The `nextflow.secret` package defines the secrets provider interface and implements the built-in local secrets store.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.secret
+    %%
+    ConfigBuilder --> SecretsLoader : build
+    BaseScript --> SecretsLoader : run
+    BashWrapperBuilder --> SecretsLoader : build
+
+    SecretsLoader --> SecretsProvider : load
+    SecretsProvider --> Secret : getSecret
+    SecretsProvider <|-- LocalSecretsProvider
+    Secret <|-- SecretImpl
+
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The default secrets provider simply stores key-value pairs in a local JSON file.
diff --git a/new-docs/nextflow-docs/developer/nextflow.trace.mdx b/new-docs/nextflow-docs/developer/nextflow.trace.mdx
new file mode 100644
index 0000000000..86ad076303
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/nextflow.trace.mdx
@@ -0,0 +1,30 @@
+
+# `nextflow.trace`
+
+The `nextflow.trace` package defines the trace observer interface and implements several built-in trace observers.
+
+## Class Diagram
+
+```mermaid
+classDiagram
+    %%
+    %% nextflow.trace
+    %%
+    Session --> TraceObserverFactory : init
+
+    TraceObserverFactory "1" --> "*" TraceObserver : create
+    TraceObserver <|-- AnsiLogObserver
+    TraceObserver <|-- GraphObserver
+    TraceObserver <|-- ReportObserver
+    TraceObserver <|-- TimelineObserver
+    TraceObserver <|-- TraceFileObserver
+    TraceObserver <|-- WorkflowStatsObserver
+```
+
+:::note
+Some classes may be excluded from the above diagram for brevity.
+:::
+
+## Notes
+
+The `TraceObserver` interface defines a set of hooks into the workflow execution, such as when a workflow starts and completes, when a task starts and completes, and when an output file is published. The `Session` maintains a list of all observers and triggers each hook when the corresponding event occurs. Implementing classes can use these hooks to perform custom behaviors. In fact, this interface is used to implement several core features, including the various execution reports, DAG renderer, and the integration with Seqera Platform.
diff --git a/new-docs/nextflow-docs/developer/packages.mdx b/new-docs/nextflow-docs/developer/packages.mdx
new file mode 100644
index 0000000000..6cf3ed167c
--- /dev/null
+++ b/new-docs/nextflow-docs/developer/packages.mdx
@@ -0,0 +1,7 @@
+import DocCardList from "@theme/DocCardList";
+
+# Packages
+
+The following pages correspond to packages in the Nextflow source code.
+
+<DocCardList />
diff --git a/docs/executor.md b/new-docs/nextflow-docs/executor.mdx
similarity index 70%
rename from docs/executor.md
rename to new-docs/nextflow-docs/executor.mdx
index 9e841fd6fe..785081a3e7 100644
--- a/docs/executor.md
+++ b/new-docs/nextflow-docs/executor.mdx
@@ -1,4 +1,4 @@
-(executor-page)=
+
 
 # Executors
 
@@ -8,8 +8,6 @@ The executor provides an abstraction between the pipeline processes and the unde
 
 In other words, you can write your pipeline script once and have it running on your computer, a cluster resource manager, or the cloud — simply change the executor definition in the Nextflow configuration file.
 
-(awsbatch-executor)=
-
 ## AWS Batch
 
 Nextflow supports the [AWS Batch](https://aws.amazon.com/batch/) service that allows job submission in the cloud without having to spin out and manage a cluster of virtual machines. AWS Batch uses Docker containers to run tasks, which greatly simplifies pipeline deployment.
@@ -22,20 +20,18 @@ The pipeline can be launched either on a local computer, or an EC2 instance. EC2
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-accelerator`
-- {ref}`process-arch` (only when using Fargate platform type for AWS Batch)
-- {ref}`process-container`
-- {ref}`process-containerOptions`
-- {ref}`process-cpus`
-- {ref}`process-disk` (only when using Fargate platform type for AWS Batch)
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-resourcelabels`
-- {ref}`process-time`
-
-See {ref}`aws-batch` for more information.
+- [accelerator][process-accelerator]
+- [arch][process-arch] (only when using Fargate platform type for AWS Batch)
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+- [cpus][process-cpus]
+- [disk][process-disk] (only when using Fargate platform type for AWS Batch)
+- [memory][process-memory]
+- [queue][process-queue]
+- [resourcelabels][process-resourcelabels]
+- [time][process-time]
 
-(azurebatch-executor)=
+See [AWS Batch][aws-batch] for more information.
 
 ## Azure Batch
 
@@ -49,24 +45,21 @@ The pipeline can be launched either on a local computer, or a cloud virtual mach
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-container`
-- {ref}`process-containerOptions`
-- {ref}`process-cpus`
-- {ref}`process-disk`
-- {ref}`process-machineType`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-resourcelabels`
-- {ref}`process-time`
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [machineType][process-machinetype]
+- [memory][process-memory]
+- [queue][process-queue]
+- [resourcelabels][process-resourcelabels]
+- [time][process-time]
 
-See {ref}`azure-batch` for more information.
-
-(bridge-executor)=
+See [Azure Batch][azure-batch] for more information.
 
 ## Bridge
 
-:::{versionadded} 22.09.1-edge
-:::
+<AddedInVersion version="22.09.1-edge" />
 
 [Bridge](https://github.com/cea-hpc/bridge) is an abstraction layer to ease batch system and resource manager usage in heterogeneous HPC environments.
 
@@ -78,18 +71,15 @@ To enable the Bridge executor, set `process.executor = 'bridge'` in the `nextflo
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-time`
-
-(flux-executor)=
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
 
 ## Flux Executor
 
-:::{versionadded} 22.11.0-edge
-:::
+<AddedInVersion version="22.11.0-edge" />
 
 The `flux` executor allows you to run your pipeline script using the [Flux Framework](https://flux-framework.org).
 
@@ -99,25 +89,22 @@ To enable the Flux executor, set `process.executor = 'flux'` in the `nextflow.co
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-queue`
-- {ref}`process-time`
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [queue][process-queue]
+- [time][process-time]
 
-:::{note}
+:::note
 Flux does not support the `memory` directive.
 :::
 
-:::{note}
+:::note
 By default, Flux will send all output to the `.command.log` file. To send this output to stdout and stderr instead, set `flux.terminalOutput = true` in your config file.
 :::
 
-(google-batch-executor)=
-
 ## Google Cloud Batch
 
-:::{versionadded} 22.07.1-edge
-:::
+<AddedInVersion version="22.07.1-edge" />
 
 [Google Cloud Batch](https://cloud.google.com/batch) is a managed computing service that allows the execution of containerized workloads in the Google Cloud Platform infrastructure.
 
@@ -129,32 +116,31 @@ To enable this executor, set `process.executor = 'google-batch'` in the `nextflo
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-accelerator`
-- {ref}`process-container`
-- {ref}`process-containerOptions`
-- {ref}`process-cpus`
-- {ref}`process-disk`
-- {ref}`process-machineType`
-- {ref}`process-memory`
-- {ref}`process-resourcelabels`
-- {ref}`process-time`
+- [accelerator][process-accelerator]
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [machineType][process-machinetype]
+- [memory][process-memory]
+- [resourcelabels][process-resourcelabels]
+- [time][process-time]
 
-See the {ref}`Google Cloud Batch <google-batch>` page for further configuration details.
-
-(htcondor-executor)=
+See [Cloud Batch][google-batch]for further configuration details.
 
 ## HTCondor
 
-:::{warning} *Experimental: may change in a future release.*
+:::warning{title="Experimental: may change in a future release"}  
 :::
 
+
 The `condor` executor allows you to run your pipeline script by using the [HTCondor](https://research.cs.wisc.edu/htcondor/) resource manager.
 
 Nextflow manages each process as a separate job that is submitted to the cluster using the `condor_submit` command.
 
 The pipeline must be launched from a node where the `condor_submit` command is available, which is typically the cluster login node.
 
-:::{note}
+:::note
 The HTCondor executor for Nextflow does not currently support HTCondor's ability to transfer input/output data to the corresponding job's compute node. Therefore, the data must be made accessible to the compute nodes through a shared file system directory from where the Nextflow workflow is executed (or specified via the `-w` option).
 :::
 
@@ -162,26 +148,21 @@ To enable the HTCondor executor, set `process.executor = 'condor'` in the `nextf
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-disk`
-- {ref}`process-memory`
-- {ref}`process-time`
-
-(hyperqueue-executor)=
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [memory][process-memory]
+- [time][process-time]
 
 ## HyperQueue
 
-:::{versionadded} 22.05.0-edge
-:::
-
-:::{versionchanged} 24.06.0-edge
+<ChangedInVersion version="24.06.0-edge">
 HyperQueue 0.17.0 or later is required.
-:::
+</ChangedInVersion>
 
-:::{versionchanged} 25.01.0-edge
+<ChangedInVersion version="25.01.0-edge">
 HyperQueue 0.20.0 or later is required.
-:::
+</ChangedInVersion>
 
 The `hyperqueue` executor allows you to run your pipeline script by using the [HyperQueue](https://github.com/It4innovations/hyperqueue) job scheduler.
 
@@ -193,13 +174,11 @@ To enable the HyperQueue executor, set `process.executor = 'hq'` in the `nextflo
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-accelerator`
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-time`
-
-(k8s-executor)=
+- [accelerator][process-accelerator]
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [time][process-time]
 
 ## Kubernetes
 
@@ -207,42 +186,38 @@ The `k8s` executor allows you to run a pipeline on a [Kubernetes](http://kuberne
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-accelerator`
-- {ref}`process-cpus`
-- {ref}`process-disk`
-- {ref}`process-memory`
-- {ref}`process-pod`
-- {ref}`process-resourcelabels`
-- {ref}`process-time`
+- [accelerator][process-accelerator]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [memory][process-memory]
+- [pod][process-pod]
+- [resourcelabels][process-resourcelabels]
+- [time][process-time]
 
-See the {ref}`Kubernetes <k8s-page>` page to learn how to set up a Kubernetes cluster to run Nextflow pipelines.
-
-(local-executor)=
+See the [Kubernetes][k8s-page] page to learn how to set up a Kubernetes cluster to run Nextflow pipelines.
 
 ## Local
 
-The `local` executor is used by default. It runs the pipeline processes on the computer where Nextflow is launched. The processes are parallelised by spawning multiple threads, taking advantage of the multi-core architecture of the CPU.
+The `local` executor is used by default. It runs the pipeline processes on the computer where Nextflow is launched. The processes are parallelized by spawning multiple threads, taking advantage of the multi-core architecture of the CPU.
 
 The `local` executor is useful for developing and testing a pipeline script on your computer, before switching to a cluster or cloud environment with production data.
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-time`
-- {ref}`process-container`
-- {ref}`process-containerOptions`
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [time][process-time]
+- [container][process-container]
+- [containerOptions][process-containeroptions]
 
-:::{note}
-While the `local` executor limits the number of concurrent tasks based on requested vs available resources, it does not enforce task resource requests. In other words, it is possible for a local task to use more CPUs and memory than it requested, in which case it may starve other tasks. An exception to this behavior is when using {ref}`container-docker` or {ref}`container-podman` containers, in which case the resource requests are enforced by the container runtime.
+:::note
+While the `local` executor limits the number of concurrent tasks based on requested vs available resources, it does not enforce task resource requests. In other words, it is possible for a local task to use more CPUs and memory than it requested, in which case it may starve other tasks. An exception to this behavior is when using [Docker][container-docker] or [Podman][container-podman] containers, in which case the resource requests are enforced by the container runtime.
 :::
 
 The local executor supports two types of tasks:
 - Script tasks (processes with a `script` or `shell` block) - executed via a Bash wrapper
 - Native tasks (processes with an `exec` block) - executed directly in the JVM.
 
-(lsf-executor)=
-
 ## LSF
 
 The `lsf` executor allows you to run your pipeline script using a [Platform LSF](http://en.wikipedia.org/wiki/Platform_LSF) cluster.
@@ -255,28 +230,23 @@ To enable the LSF executor, set `process.executor = 'lsf'` in the `nextflow.conf
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-time`
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
 
-:::{note}
-LSF supports both *per-core* and *per-job* memory limits. Nextflow assumes that LSF works in the *per-core* mode, thus it divides the requested {ref}`process-memory` by the number of requested {ref}`process-cpus`.
+:::note
+LSF supports both *per-core* and *per-job* memory limits. Nextflow assumes that LSF works in the *per-core* mode, thus it divides the requested [memory][process-memory] by the number of requested [cpus][process-cpus].
 
-When LSF is configured to work in the *per-job* memory limit mode, you must specify this limit with the `perJobMemLimit` option in the {ref}`config-executor` scope of your Nextflow config file.
+When LSF is configured to work in the *per-job* memory limit mode, you must specify this limit with the `perJobMemLimit` option in the [`executor`][config-executor] scope of your Nextflow config file.
 
 See also the [Platform LSF documentation](https://www.ibm.com/support/knowledgecenter/SSETD4_9.1.3/lsf_config_ref/lsf.conf.lsb_job_memlimit.5.dita).
 :::
 
-(moab-executor)=
-
 ## Moab
 
-:::{versionadded} 19.07.0
-:::
-
-:::{warning} *Experimental: may change in a future release.*
+:::warning{title="Experimental: may change in a future release"}
 :::
 
 The `moab` executor allows you to run your pipeline script using the [Moab](https://en.wikipedia.org/wiki/Moab_Cluster_Suite) resource manager by [Adaptive Computing](http://www.adaptivecomputing.com/).
@@ -289,13 +259,11 @@ To enable the `Moab` executor, set `process.executor = 'moab'` in the `nextflow.
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-time`
-
-(nqsii-executor)=
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
 
 ## NQSII
 
@@ -309,19 +277,14 @@ To enable the NQSII executor, set `process.executor = 'nqsii'` in the `nextflow.
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-time`
-
-(oar-executor)=
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
 
 ## OAR
 
-:::{versionadded} 19.11.0-edge
-:::
-
 The `oar` executor allows you to run your pipeline script using the [OAR](https://oar.imag.fr) resource manager.
 
 Nextflow manages each process as a separate job that is submitted to the cluster using the `oarsub` command.
@@ -332,28 +295,25 @@ To enable the OAR executor set `process.executor = 'oar'` in the `nextflow.confi
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-time`
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
 
 When specifying `clusterOptions` as a string, multiple options must be separated by semicolons to ensure that the job script is formatted correctly:
 ```groovy
 clusterOptions = '-t besteffort;--project myproject'
 ```
 
-:::{versionadded} 24.04.0
-:::
+<AddedInVersion version="24.04.0" />
 
 The same behavior can now be achieved using a string list:
 ```groovy
 clusterOptions = [ '-t besteffort', '--project myproject' ]
 ```
 
-See {ref}`process-clusteroptions` for details.
-
-(pbs-executor)=
+See [clusterOptions][process-clusteroptions] for details.
 
 ## PBS/Torque
 
@@ -367,13 +327,11 @@ To enable the PBS executor, set `process.executor = 'pbs'` in the `nextflow.conf
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-time`
-
-(pbspro-executor)=
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
 
 ## PBS Pro
 
@@ -387,13 +345,11 @@ To enable the PBS Pro executor, set `process.executor = 'pbspro'` in the `nextfl
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-time`
-
-(sge-executor)=
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
 
 ## SGE
 
@@ -407,14 +363,12 @@ To enable the SGE executor, set `process.executor = 'sge'` in the `nextflow.conf
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-penv`
-- {ref}`process-queue`
-- {ref}`process-time`
-
-(slurm-executor)=
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [penv][process-penv]
+- [queue][process-queue]
+- [time][process-time]
 
 ## SLURM
 
@@ -428,25 +382,23 @@ To enable the SLURM executor, set `process.executor = 'slurm'` in the `nextflow.
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-time`
+- [clusterOptions][process-clusteroptions]
+- [cpus][process-cpus]
+- [memory][process-memory]
+- [queue][process-queue]
+- [time][process-time]
 
-:::{note}
+:::note
 SLURM partitions can be specified with the `queue` directive.
 :::
 
-:::{note}
+:::note
 Nextflow does not provide direct support for SLURM multi-clusters. If you need to submit workflow executions to a cluster other than the current one, specify it with the `SLURM_CLUSTERS` variable in the launch environment.
 :::
 
-:::{versionadded} 23.07.0-edge
+<AddedInVersion version="23.07.0-edge">
 Some SLURM clusters require memory allocations to be specified with `--mem-per-cpu` instead of `--mem`. You can specify `executor.perCpuMemAllocation = true` in the Nextflow configuration to enable this behavior. Nextflow will automatically compute the memory per CPU for each task (by default 1 CPU is used).
-:::
-
-(tcs-executor)=
+</AddedInVersion>
 
 ## TCS
 
@@ -460,11 +412,12 @@ To enable the TCS executor, set `process.executor = 'tcs'` in the `nextflow.conf
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 
-- {ref}`process-clusterOptions`
-- {ref}`process-time`
+- [clusterOptions][process-clusteroptions]
+- [time][process-time]
 
-:::{note}
-Use `clusterOptions` to specify system-dependent options such as queue (resource group), CPU, and node. These options vary across target systems and are not standardized. They correspond to `-L` options in the arguments of the `pjsub` command and should be configured according to the requirements of the specific cluster environment.
+:::note
+Use `clusterOptions` to specify system-dependent options such as queue (resource group), CPU, and node. These options vary across target systems and are not standardized.
+They correspond to `-L` options in the arguments of the `pjsub` command and should be configured according to the requirements of the specific cluster environment.
 
 For example:
 
@@ -477,3 +430,24 @@ process {
 ```
 :::
 
+[aws-batch]: /nextflow_docs/nextflow_repo/docs/aws.mdx#aws-batch
+[azure-batch]: /nextflow_docs/nextflow_repo/docs/azure.mdx#azure-batch
+[config-executor]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#executor
+[container-docker]: /nextflow_docs/nextflow_repo/docs/container.mdx#docker
+[container-podman]: /nextflow_docs/nextflow_repo/docs/container.mdx#podman
+[google-batch]: /nextflow_docs/nextflow_repo/docs/google.mdx#cloud-batch
+[k8s-page]: /nextflow_docs/nextflow_repo/docs/kubernetes.mdx
+[process-accelerator]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#accelerator
+[process-arch]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#arch
+[process-clusteroptions]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#clusteroptions
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-containeroptions]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#containeroptions
+[process-cpus]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cpus
+[process-disk]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#disk
+[process-machinetype]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#machinetype
+[process-memory]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#memory
+[process-penv]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#penv
+[process-pod]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#pod
+[process-queue]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#queue
+[process-resourcelabels]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#resourcelabels
+[process-time]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#time
\ No newline at end of file
diff --git a/docs/fusion.md b/new-docs/nextflow-docs/fusion.mdx
similarity index 90%
rename from docs/fusion.md
rename to new-docs/nextflow-docs/fusion.mdx
index 1f9144749e..e19ce10653 100644
--- a/docs/fusion.md
+++ b/new-docs/nextflow-docs/fusion.mdx
@@ -1,13 +1,10 @@
-(fusion-page)=
+
 
 # Fusion file system
 
-:::{versionadded} 22.10.0
-:::
+<AddedInVersion version="22.10.0" />
 
-:::{versionadded} 23.02.0-edge
-Support for Google Cloud Storage.
-:::
+<AddedInVersion version="23.02.0-edge" />
 
 Cloud object stores such as AWS S3 are scalable and cost-effective, but they don't present a POSIX (Portable Operating System Interface). This means containerized applications must copy data to and from cloud storage for every task — a slow and inefficient process.
 
@@ -15,7 +12,7 @@ Fusion is a virtual, lightweight, distributed file system that bridges the gap b
 
 See [Fusion file system](https://docs.seqera.io/fusion) for more information about Fusion features.
 
-:::{note}
+:::note
 Fusion requires a license for use in Seqera Platform compute environments or directly in Nextflow. Fusion can be trialed at no cost. See the [Fusion licensing documentation](https://docs.seqera.io/fusion/licensing) for more information.
 :::
 
@@ -25,8 +22,7 @@ Fusion integrates with Nextflow directly and does not require any installation o
 
 To enable Fusion in your Nextflow pipeline, add the following to your `nextflow.config` file:
 
-```{code-block} nextflow
-:class: copyable
+```nextflow
 fusion.enabled = true
 wave.enabled = true
 tower.accessToken = '<PLATFORM_ACCESS_TOKEN>'
diff --git a/docs/git.md b/new-docs/nextflow-docs/git.mdx
similarity index 85%
rename from docs/git.md
rename to new-docs/nextflow-docs/git.mdx
index a7ee556ae2..499d089331 100644
--- a/docs/git.md
+++ b/new-docs/nextflow-docs/git.mdx
@@ -1,4 +1,4 @@
-(git-page)=
+
 
 # Git
 
@@ -11,41 +11,51 @@ The configuration properties for each Git provider are defined inside the `provi
 ```groovy
 providers {
     <provider-name> {
-        property = value
-        // ...
+property = value
+// ...
     }
 }
 ```
 
 In the above template replace `<provider-name>` with one of the "default" servers (i.e. `bitbucket`, `github` or `gitlab`) or a custom identifier representing a private SCM server installation.
 
-:::{versionadded} 20.10.0
-A custom location for the SCM file can be specified using the `NXF_SCM_FILE` environment variable.
-:::
-
 The following configuration properties are supported for each provider configuration:
 
-`providers.<provider>.user`
-: User name required to access private repositories on the SCM server.
+##### `providers.<provider>.user`
+
+User name required to access private repositories on the SCM server.
+
+##### `providers.<provider>.token`
+
+*Required only for private Gitlab servers and supported for BitBucket*
+
+Private API access token.
+
+User password required to access private repositories on the SCM server.
+
+##### `providers.<provider>.token`
+
+*Required only for private Gitlab servers.*
 
-`providers.<provider>.password`
-: User password required to access private repositories on the SCM server.
+Private API access token.
 
-`providers.<provider>.token`
-: *Required only for private Gitlab servers and supported for BitBucket*
-: Private API access token.
+##### `providers.<provider>.platform`
 
-`providers.<provider>.platform`
-: *Required only for private SCM servers*
-: Git provider name, either: `github`, `gitlab` or `bitbucket`.
+*Required only for private SCM servers.*
 
-`providers.<provider>.server`
-: *Required only for private SCM servers*
-: SCM server name including the protocol prefix e.g. `https://github.com`.
+Git provider name, either: `github`, `gitlab`, or `bitbucket`.
 
-`providers.<provider>.endpoint`
-: *Required only for private SCM servers*
-: SCM API `endpoint` URL e.g. `https://api.github.com` (default: the same as `providers.<provider>.server`).
+##### `providers.<provider>.server`
+
+*Required only for private SCM servers.*
+
+SCM server name including the protocol prefix, e.g., `https://github.com`.
+
+##### `providers.<provider>.endpoint`
+
+*Required only for private SCM servers.*
+
+SCM API `endpoint` URL, e.g., `https://api.github.com` (default: the same as `providers.<provider>.server`).
 
 ## Git providers
 
@@ -62,11 +72,11 @@ providers {
 }
 ```
 
-:::{versionadded} 25.07.0-edge
+<AddedInVersion version="25.07.0-edge">
 API tokens are supported for BitBucket authentication. When both `token` and `password` are provided, the API token takes priority over the app password.
-:::
+</AddedInVersion>
 
-:::{note}
+:::note
 API tokens are substitute passwords for a user account which you can use for scripts and integrating tools in order to avoid putting your real password into configuration files. Learn more about [app passwords](https://support.atlassian.com/bitbucket-cloud/docs/app-passwords/) and [API tokens](https://support.atlassian.com/bitbucket-cloud/docs/using-api-tokens/).
 :::
 
@@ -74,11 +84,11 @@ API tokens are substitute passwords for a user account which you can use for scr
 
 [Bitbucket Server](https://confluence.atlassian.com/bitbucketserver) is a self-hosted Git repository and management platform.
 
-:::{note}
-Bitbucket Server uses a different API from the [Bitbucket](https://bitbucket.org/) Cloud service. Make sure to use the right configuration whether you are using the cloud service or a self-hosted installation.
+:::note
+Bitbucket Servers use a different API from the [Bitbucket](https://bitbucket.org/) Cloud service. Make sure to use the right configuration whether you are using the cloud service or a self-hosted installation.
 :::
 
-To access your local Bitbucket Server create an entry in the [SCM configuration file](#git-configuration) as shown below:
+To access your local Bitbucket Server, create an entry in the [SCM configuration file](#git-configuration) as shown below:
 
 ```groovy
 providers {
@@ -107,9 +117,9 @@ providers {
 
 GitHub requires the use of a personal access token (PAT) in place of a password when accessing APIs. Learn more about PAT and how to create it at [this link](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token).
 
-:::{versionadded} 23.01.0-edge
+<AddedInVersion version="23.01.0-edge">
 Nextflow automatically uses the `GITHUB_TOKEN` environment variable to authenticate access to the GitHub repository if no credentials are provided via the `scm` file. This is useful especially when accessing pipeline code from a GitHub Action. Read more about the token authentication in the [GitHub documentation](https://docs.github.com/en/actions/security-guides/automatic-token-authentication).
-:::
+</AddedInVersion>
 
 ### GitLab
 
@@ -125,7 +135,7 @@ providers {
 }
 ```
 
-:::{tip}
+:::tip
 The GitLab *token* string can be used as the `password` value in the above setting. When doing that the `token` field can be omitted.
 :::
 
@@ -161,17 +171,12 @@ providers {
 }
 ```
 
-:::{tip}
+:::tip
 The Personal access token can be generated in the repository `Clone Repository` dialog.
 :::
 
-(aws-codecommit)=
-
 ### AWS CodeCommit
 
-:::{versionadded} 22.06.0-edge
-:::
-
 Nextflow supports [AWS CodeCommit](https://aws.amazon.com/codecommit/) as a Git provider to access and to share pipelines code.
 
 To access your project hosted on AWS CodeCommit with Nextflow provide the repository credentials using the configuration snippet shown below:
@@ -188,7 +193,7 @@ providers {
 
 In the above snippet replace `<AWS ACCESS KEY>` and `<AWS SECRET KEY>` with your AWS credentials, and `my_aws_repo` with a name of your choice.
 
-:::{tip}
+:::tip
 The `user` and `password` settings are optional. If omitted, the [AWS default credentials provider chain](https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/credentials.html) is used.
 :::
 
@@ -200,7 +205,7 @@ nextflow run https://git-codecommit.eu-west-1.amazonaws.com/v1/repos/my-repo
 
 In the above example replace `my-repo` with your own repository. Note also that AWS CodeCommit has different URLs depending on the region in which you are working.
 
-:::{note}
+:::note
 The support for protocols other than HTTPS is not available at this time.
 :::
 
@@ -236,10 +241,10 @@ Or, alternatively, using the Git clone URL:
 nextflow run http://gitlab.acme.org/acme/hello.git
 ```
 
-:::{note}
+:::note
 You must also specify the server API endpoint URL if it differs from the server base URL. For example, for GitHub Enterprise V3, add `endpoint = 'https://git.your-domain.com/api/v3'`.
 :::
 
-:::{warning}
+:::warning
 When accessing a private SCM installation over `https` from a server that uses a custom SSL certificate, you may need to import the certificate into your local Java keystore. See [Import the Certificate as a Trusted Certificate](https://docs.oracle.com/javase/tutorial/security/toolsign/rstep2.html) for more information.
 :::
diff --git a/docs/google.md b/new-docs/nextflow-docs/google.mdx
similarity index 78%
rename from docs/google.md
rename to new-docs/nextflow-docs/google.mdx
index d2188a4e8f..06fd25d49e 100644
--- a/docs/google.md
+++ b/new-docs/nextflow-docs/google.mdx
@@ -1,20 +1,18 @@
-(google-page)=
 
-# Google Cloud
 
-(google-credentials)=
+# Google Cloud
 
 ## Credentials
 
 Credentials for submitting requests to the Google Cloud Batch API are picked up from your environment using [Application Default Credentials](https://github.com/googleapis/google-auth-library-java#google-auth-library-oauth2-http). Application Default Credentials are designed to use the credentials most natural to the environment in which a tool runs.
 
-The most common case will be to pick up your end-user Google credentials from your workstation. You can create these by running the command:
+The most common case will be to pick up your end-user Google credentials from your workstation. You can create these by running the following command and running through the authentication flow:
 
 ```bash
 gcloud auth application-default login
 ```
 
-and running through the authentication flow. This will write a credential file to your gcloud configuration directory that will be used for any tool you run on your workstation that picks up default credentials.
+This will write a credential file to your gcloud configuration directory that will be used for any tool you run on your workstation that picks up default credentials.
 
 The next most common case would be when running on a Compute Engine VM. In this case, Application Default Credentials will pick up the Compute Engine Service Account credentials for that VM.
 
@@ -37,29 +35,24 @@ Then, define the following variable replacing the path in the example with the o
 export GOOGLE_APPLICATION_CREDENTIALS="/path/your/file/creds.json"
 ```
 
-See [Get started with Nextflow on Google Cloud Batch](https://www.nextflow.io/blog/2023/nextflow-with-gbatch.html) for more information on how to use Google Cloud Batch, 
+See [Get started with Nextflow on Google Cloud Batch](https://www.nextflow.io/blog/2023/nextflow-with-gbatch.html) for more information on how to use Google Cloud Batch,
 including how to set the required roles for your service account.
 
-(google-batch)=
-
 ## Cloud Batch
 
-:::{versionadded} 22.07.1-edge
-:::
+<AddedInVersion version="22.07.1-edge" />
 
 [Google Cloud Batch](https://cloud.google.com/batch) is a managed computing service that allows the execution of containerized workloads in the Google Cloud Platform infrastructure.
 
 Nextflow provides built-in support for Google Cloud Batch, allowing the seamless deployment of Nextflow pipelines in the cloud, in which tasks are offloaded to the Cloud Batch service.
 
-Read the {ref}`Google Cloud Batch executor <google-batch-executor>` section to learn more about the `google-batch` executor in Nextflow.
-
-(google-batch-config)=
+Read the [Google Cloud Batch executor][google-batch-executor] section to learn more about the `google-batch` executor in Nextflow.
 
 ### Configuration
 
 Make sure to have defined in your environment the `GOOGLE_APPLICATION_CREDENTIALS` variable. See the [Credentials](#credentials) section for details.
 
-:::{note}
+:::note
 Make sure your Google account is allowed to access the Google Cloud Batch service by checking the [APIs & Services](https://console.cloud.google.com/apis/dashboard) dashboard.
 :::
 
@@ -85,13 +78,11 @@ google {
 
 Notes:
 
-- A container image must be specified to execute processes. You can use a different Docker image for each process using one or more {ref}`config-process-selectors`.
+- A container image must be specified to execute processes. You can use a different Docker image for each process using one or more [process selectors][config-process-selectors].
 - Make sure to specify the project ID, not the project name.
 - Make sure to specify a location where Google Batch is available. Refer to the [Google Batch documentation](https://cloud.google.com/batch/docs/get-started#locations) for region availability.
 
-Read the {ref}`Google configuration<config-google>` section to learn more about advanced configuration options.
-
-(google-batch-process)=
+Read the [Google configuration][config-google] section to learn more about advanced configuration options.
 
 ### Process definition
 
@@ -122,8 +113,7 @@ process other_task {
 }
 ```
 
-:::{versionadded} 23.02.0-edge
-:::
+<AddedInVersion version="23.02.0-edge" />
 
 The `machineType` directive can also be a comma-separated list of patterns. The pattern can contain a `*` to match any
 number of characters and `?` to match any single character. Examples of valid patterns: `c2-*`, `m?-standard*`, `n*`.
@@ -141,8 +131,7 @@ process my_task {
 }
 ```
 
-:::{versionadded} 23.12.0-edge
-:::
+<AddedInVersion version="23.12.0-edge" />
 
 The `machineType` directive can also be an [Instance Template](https://cloud.google.com/compute/docs/instance-templates),
 specified as `template://<instance-template>`. For example:
@@ -160,7 +149,7 @@ process my_task {
 }
 ```
 
-:::{note}
+:::note
 Using an instance template will overwrite the `accelerator` and `disk` directives, as well as the following Google Batch
 config options: `bootDiskImage`, `cpuPlatform`, `preemptible`, and `spot`.
 :::
@@ -170,9 +159,7 @@ To use an instance template with GPUs, you must also set the `google.batch.insta
 To use an instance template with Fusion, the instance template must include a `local-ssd` disk named `fusion` with 375 GB.
 See the [Google Batch documentation](https://cloud.google.com/compute/docs/disks/local-ssd) for more details about local SSDs.
 
-
-:::{versionadded} 23.06.0-edge
-:::
+<AddedInVersion version="23.06.0-edge" />
 
 The `disk` directive can be used to set the boot disk size or provision a disk for scratch storage. If the disk type is specified with the `type` option, a new disk will be mounted to the task VM at `/tmp` with the requested size and type. Otherwise, it will set the boot disk size, overriding the `google.batch.bootDiskSize` config option. See the [Google Batch documentation](https://cloud.google.com/compute/docs/disks) for more information about the available disk types.
 
@@ -199,11 +186,11 @@ The pipeline execution must specify a Google Storage bucket where the workflow's
 nextflow run <script or project name> -work-dir gs://my-bucket/some/path
 ```
 
-:::{tip}
+:::tip
 Any input data **not** stored in a Google Storage bucket will automatically be transferred to the pipeline work bucket. Use this feature with caution being careful to avoid unnecessary data transfers.
 :::
 
-:::{warning}
+:::warning
 The Google Storage path needs to contain at least sub-directory. Do not use only the bucket name e.g. `gs://my-bucket`.
 :::
 
@@ -217,8 +204,7 @@ google {
 }
 ```
 
-:::{versionadded} 23.11.0-edge
-:::
+<AddedInVersion version="23.11.0-edge" />
 
 Since this type of virtual machines can be retired by the provider before the job completion, it is advisable to add the following retry strategy to your config file to instruct Nextflow to automatically re-execute a job if the virtual machine was terminated preemptively:
 
@@ -231,10 +217,9 @@ process {
 
 ### Fusion file system
 
-:::{versionadded} 23.02.0-edge
-:::
+<AddedInVersion version="23.02.0-edge" />
 
-The Google Batch executor supports the use of {ref}`fusion-page`. Fusion allows the use of Google Cloud Storage as a virtual distributed file system, optimizing the data transfer and speeding up most job I/O operations.
+The Google Batch executor supports the use of [Fusion][fusion-page]. Fusion allows the use of Google Cloud Storage as a virtual distributed file system, optimizing the data transfer and speeding up most job I/O operations.
 
 See [Google Cloud Batch](https://docs.seqera.io/fusion/guide/gcp-batch) for more information about configuring Fusion for Google Cloud Batch.
 
@@ -242,21 +227,21 @@ See [Google Cloud Batch](https://docs.seqera.io/fusion/guide/gcp-batch) for more
 
 Currently, the following Nextflow directives are supported by the Google Batch executor:
 
-- {ref}`process-accelerator`
-- {ref}`process-container`
-- {ref}`process-containeroptions`
-- {ref}`process-cpus`
-- {ref}`process-disk`
-- {ref}`process-executor`
-- {ref}`process-machinetype`
-- {ref}`process-memory`
-- {ref}`process-time`
+- [accelerator][process-accelerator]
+- [container][process-container]
+- [containerOptions][process-containeroptions]
+- [cpus][process-cpus]
+- [disk][process-disk]
+- [executor][process-executor]
+- [machineType][process-machinetype]
+- [memory][process-memory]
+- [time][process-time]
 
 ### Hybrid execution
 
 Nextflow allows the use of multiple executors in the same workflow. This feature enables the deployment of hybrid workloads, in which some jobs are executed in the local computer or local computing cluster, and some jobs are offloaded to Google Cloud.
 
-To enable this feature, use one or more {ref}`config-process-selectors` in your Nextflow configuration file to apply the Google Cloud executor to the subset of processes that you want to offload. For example:
+To enable this feature, use one or more [process selectors][config-process-selectors] in your Nextflow configuration file to apply the Google Cloud executor to the subset of processes that you want to offload. For example:
 
 ```groovy
 process {
@@ -278,11 +263,11 @@ Then launch the pipeline with the `-bucket-dir` option to specify a Google Stora
 nextflow run <script or project name> -bucket-dir gs://my-bucket/some/path
 ```
 
-:::{warning}
+:::warning
 The Google Storage path needs to contain at least one subdirectory (e.g. `gs://my-bucket/work` rather than `gs://my-bucket`).
 :::
 
-:::{note}
+:::note
 Nextflow will automatically manage the transfer of input and output files between the local and cloud environments when using hybrid workloads.
 :::
 
@@ -292,3 +277,16 @@ Nextflow will automatically manage the transfer of input and output files betwee
 
 - Currently, it's not possible to specify a disk type different from the default one assigned by the service depending on the chosen instance type.
 
+[config-google]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#google
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[google-batch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#google-cloud-batch
+[process-accelerator]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#accelerator
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-containeroptions]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#containeroptions
+[process-cpus]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cpus
+[process-disk]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#disk
+[process-executor]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#executor
+[process-machinetype]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#machinetype
+[process-memory]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#memory
+[process-time]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#time
diff --git a/new-docs/nextflow-docs/guides/aws-java-sdk-v2.mdx b/new-docs/nextflow-docs/guides/aws-java-sdk-v2.mdx
new file mode 100644
index 0000000000..9c54761abd
--- /dev/null
+++ b/new-docs/nextflow-docs/guides/aws-java-sdk-v2.mdx
@@ -0,0 +1,36 @@
+# AWS Java SDK v2
+
+AWS Java SDK v1 will reach end of life at the end of 2025. Starting in Nextflow 25.10, Nextflow uses AWS Java SDK v2 in the `nf-amazon` plugin.
+
+This migration introduces several breaking changes to the `aws.client` config scope, including new and removed options. This page describes these changes and how they affect your Nextflow configuration.
+
+## New HTTP client
+
+The HTTP client in SDK v2 does not support overriding certain advanced HTTP options. As a result, the following config options are no longer supported:
+
+- `aws.client.protocol`
+- `aws.client.signerOverride`
+- `aws.client.socketRecvBufferSizeHint`
+- `aws.client.socketSendBufferSizeHint`
+- `aws.client.userAgent`
+
+## Parallel S3 operations
+
+Nextflow manages S3 transfers, including uploads, downloads, and S3-to-S3 copies, separately from other S3 API calls such as listing a directory or retrieving object metadata.
+
+Use the `aws.client.targetThroughputInGbps` option to control the concurrency of S3 transfers based on the available network bandwidth. This setting defaults to `10`, which allows Nextflow to perform concurrent S3 transfers up to 10 Gbps of network throughput.
+
+Use the `aws.client.maxConnections` config option to control the maximum number of concurrent HTTP connections for all other S3 API calls.
+
+## Multi-part transfers
+
+Nextflow transfers large files to and from S3 as multipart transfers. Use the `aws.client.minimumPartSize` and `aws.client.multipartThreshold` configuration options to control when and how multipart transfers are performed.
+
+Concurrent multipart downloads can consume a large amount of heap memory due to the buffer allocated by each transfer. To avoid out-of-memory errors, the size consumed by these buffers is limited to 400 MB by default. Use the `aws.client.maxDownloadHeapMemory` option to control this value.
+
+The following multipart upload config options are no longer supported:
+
+- `aws.client.uploadChunkSize`
+- `aws.client.uploadMaxAttempts`
+- `aws.client.uploadMaxThreads`
+- `aws.client.uploadRetrySleep`
diff --git a/docs/guides/gradle-plugin.md b/new-docs/nextflow-docs/guides/gradle-plugin.mdx
similarity index 68%
rename from docs/guides/gradle-plugin.md
rename to new-docs/nextflow-docs/guides/gradle-plugin.mdx
index f0801c241d..41ac44044e 100644
--- a/docs/guides/gradle-plugin.md
+++ b/new-docs/nextflow-docs/guides/gradle-plugin.mdx
@@ -1,4 +1,4 @@
-(gradle-plugin-page)=
+
 
 # Using the Nextflow Gradle plugin
 
@@ -6,18 +6,15 @@ Nextflow provides a new `plugin create` command that simplifies the creation of
 
 The [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle) configures default dependencies needed for Nextflow integration and defines Gradle tasks for building, testing, and publishing Nextflow plugins. The Gradle plugin is versioned and published to the [Gradle Plugin Portal](https://plugins.gradle.org/), allowing developers to manage it like any other dependency. As the plugin ecosystem evolves, the Gradle plugin will enable easier maintenance and adoption of improvements. This page introduces [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle) and how to use it.
 
-:::{note}
-The Nextflow Gradle plugin and plugin registry are currently available as a public preview. See the {ref}`Migrating to the Nextflow plugin registry <plugin-registry-page>` for more information.
+:::note
+The Nextflow Gradle plugin and plugin registry are currently available as a public preview. See the [Migrating to the Nextflow plugin registry][plugin-page-migrate] for more information.
 :::
 
-(gradle-plugin-create)=
-
 ## Creating a plugin
 
-:::{versionadded} 25.04.0
-:::
+<AddedInVersion version="25.04.0" />
 
-The best way to create a plugin with the Nextflow Gradle plugin is to use the `nextflow plugin create` sub-command and create a plugin project based on the [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/). See {ref}`dev-plugins-template` for more information about the Nextflow plugin template.
+The best way to create a plugin with the Nextflow Gradle plugin is to use the `nextflow plugin create` sub-command and create a plugin project based on the [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/). See [Nextflow plugin template][dev-plugins-template] for more information about the Nextflow plugin template.
 
 To create Nextflow plugins with the Gradle plugin:
 
@@ -25,9 +22,9 @@ To create Nextflow plugins with the Gradle plugin:
 
 2. Follow the prompts to add your plugin name, organization name, and project path.
 
-3. Develop your plugin extension points. See {ref}`dev-plugins-extension-points` for more information.
+3. Develop your plugin extension points. See [Extension points][dev-plugins-extension-points] for more information.
 
-4. Develop your tests. See {ref}`gradle-plugin-test` for more information.
+4. Develop your tests. See [Testing a plugin][gradle-plugin-test] for more information.
 
 5. In the plugin root directory, run `make assemble`.
 
@@ -39,7 +36,7 @@ To install plugins locally:
 
 1. In the plugin root directory, run `make install`.
 
-    :::{note}
+    :::note
     Running `make install` will add your plugin to your `$HOME/.nextflow/plugins` directory.
     :::
 
@@ -51,12 +48,10 @@ To install plugins locally:
 
     Replace `<PLUGIN_NAME>@<VERSION>` with your plugin name and version.
 
-    :::{note}
-    Plugins can also be configured via Nextflow configuration files. See {ref}`using-plugins-page` for more information.
+    :::note
+    Plugins can also be configured via Nextflow configuration files. See [Using plugins][using-plugins-page] for more information.
     :::
 
-(gradle-plugin-test)=
-
 ## Testing a plugin
 
 Testing your Nextflow plugin requires unit tests and end-to-end tests.
@@ -77,15 +72,13 @@ End-to-end tests are comprehensive tests that verify the behavior of an entire p
 
 End-to-end tests should be tailored to the needs of your plugin, but generally take the form of a small Nextflow pipeline. See the `validation` directory in the [plugin template](https://github.com/nextflow-io/nf-plugin-template) for an example end-to-end test.
 
-(gradle-plugin-publish)=
-
 ## Publishing a plugin
 
 The Nextflow Gradle plugin allows you to publish plugins to the [Nextflow plugin registry](https://registry.nextflow.io/) from the command line.
 
 To publish plugins to the [Nextflow plugin registry](https://registry.nextflow.io/):
 
-1. {ref}`Claim your plugin <plugin-registry-claim>` in the registry.
+1. [Claim your plugin][plugin-registry-claim] in the registry.
 
     :::{note}
     You can claim a plugin even if it doesn't exist in the registry yet.
@@ -99,10 +92,20 @@ To publish plugins to the [Nextflow plugin registry](https://registry.nextflow.i
     npr.apiKey=<API_KEY>
     ```
 
-    Replace `<API_KEY>` with your plugin registry API key. See {ref}`plugin-registry-access-token` for more information.
+    Replace `<API_KEY>` with your plugin registry API key. See [Creating an access token][plugin-registry-access-token] for more information.
 
 4. Run `make release`.
 
 ## Additional resources
 
 For additional Nextflow Gradle plugin configuration options, see the [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle) repository.
+
+[plugin-registry-claim]: /nextflow_docs/nextflow_repo/docs/plugins/plugin-registry.html#claiming-a-plugin
+[dev-plugins-extension-points]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#extension-points
+[dev-plugins-template]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#nextflow-plugin-template
+[gradle-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx
+[gradle-plugin-test]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#testing-a-plugin
+[plugin-page-migrate]: /nextflow_docs/nextflow_repo/docs/guides/migrate-plugin.mdx
+[plugin-registry-access-token]: /nextflow_docs/nextflow_repo/docs/plugins/plugin-registry.mdx#creating-an-access-token
+[plugin-registry-page]: /nextflow_docs/nextflow_repo/docs/plugins/plugin-registry.mdx
+[using-plugins-page]: /nextflow_docs/nextflow_repo/docs/plugins/using-plugins.mdx
diff --git a/new-docs/nextflow-docs/guides/migrate-plugin.mdx b/new-docs/nextflow-docs/guides/migrate-plugin.mdx
new file mode 100644
index 0000000000..dcf3cb142e
--- /dev/null
+++ b/new-docs/nextflow-docs/guides/migrate-plugin.mdx
@@ -0,0 +1,143 @@
+(migrate-plugin-page)=
+
+# Migrating to the Nextflow plugin registry
+
+The [Nextflow plugin registry](https://registry.nextflow.io/) is a central repository for Nextflow plugins. It hosts an index of plugin metadata that supports plugin discovery, accessibility, and version tracking. The [legacy plugin index](https://github.com/nextflow-io/plugins) will be deprecated in favor of the Nextflow plugin registry.
+
+Starting with Nextflow 25.04, the plugin registry can be used as a direct replacement for the legacy plugin index. This page describes the migration timeline, it's impact on users and developers, and how to migrate existing plugins.
+
+## Migration timeline
+
+The migration timeline is tentative and subject to modification.
+
+<h3>Nextflow 25.04</h3>
+
+The Nextflow plugin registry is available as a private beta. Nextflow 25.04 can use the Nextflow plugin registry as an opt-in feature. The Nextflow plugin registry will be automatically kept up-to-date with the [legacy plugin index](https://github.com/nextflow-io/plugins).
+
+During this time, plugin developers are encouraged to experiment with the Gradle plugin and plugin registry.
+
+<h3>Nextflow 25.10</h3>
+
+The Nextflow plugin registry will be generally available. Nextflow 25.10 will use the plugin registry by default. The legacy plugin index will be **closed to new pull requests**.
+
+Developers will be required to publish to the Nextflow plugin registry. To ensure continued support for older versions of Nextflow, the legacy plugin index will be automatically kept up-to-date with the Nextflow plugin registry.
+
+<h3>Nextflow 26.04</h3>
+
+Nextflow 26.04 will only be able to use the Nextflow plugin registry.
+
+At some point in the future, the legacy plugin index will be **frozen** -- it will no longer receives updates from the Nextflow plugin registry. To ensure continued support for older versions of Nextflow, the legacy plugin index will remain available indefinitely.
+
+## Migration impact on plugin users
+
+No immediate actions are required for plugin users. The plugin configuration has not changed.
+
+## Impact on plugin developers
+
+Plugin developers will need to update their plugin to publish to the Nextflow plugin registry instead of the legacy plugin index. The best way to do this is to migrate to the [Nextflow Gradle plugin][gradle-plugin-page], which simplifies the development process and supports publishing to the plugin registry from the command line.
+
+## Migrating to the Nextflow Gradle plugin
+
+To migrate an existing Nextflow plugin to the [Nextflow Gradle plugin][gradle-plugin-page]:
+
+1. Remove the following files and folders:
+    - `buildSrc/`
+    - `launch.sh`
+    - `plugins/build.gradle`
+
+2. If your plugin has a `plugins` directory, move the `src` directory to the project root.
+
+    :::note
+    Plugin sources should be in `src/main/groovy` or `src/main/java`.
+    :::
+
+3. Replace the contents of `settings.gradle` with the following:
+
+    ```groovy
+    rootProject.name = '<PLUGIN_NAME>'
+    ```
+
+    Replace `<PLUGIN_NAME>` with your plugin name.
+
+4. In the project root, create a new `build.gradle` file with the following configuration:
+
+    ```groovy
+    // Plugins
+    plugins {
+        id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.6'
+    }
+
+    // Dependencies (optional)
+    dependencies {
+        <DEPENDENCY>
+    }
+
+    // Plugin version
+    version = '<PLUGIN_VERSION>'
+
+    nextflowPlugin {
+        // Minimum Nextflow version
+        nextflowVersion = '<MINIMUM_NEXTFLOW_VERSION>'
+
+        // Plugin metadata
+        provider = '<PROVIDER>'
+        className = '<CLASS_NAME>'
+        extensionPoints = [
+            '<EXTENSION_POINT>'
+        ]
+
+    }
+    ```
+
+    Replace the following:
+
+    - `<DEPENDENCY>`: (Optional) Your plugins dependency libraries. For example, `commons-io:commons-io:2.18.0`.
+    - `<PLUGIN_VERSION>:` Your plugin version. For example, `0.5.0`.
+    - `<MINIMUM_NEXTFLOW_VERSION>`: The minimum Nextflow version required to run your plugin. For example, `25.04.0`.
+    - `<PROVIDER>`: Your name or organization. For example, `acme`.
+    - `<CLASS_NAME>`: Your plugin class name. For example, `acme.plugin.MyPlugin`.
+    - `<EXTENSION_POINT>`: Your extension point identifiers that the plugin will implement or expose. For example, `acme.plugin.MyFactory`.
+
+5. Replace the contents of `Makefile` with the following:
+
+    ```Makefile
+    # Build the plugin
+    assemble:
+        ./gradlew assemble
+
+    clean:
+        rm -rf .nextflow*
+        rm -rf work
+        rm -rf build
+        ./gradlew clean
+
+    # Run plugin unit tests
+    test:
+        ./gradlew test
+
+    # Install the plugin into local nextflow plugins dir
+    install:
+        ./gradlew install
+
+    # Publish the plugin
+    release:
+        ./gradlew releasePlugin
+    ```
+
+6. Update `README.md` with information about the structure of your plugin.
+
+7. In the plugin root directory, run `make assemble`.
+
+Alternatively, use the `nextflow plugin create` command to re-create your plugin with the plugin template and add your existing plugin code. See [Nextflow plugin template][dev-plugins-template] for more information about the plugin template.
+
+## Publishing to the Nextflow plugin registry
+
+The Nextflow Gradle plugin supports publishing plugins from the command line. See [Publishing a plugin][gradle-plugin-publish] for more information.
+
+:::warning
+Once you migrate to the Gradle plugin, you will no longer be able to publish to the legacy plugin index. See the [Migration timeline](#migration-timeline) for more information.
+:::
+
+[dev-plugins-template]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#nextflow-plugin-template
+[gradle-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx
+[gradle-plugin-publish]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#publishing-a-plugin
diff --git a/new-docs/nextflow-docs/guides/updating-spot-retries.mdx b/new-docs/nextflow-docs/guides/updating-spot-retries.mdx
new file mode 100644
index 0000000000..75b0802fd1
--- /dev/null
+++ b/new-docs/nextflow-docs/guides/updating-spot-retries.mdx
@@ -0,0 +1,84 @@
+# Spot Instance failures and retries
+
+This page describes changes in how Nextflow handles Spot Instance failures and retries on AWS and Google Cloud, the impact of those changes, and how to configure spot retry behavior for your pipelines. These changes apply to Nextflow 24.10 and later.
+
+## Retry behavior
+
+Up to version 24.10, Nextflow would silently retry Spot Instance failures up to `5` times when using AWS Batch or Google Batch. These retries were controlled by cloud-specific configuration parameters (e.g., `aws.batch.maxSpotAttempts`) and happened in cloud infrastructure without explicit visibility to Nextflow.
+
+### Before Nextflow 24.10
+
+By default, Nextflow would instruct AWS and Google to automatically retry jobs lost to Spot reclamation up to `5` times. Retries were handled by the cloud provider _within_ a Nextflow task. It was often unclear that tasks were restarted as there was no explicit message. Task runtimes and associated cloud costs were increased because they included the runtime of the reclaimed and retried tasks. Due to the high likelihood of reclamation before completion, long-running tasks running on Spot Instances frequently required retries, leading to inefficient allocation of resources and higher costs.
+
+### After Nextflow 24.10
+
+The default Spot reclamation retry setting changed to `0` on AWS and Google. By default, no _internal_ retries are attempted on these platforms. Spot reclamations lead to an immediate failure, exposed to Nextflow in the same way as other generic failures (for example, returning `exit code 1` on AWS). Nextflow treats these failures like any other job failure, unless a retry strategy is configured.
+
+## Impact on existing workflows
+
+If you rely on silent Spot retries (the previous default behavior), you may now see more tasks fail with the following characteristics:
+
+- **AWS**: Generic failure with `exit code 1`. You may see messages indicating the host machine was terminated.
+
+- **Google**: Spot reclamation typically produces a specific code, but is now surfaced as a recognizable task failure in Nextflow logs.
+
+Since the default for Spot retries is now `0`, you must actively enable a retry strategy if you want Nextflow to handle reclaimed Spot Instances automatically.
+
+## Possible actions
+
+There are four possible actions.
+
+### Do nothing
+
+If you do not configure anything, you will observe more pipeline failures when Spot Instances are reclaimed. This approach provides clearer visibility into failures. Failed tasks can be re-run with the `-resume` option. However, frequent task reclamation may lead to a higher failure rate and each retry requires manual intervention.
+
+:::note
+If you resume the pipeline using the resume option, it will pick up at the point the pipeline was interrupted and start with a retry of that task.
+:::
+
+### Re-enable Spot retries
+
+You can re-enable Spot retries for each provider in your Nextflow config:
+
+```groovy
+aws.batch.maxSpotAttempts = 5
+google.batch.maxSpotAttempts = 5
+```
+
+The above example sets the maximum number of Spot retries to `5` for both AWS and Google.
+
+### Make Spot failures visible and retry them
+
+You can set `maxRetries` to enable Nextflow-level retries for any failure:
+
+```groovy
+process.maxRetries = 5
+```
+
+The above example sets retries to `5` for any failures across all providers.
+
+### Use Fusion Snapshots
+
+*This option is only available for AWS Batch.*
+
+If you have long-running tasks where progress lost due to Spot reclamation is costly, consider [Fusion Snapshots](https://docs.seqera.io/fusion/guide/snapshots) (if supported by your environment). Fusion Snapshots allow you to resume a partially completed task on a new machine if a Spot Instance is reclaimed, thereby reducing wasted compute time.
+
+Key features of Fusion Snapshots:
+
+- Jobs do not need to start from scratch after reclamation.
+- Especially useful for tasks that take many hours or days to complete.
+- May significantly reduce costs and run times in high-reclamation environments.
+
+See [Fusion Snapshots for AWS Batch](https://docs.seqera.io/fusion/guide/snapshots) for more information.
+
+## Best practices
+
+Best practices for Spot Instance failures and retries:
+
+- **Evaluate job duration**: If your tasks are very long (multiple hours or more), Spot Instances can cause repeated interruptions. Consider using on-demand instances or Fusion Snapshots.
+
+- **Set sensible retry limits**: If you enable Spot retries, choose a retry count that balances the cost savings of Spot usage against the overhead of restarting tasks.
+
+- **Monitor logs and exit codes**: Failures due to Spot reclamation will now appear in Nextflow logs. Monitor failures and fine-tune your strategy.
+
+- **Consider partial usage of Spot**: Some workflows may mix on-demand instances for critical or long tasks and Spot Instances for shorter, less critical tasks. This can optimize cost while minimizing wasted compute time.
diff --git a/new-docs/nextflow-docs/index.mdx b/new-docs/nextflow-docs/index.mdx
new file mode 100644
index 0000000000..054e96edaa
--- /dev/null
+++ b/new-docs/nextflow-docs/index.mdx
@@ -0,0 +1,70 @@
+
+# Nextflow
+
+*"Dataflow variables are spectacularly expressive in concurrent programming"*
+<br />[Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum](https://dl.acm.org/doi/abs/10.1145/72551.72552)
+
+<div style={{ display: "flex", flexWrap: "wrap", gap: "8px", alignItems: "center" }}>
+    <a href="https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush">
+        <img src="https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg" alt="Nextflow CI" />
+    </a>
+    <a href="https://github.com/nextflow-io/nextflow/releases/latest">
+        <img src="https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout" alt="Nextflow version" />
+    </a>
+    <a href="https://twitter.com/nextflowio">
+        <img src="https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=58bd9f&&label=%40nextflow&style=popout" alt="Nextflow Twitter" />
+    </a>
+    <a href="https://www.nature.com/articles/nbt.3820">
+        <img src="https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=58bd9f&style=popout" alt="Nextflow publication" />
+    </a>
+    <a href="http://bioconda.github.io/recipes/nextflow/README.html">
+        <img src="https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=58bd9f&style=popout" alt="install with bioconda" />
+    </a>
+    <a href="https://github.com/nextflow-io/nextflow/blob/master/COPYING">
+        <img src="https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout" alt="Nextflow license" />
+    </a>
+</div>
+
+<br />
+
+Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It uses a dataflow programming model that simplifies writing parallel and distributed pipelines by allowing you to focus on data flow and computation. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, and cloud. Additionally, Nextflow supports a range of compute environments, software container runtimes, and package managers, allowing workflows to be executed in reproducible and isolated environments.
+
+## Get started
+
+To get started with Nextflow:
+
+1. See the Nextflow [overview][overview-page] to learn key concepts
+2. Download and [install][install-page] Nextflow
+3. Set up an [environment][devenv-page] with the [Nextflow VS Code extension][devenv-nextflow]
+4. Run [your first script][your-first-script]
+
+To continue learning about Nextflow, visit the [Nextflow community training portal](https://training.nextflow.io/latest/) and find a training course that is right for you. Seqera, the company that develops Nextflow, also runs a variety of training events. See [Seqera Events](https://seqera.io/events/) for more information.
+
+## Community
+
+You can post questions in the [Nextflow community forum](https://community.seqera.io) or the [Nextflow Slack](https://www.nextflow.io/slack-invite.html). Bugs and feature requests should be reported as [GitHub issues](https://github.com/nextflow-io/nextflow/issues/new/choose).
+
+The Nextflow community is highly active with regular community meetings, events, a podcast, and more. You can view this material on the [Nextflow](https://www.youtube.com/@Nextflow) YouTube channel.
+
+The [nf-core](https://nf-co.re/) project is a community effort aggregating high-quality Nextflow workflows that can be used by everyone.
+
+## Contributing
+
+Contributions to Nextflow are welcome. See [Contributing][contributing-page] for more details.
+
+## License
+
+Nextflow is released under the Apache 2.0 license. Nextflow is a [registered trademark](https://github.com/nextflow-io/trademark).
+
+## Citations
+
+If you use Nextflow in your work, please cite:
+
+P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nature Biotechnology 35, 316–319 (2017) doi:[10.1038/nbt.3820](http://www.nature.com/nbt/journal/v35/n4/full/nbt.3820.html)
+
+[contributing-page]: /nextflow_docs/nextflow_repo/docs/developer/index.mdx
+[overview-page]: /nextflow_docs/nextflow_repo/docs/overview.mdx
+[install-page]: /nextflow_docs/nextflow_repo/docs/install.mdx
+[devenv-page]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx
+[devenv-nextflow]: /nextflow_docs/nextflow_repo/docs/developer-env.mdx#nextflow
+[your-first-script]: /nextflow_docs/nextflow_repo/docs/your-first-script.mdx
diff --git a/docs/install.md b/new-docs/nextflow-docs/install.mdx
similarity index 77%
rename from docs/install.md
rename to new-docs/nextflow-docs/install.mdx
index 98e1c86134..d66965c395 100644
--- a/docs/install.md
+++ b/new-docs/nextflow-docs/install.mdx
@@ -1,27 +1,24 @@
-(install-page)=
+
 
 # Installation
 
 Nextflow can be used on any POSIX-compatible system (Linux, macOS, etc), and on Windows through [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux). This page describes how to install Nextflow.
 
-:::{note}
-New versions of Nextflow are released regularly. See {ref}`updating-nextflow-page` for more information about Nextflow release cadence, how to update Nextflow, and how select your version of Nextflow.
+:::note
+New versions of Nextflow are released regularly. See [Updating Nextflow][updating-nextflow] for more information about Nextflow release cadence, how to update Nextflow, and how select your version of Nextflow.
 :::
 
-(install-requirements)=
-
 ## Requirements
 
 Nextflow requires Bash 3.2 (or later) and [Java 17 (or later, up to 25)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. To see which version of Java you have, run the following command:
 
-```{code-block} bash
-:class: copyable
+```bash
 java -version
 ```
 
-:::{versionchanged} 24.11.0-edge
+<DeprecatedInVersion version="24.11.0-edge">
 Support for Java versions prior to 17 was dropped.
-:::
+</DeprecatedInVersion>
 
 If you don't have a compatible version of Java installed, it is recommended that you install it through [SDKMAN!](https://sdkman.io/), and that you use the latest Long-Term-Support (LTS) version of Temurin. See [Which version of JDK should I use?](https://whichjdk.com/) for more information about different versions of Java.
 
@@ -29,8 +26,7 @@ To install Java with SDKMAN:
 
 1. [Install SDKMAN](https://sdkman.io/install):
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     curl -s https://get.sdkman.io | bash
     ```
 
@@ -38,20 +34,16 @@ To install Java with SDKMAN:
 
 3. Install Java:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     sdk install java 17.0.10-tem
     ```
 
 4. Confirm that Java is installed correctly:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     java -version
     ```
 
-(install-nextflow)=
-
 ## Install Nextflow
 
 Nextflow is distributed as an easy to use self-installing package. It is also distributed via Conda and as a standalone distribution.
@@ -64,42 +56,38 @@ To install Nextflow with the self-installing package:
 
 1. Download Nextflow:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     curl -s https://get.nextflow.io | bash
     ```
 
-    :::{tip}
+    :::tip
     Set `export CAPSULE_LOG=none` to make the installation logs less verbose.
     :::
 
 2. Make Nextflow executable:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     chmod +x nextflow
     ```
 
 3. Move Nextflow into an executable path. For example:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     mkdir -p $HOME/.local/bin/
     mv nextflow $HOME/.local/bin/
     ```
 
-    :::{tip}
+    :::tip
     Ensure the directory `$HOME/.local/bin/` is included in your `PATH` variable. Temporarily add this directory to `PATH` by setting `export PATH="$PATH:$HOME/.local/bin"`. Add the directory to `PATH` permanently by adding the export command to your shell configuration file, such as `~/.bashrc` or `~/.zshrc`. Alternatively, move the `nextflow` executable to a directory already in your `PATH`.
     :::
 
-    :::{warning}
+    :::warning
     Nextflow updates its executable during the self-install process, therefore the update can fail if the executable is placed in a directory with restricted permissions.
     :::
 
 4. Confirm Nextflow is installed correctly:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     nextflow info
     ```
 
@@ -109,31 +97,26 @@ To install Nextflow with Conda:
 
 1. Create an environment with Nextflow:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     conda create --name nf-env bioconda::nextflow
     ```
 
 2. Activate the environment:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     source activate nf-env
     ```
 
 3. Confirm Nextflow is installed correctly:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     nextflow info
     ```
 
-:::{warning}
+:::warning
 Installing Nextflow via Conda may lead to outdated versions, dependency conflicts, and Java compatibility issues. Using the self-installing package is recommended for a more reliable and up-to-date installation.
 :::
 
-(install-standalone)=
-
 ### Standalone distribution
 
 The Nextflow standalone distribution (i.e., the `dist` release) is a self-contained `nextflow` executable that can run without needing to download core dependencies at runtime. This distribution is useful for offline environments as well as building and testing Nextflow locally.
@@ -144,19 +127,17 @@ To use the standalone distribution:
 
 2. Grant execution permissions to the downloaded file. For example:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     chmod +x nextflow-24.10.1-dist
     ```
 
 3. Use it as a drop-in replacement for `nextflow` command. For example:
 
-    ```{code-block} bash
-    :class: copyable
+    ```bash
     ./nextflow-24.10.1-dist run info
     ```
 
-:::{note}
+:::note
 The standalone distribution will still download core and third-party plugins as needed at runtime.
 :::
 
@@ -172,6 +153,9 @@ Launching from Seqera provides you with:
 - Advanced analytics with resource optimization.
 
 Seqera Cloud Basic is free for small teams. Researchers at qualifying academic institutions can apply for free access to Seqera Cloud Pro.
-See [Seqera Platform Cloud](https://docs.seqera.io/platform) to get started.
+See the [Seqera Platform documentation](https://docs.seqera.io/platform) for tutorials to get started.
+
+If you have installed Nextflow locally, you can use the [`nextflow auth`][cli-auth] command to authenticate with Seqera and automatically configure workflow monitoring.
 
-If you have installed Nextflow locally, you can use the {ref}`nextflow auth <cli-auth>` command to authenticate with Seqera and automatically configure workflow monitoring.
+[cli-auth]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#cli-auth
+[updating-nextflow]: /nextflow_docs/nextflow_repo/docs/updating-nextflow.mdx
diff --git a/docs/kubernetes.md b/new-docs/nextflow-docs/kubernetes.mdx
similarity index 75%
rename from docs/kubernetes.md
rename to new-docs/nextflow-docs/kubernetes.mdx
index 7fd0494692..88f6dde159 100644
--- a/docs/kubernetes.md
+++ b/new-docs/nextflow-docs/kubernetes.mdx
@@ -1,12 +1,12 @@
-(k8s-page)=
+
 
 # Kubernetes
 
 [Kubernetes](https://kubernetes.io/) is a cloud-native open-source system for deployment, scaling, and management of containerized applications.
 
-It provides clustering and file system abstractions that allows the execution of containerised workloads across different cloud platforms and on-premises installations.
+It provides clustering and file system abstractions that allows the execution of containerized workloads across different cloud platforms and on-premises installations.
 
-The built-in support for Kubernetes provided by Nextflow streamlines the execution of containerised workflows in Kubernetes clusters.
+The built-in support for Kubernetes provided by Nextflow streamlines the execution of containerized workflows in Kubernetes clusters.
 
 ## Concepts
 
@@ -16,8 +16,8 @@ Kubernetes abstracts also the storage provisioning through the definition of one
 
 When using the `k8s` executor Nextflow deploys the workflow execution as a Kubernetes pod. This pod orchestrates the workflow execution and submits a separate pod execution for each job that need to be carried out by the workflow application.
 
-```{image} _static/nextflow-k8s-min.png
-```
+
+![Nextflow k8s](_static/nextflow-k8s-min.png)
 
 ## Requirements
 
@@ -25,10 +25,10 @@ At least a [Persistent Volume](https://kubernetes.io/docs/concepts/storage/persi
 
 Such volume needs to be accessible through a [Persistent Volume Claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/#persistentvolumeclaims), which will be used by Nextflow to run the application and store the scratch data and the pipeline final result.
 
-The workflow application has to be containerised using the usual Nextflow {ref}`container<process-container>` directive.
+The workflow application has to be containerized using the usual Nextflow [container][process-container] directive.
 
-:::{tip}
-When using {ref}`wave-page` and {ref}`fusion-page` there is no need to use a shared file system and configure a persistent volume claim for the deployment of Nextflow pipeline with Kubernetes. You can ignore this requirement when using the Fusion file system. See the {ref}`fusion-page` for further information.
+:::tip
+When using [Wave][wave-page] and [Fusion][fusion-page] there is no need to use a shared file system and configure a persistent volume claim for the deployment of Nextflow pipeline with Kubernetes. You can ignore this requirement when using the Fusion file system. See the [Fusion][fusion-page] for further information.
 :::
 
 ## Execution
@@ -37,7 +37,7 @@ The workflow execution needs to be submitted from a computer able to connect to
 
 Nextflow uses the Kubernetes configuration file available at the path `$HOME/.kube/config` or the file specified by the environment variable `KUBECONFIG`.
 
-You can verify such configuration with the command below:
+You can verify such configuration with the following command:
 
 ```console
 $ kubectl cluster-info
@@ -47,7 +47,7 @@ KubeDNS is running at https://your-host:6443/api/v1/namespaces/kube-system/servi
 
 ### Launch with `kuberun`
 
-:::{warning}
+:::warning
 The `kuberun` is considered an obsolete approach for the deployment of Nextflow pipeline with Kubernetes and is no longer maintained. For a better alternative, consider using [Launch with Fusion](#launch-with-fusion).
 :::
 
@@ -59,7 +59,7 @@ nextflow kuberun <pipeline-name> -v vol-claim:/mount/path
 
 This command will create and execute a pod running the nextflow orchestrator for the specified workflow. In the above example replace `<pipeline-name>` with an existing nextflow project or the absolute path of a workflow already deployed in the Kubernetes cluster.
 
-The `-v` command line option is required to specify the volume claim name and mount path to use for the workflow execution. In the above example replace `vol-claim` with the name of an existing persistent volume claim and `/mount/path` with the path where the volume is required to be mount in the container. Volume claims can also be specified in the Nextflow configuration file, see the {ref}`Kubernetes configuration section<config-k8s>` for details.
+The `-v` command line option is required to specify the volume claim name and mount path to use for the workflow execution. In the above example replace `vol-claim` with the name of an existing persistent volume claim and `/mount/path` with the path where the volume is required to be mount in the container. Volume claims can also be specified in the Nextflow configuration file. See [k8s][config-k8s>] for details.
 
 Once the pod execution starts, the application in the foreground prints the console output produced by the running workflow pod.
 
@@ -73,16 +73,15 @@ nextflow kuberun login -v vol-claim:/mount/path
 
 This command creates a pod, sets up the volume claim(s), configures the Nextflow environment and finally launches a Bash login session.
 
-:::{warning}
+:::warning
 The pod is automatically destroyed once the shell session terminates. Do not use it to launch long-running workflows in the background.
 :::
 
 ### Launch with Fusion
 
-:::{versionadded} 22.10.0
-:::
+<AddedInVersion version="22.10.0" />
 
-The use of {ref}`fusion-page` allows deploying a Nextflow pipeline to a remote (or local) cluster without the need to use a shared file system and configure a persistent volume claim for the deployment of Nextflow pipeline with Kubernetes.
+The use of [Fusion][fusion-page] allows deploying a Nextflow pipeline to a remote (or local) cluster without the need to use a shared file system and configure a persistent volume claim for the deployment of Nextflow pipeline with Kubernetes.
 
 This also makes unnecessary the use of the special `kuberun` command for the pipeline execution.
 
@@ -106,11 +105,11 @@ k8s {
 
 In the above snippet replace `vol-claim` with the name of an existing persistent volume claim and replace `/mount/path` with the actual desired mount path (default: `/workspace`) and `storageSubPath` with the directory in the volume to be mounted (default: `/`).
 
-:::{warning}
+:::warning
 The running pod must have been created with the same persistent volume claim name and mount as the one specified in your Nextflow configuration file. Note also that the `run` command does not support the `-v` option.
 :::
 
-:::{tip}
+:::tip
 It is also possible to mount multiple volumes using the `pod` directive, for example:
 
 ```groovy
@@ -120,7 +119,7 @@ k8s.pod = [ [volumeClaim: "other-pvc", mountPath: "/other" ]]
 
 ## Pod settings
 
-The process {ref}`process-pod` directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the {ref}`k8s-executor` executor. See the {ref}`process-pod` directive for more details.
+The process [pod][process-pod] directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the [Kubernetes][k8s-executor] executor. See the [pod][process-pod] directive for more details.
 
 ## Limitations
 
@@ -128,4 +127,11 @@ The `kuberun` command does not allow the execution of local Nextflow scripts. It
 
 ## Advanced configuration
 
-Read the {ref}`Kubernetes configuration<config-k8s>` and {ref}`executor <k8s-executor>` sections to learn more about advanced configuration options.
+See [k8s][config-k8s] and [Kubernetes][k8s-executor] to learn more about advanced configuration options.
+
+[config-k8s]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#k8s
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[k8s-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#kubernetes
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-pod]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#pod
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/make-html.sh b/new-docs/nextflow-docs/make-html.sh
new file mode 100755
index 0000000000..da26d88bf2
--- /dev/null
+++ b/new-docs/nextflow-docs/make-html.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+docker run -v $(pwd):/tmp $(wave -f Dockerfile --context .) -- make html
+echo "Done. See _build/html/index.html"
diff --git a/new-docs/nextflow-docs/migrations/24-04.mdx b/new-docs/nextflow-docs/migrations/24-04.mdx
new file mode 100644
index 0000000000..9f9776d45a
--- /dev/null
+++ b/new-docs/nextflow-docs/migrations/24-04.mdx
@@ -0,0 +1,146 @@
+# Migrating to 24.04
+
+[Nextflow 24.04](https://github.com/nextflow-io/nextflow/releases/tag/v24.04.0) was released on May 20, 2024.
+
+## New features
+
+### Topic channels (first preview)
+
+A topic channel is a channel that can receive values from multiple sources, based on a matching name or *topic*.
+
+Topic channels are particularly useful for collecting metadata from various points in a pipeline without writing all of the channel logic that is normally required (e.g., using the `mix` operator).
+
+See [topic][channel-topic] for details.
+
+### Process `eval` outputs
+
+A process `eval` output is a new type of process output that captures the standard output of an arbitrary shell command.
+
+This output type is a simpler way to capture command outputs, such as the version of a command-line tool, instead of using a `path` or `env` output.
+
+See [Eval output (`eval`)][process-out-eval] for details.
+
+### Resource limits
+
+The `resourceLimits` process directive allows you to define global limits on the resources requested by individual tasks.
+
+This directive is useful for ensuring that a task's resource requirements never exceed system-wide limits. It is especially important for preventing tasks from becoming unschedulable when using retry with [dynamic resources][dynamic-task-resources].
+
+See [resourceLimits][process-resourcelimits] for details.
+
+### Job arrays
+
+The `array` directive allows a process to submit jobs as *job arrays*, a feature used by many batch schedulers to submit many similar jobs in an efficient manner.
+
+:::tip
+On Google Batch, the `array` directive can be used in conjunction with the `cpus`, `memory`, and `machineType` directives to pack multiple tasks onto the same VM.
+:::
+
+See [array][process-array] for details.
+
+### Workflow outputs (first preview)
+
+Workflow outputs are a new way to publish outputs at the workflow level:
+
+```nextflow
+nextflow.preview.output = true
+
+workflow {
+  main:
+  ch_fastqc = fastqc(data)
+  multiqc(ch_fastqc.collect())
+
+  publish:
+  ch_fastqc >> 'qc'
+  multiqc.out >> 'summary'
+}
+
+output {
+  directory 'results'
+  mode 'copy'
+}
+```
+
+This syntax allows you to publish channels in a workflow, instead of publishing file patterns in a process using `publishDir`.
+
+See [Workflow outputs][workflow-output-def] for details.
+
+## Enhancements
+
+### Colored logs
+
+Nextflow's console output now features colored logs and improved organization to highlight the most important information about a pipeline while it's running.
+
+### AWS Fargate
+
+Nextflow now supports AWS Fargate for the AWS Batch executor. See [AWS Fargate][aws-fargate] for details.
+
+### OCI auto-pull mode for Singularity and Apptainer
+
+The `singularity.ociAutoPull` (`apptainer.ociAutoPull`) config option enables OCI auto-pull mode for Singularity (Apptainer). When enabled, this setting allows Singularity (Apptainer) to download and convert Docker images during task execution rather than on the Nextflow head node.
+
+See [singularity][config-singularity] and [apptainer][config-apptainer] for details.
+
+### Improved publish error handling
+
+The publishing logic used by `publishDir` and workflow outputs will automatically retry failed publish operations with exponential backoff, providing better resilience against transient errors. The retry behavior can be controlled using the `nextflow.publish.retryPolicy.*` config settings.
+
+Additionally, the `failOnError` option of the `publishDir` directive is now `true` by default. This means that, by default, publish errors (after retries) will cause the pipeline to fail. To restore the previous behavior, set `failOnError` to `false` for each `publishDir` directive.
+
+:::note
+The `nextflow.publish` config settings have since been moved to `workflow.output`. See [workflow][config-workflow] for details.
+:::
+
+### GA4GH TES 1.1
+
+The TES executor has been updated to be compliant with version 1.1 of the [TES API specification](https://ga4gh.github.io/task-execution-schemas/docs/). Notable improvements include support for directory outputs, glob outputs, and the `bin` directory.
+
+:::note
+The `nf-ga4gh` plugin has since been moved into its own repository, [nextflow-io/nf-ga4gh](https://github.com/nextflow-io/nf-ga4gh). Refer to this repository for documentation and the latest updates on GA4GH integrations for Nextflow.
+:::
+
+## Breaking changes
+
+- Support for [Glacier auto-retrieval][config-aws] was removed. Consider using the AWS CLI to restore Glacier objects before or at the beginning of your pipeline.
+
+- The `seqera` and `defaults` channels were removed from the list of default conda channels used by Wave. They can be restored with the following setting:
+
+  ```groovy
+  conda.channels = ['seqera', 'conda-forge', 'bioconda', 'defaults']
+
+## Miscellaneous
+
+- New config option: `azure.batch.pools.<name>.lowPriority`
+- New config option: `azure.batch.pools.<name>.startTask.script`
+- New config option: `azure.batch.pools.<name>.startTask.privileged`
+- New config option: `executor.account`
+- New config option: `fusion.cacheSize`
+- New config option: `google.batch.maxSpotAttempts`
+- New config option: `k8s.cpuLimits`
+- New config option: `k8s.fuseDevicePlugin`
+- New environment variable: `NXF_CLOUDINFO_ENABLED`
+- New environment variable: `NXF_CACHE_DIR`
+- New plugin extension point: `TaskTipProvider`
+- New `pod` directive option: `schedulerName`
+- New `pod` directive option: `ttlSecondsAfterFinished`
+- New workflow metadata: `workflow.fusion.enabled`
+- New workflow metadata: `workflow.fusion.version`
+- New workflow metadata: `workflow.preview`
+- New workflow metadata: `workflow.wave.enabled`
+- Support Google Batch [instance templates][google-batch-process]
+- Support the use of [secrets in the pipeline script][secrets-pipeline-script]
+- Upgrade to Groovy 4
+
+[aws-fargate]: /nextflow_docs/nextflow_repo/docs/aws.mdx#aws-fargate
+[config-aws]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#aws
+[config-apptainer]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#apptainer
+[config-singularity]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#singularity
+[channel-topic]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#topic
+[config-workflow]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#workflow
+[dynamic-task-resources]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-task-resources
+[google-batch-process]: /nextflow_docs/nextflow_repo/docs/google.mdx#process-definition
+[process-array]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#array
+[process-out-eval]: /nextflow_docs/nextflow_repo/docs/process.mdx#eval-output-eval
+[process-resourcelimits]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#resourcelimits
+[secrets-pipeline-script]: /nextflow_docs/nextflow_repo/docs/secrets.mdx#pipeline-script
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
diff --git a/new-docs/nextflow-docs/migrations/24-10.mdx b/new-docs/nextflow-docs/migrations/24-10.mdx
new file mode 100644
index 0000000000..bfb9e337ec
--- /dev/null
+++ b/new-docs/nextflow-docs/migrations/24-10.mdx
@@ -0,0 +1,76 @@
+# Migrating to 24.10
+
+[Nextflow 24.10](https://github.com/nextflow-io/nextflow/releases/tag/v24.10.0) was released on October 27, 2024.
+
+## New features
+
+### Language server
+
+The [Nextflow language server](https://github.com/nextflow-io/language-server) implements the Language Server Protocol (LSP) for Nextflow scripts and config files. It can be integrated with any editor that functions as an LSP client, and is used by the official [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow). See [VS Code integration][vscode-page] for details.
+
+The language server parses scripts and config files according to the [Nextflow language specification][syntax-page], which is more strict than the Nextflow CLI. See [Preparing for strict syntax][strict-syntax-page] for details.
+
+### Workflow outputs (second preview)
+
+The second preview of workflow outputs introduces the following breaking changes from the [previous version][workflow-outputs-first-preview]:
+
+- The `publish:` section within processes has been removed. Channels should now be published only from workflows, ideally the entry workflow.
+
+- The `directory` output directive has been replaced with the `outputDir` config option and `-output-dir` command line option, which defaults to `results`. Other directives, such as `mode`, have been replaced with config options under `workflow.output.*`.
+
+  In other words, only target blocks can be specified in the output block, but target blocks can still specify directives such as `mode`.
+
+- Target names cannot begin or end with a slash (`/`).
+
+See [Workflow outputs][workflow-output-def] to learn more about the workflow output definition.
+
+## Enhancements
+
+### Azure Managed Identities
+
+Nextflow now supports managed identities for the Azure Batch executor. See [Managed identities][azure-managed-identities] for details.
+
+### Task previous execution trace
+
+The `task` variable in the process definition has two new properties, `task.previousTrace` and `task.previousException`, which allows a task to access the runtime metadata of the previous attempt. See [Dynamic task resources with previous execution trace][task-previous-execution-trace] for details.
+
+## Breaking changes
+
+- The `all` release of Nextflow has been replaced with the `dist` release, which includes fewer core plugins by default and supports third-party plugins. See [Standalone distribution][install-standalone] for details.
+
+- The `nf-ga4gh` plugin has been moved into its own repository, [nextflow-io/nf-ga4gh](https://github.com/nextflow-io/nf-ga4gh). To continue using the TES executor, you must explicitly declare the `nf-ga4gh` plugin in your Nextflow configuration. Refer to the plugin repository for documentation and updates on GA4GH integrations.
+
+- The [HyperQueue][hyperqueue-executor] executor now requires HyperQueue 0.17.0 or later.
+
+- The use of [Grape](https://docs.groovy-lang.org/latest/html/documentation/grape.html) dependencies with the `@Grab` annotation is no longer supported. Code that requires third-party libraries should be migrated to a plugin.
+
+- Automatic spot retries for AWS Batch and Google Batch have been disabled by default. See [Spot Instance failures and retries][spot-retries-page] for details.
+
+## Deprecations
+
+- The use of `addParams` and `params` clauses in include declarations is deprecated. See [Module parameters][module-params] for details.
+
+## Miscellaneous
+
+- New config option: `aws.client.requesterPays`
+- New config option: `google.batch.autoRetryExitCodes`
+- New config option: `google.batch.bootDiskImage`
+- New config option: `manifest.contributors`
+- New config option: `wave.mirror`
+- New config option: `wave.scan.mode`
+- New config option: `wave.scan.allowedLevels`
+- New config option: `workflow.failOnIgnore`
+- Rename `nextflow.publish.retryPolicy` config scope to `workflow.output.retryPolicy`
+
+
+[azure-managed-identities]: /nextflow_docs/nextflow_repo/docs/azure.mdx#managed-identities
+[hyperqueue-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#hyperqueue
+[install-standalone]: /nextflow_docs/nextflow_repo/docs/install.mdx#standalone-distribution
+[module-params]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-parameters
+[spot-retries-page]: /nextflow_docs/nextflow_repo/docs/guides/updating-spot-retries.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[task-previous-execution-trace]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-task-resources-with-previous-execution-trace
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-outputs-first-preview]: /nextflow_docs/nextflow_repo/docs/migrations/24-04.mdx#workflow-outputs-first-preview
+[vscode-page]: /nextflow_docs/nextflow_repo/docs/vscode.mdx
diff --git a/new-docs/nextflow-docs/migrations/25-04.mdx b/new-docs/nextflow-docs/migrations/25-04.mdx
new file mode 100644
index 0000000000..2ddceda137
--- /dev/null
+++ b/new-docs/nextflow-docs/migrations/25-04.mdx
@@ -0,0 +1,123 @@
+# Migrating to 25.04
+
+[Nextflow 25.04](https://github.com/nextflow-io/nextflow/releases/tag/v25.04.0) was released on May 8, 2025.
+
+## New features
+
+### Strict syntax
+
+The *strict syntax* is a strict parser for Nextflow DSL2 that implements the [Nextflow language specification][syntax-page]. Originally introduced by the [Nextflow language server](https://github.com/nextflow-io/language-server) alongside Nextflow 24.10, the strict syntax is now available in the Nextflow CLI.
+
+The strict syntax is disabled by default. It can be enabled by setting the environment variable `NXF_SYNTAX_PARSER=v2`. See [strict syntax][strict-syntax-page] for details.
+
+### Linting and formatting
+
+The `nextflow lint` command checks Nextflow scripts and config files for errors using the [strict syntax][strict-syntax-page]. It can also format Nextflow files using the same formatter as the Nextflow language server. See [lint][cli-lint] for details.
+
+### Workflow outputs (third preview)
+
+The third preview of workflow outputs introduces the following breaking changes from the [previous version][workflow-outputs-second-preview]:
+
+- The `publish:` section can only be specified in the entry workflow.
+
+- Workflow outputs in the `publish:` section are assigned instead of using the `>>` operator. Output names must be valid identifiers.
+
+- By default, output files are published to the base output directory, rather than a subdirectory corresponding to the output name.
+
+- The syntax for dynamic publish paths has changed. Instead of defining a closure that returns a closure with the `path` directive, the outer closure should use the `>>` operator to publish individual files. See [Publishing files][workflow-publishing-files] for details.
+
+- The `mapper` index directive has been removed. Use a `map` operator in the workflow body instead.
+
+See [Workflow outputs][workflow-output-def] to get started.
+
+### Topic channels (out of preview)
+
+[Topic channels][channel-topic], introduced in Nextflow 24.04 as a preview feature, have been brought out of preview, which means that they can be used without the `nextflow.preview.topic` feature flag.
+
+### Data lineage
+
+This release introduces built-in provenance tracking, also known as *data lineage*. When `lineage.enabled` is set to `true` in your configuration, Nextflow will record every workflow run, task execution, output file, and the links between them.
+
+You can explore this lineage from the command line using the [lineage][cli-lineage] command. Additionally, you can refer to files in the lineage store from a Nextflow script using the `lid://` path prefix as well as the [fromLineage][channel-from-lineage] channel factory.
+
+See the [Data lineage][data-lineage-page] guide to get started.
+
+<h3>Simplified plugin development</h3>
+
+The `nextflow plugin create` sub-command creates the scaffold for a Nextflow plugin using the official [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/). It is simpler and easier to maintain than the previous plugin boilerplate.
+
+See the [Using the Nextflow Gradle plugin][gradle-plugin-page] guide for details.
+
+## Enhancements
+
+### Improved `inspect` command
+
+Previously, the `nextflow inspect` command included all processes that were invoked in a preview run. Now, the `inspect` command includes all processes that are *included* by the entry workflow (directly or indirectly), which has several benefits:
+
+- It includes all processes that could potentially be invoked by the workflow, not just the processes that are invoked for a particular run configuration.
+
+- It's faster, as it doesn't need to evaluate the entry workflow -- only the includes.
+
+- It can be run as `nextflow inspect <PIPELINE>`, without specifying any parameters or config profiles.
+
+See [inspect][cli-inspect] to learn more about the `inspect` command.
+
+### Plugin version ranges
+
+When specifying a plugin, the plugin version can now be prefixed with `~` to pin the major and minor version while allowing the latest patch release. This syntax makes it possible to pin the plugin version while automatically using new patch releases.
+
+See [Plugins][plugins-page] for details.
+
+### Improved publish error handling
+
+Nextflow will terminate the run if the thread pool responsible for publishing files takes too long. Previously, this timeout was reported as a warning. Now, it is reported as an error.
+
+The previous behavior can be restored with the following config setting:
+
+```groovy
+workflow.output.ignoreErrors = true
+```
+
+## Breaking changes
+
+- Nextflow now requires Java 17 or newer. See [Requirements][install-requirements] for instructions to install Java 17.
+
+- The [HyperQueue][hyperqueue-executor] executor now requires HyperQueue 0.20.0 or later.
+
+## Deprecations
+
+- The process `shell` section has been deprecated. See [Shell][process-shell] for details.
+
+- Nextflow will report a warning if it encounters a process `shell` directive that contains newlines. This warning will become an error in a future release.
+
+- The `-with-weblog` CLI option has been deprecated. See [nextflow-io/nf-weblog](https://github.com/nextflow-io/nf-weblog) to learn how to use the `nf-weblog` plugin.
+
+## Miscellaneous
+
+- New config option: `aws.batch.terminateUnschedulableJobs`
+- New config option: `azure.batch.jobMaxWallClockTime`
+- New config option: `fusion.snapshots`
+- New config option: `google.batch.gcsfuseOptions`
+- New config option: `google.batch.networkTags`
+- New config option: `workflow.output.copyAttributes`
+- New environment variable: `NXF_PLUGINS_ALLOWED`
+- New plugin extension point: `TraceObserverFactoryV2`
+- New standard library function: `env()`
+- Support `disk` directive for Azure Batch
+
+[channel-from-lineage]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#fromlineage
+[channel-topic]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#topic
+[cli-inspect]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#inspect
+[cli-lineage]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lineage
+[cli-lint]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lint
+[data-lineage-page]: /nextflow_docs/nextflow_repo/docs/tutorials/data-lineage.mdx
+[gradle-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx
+[hyperqueue-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#hyperqueue
+[install-requirements]: /nextflow_docs/nextflow_repo/docs/install.mdx#requirements
+[plugins-page]: /nextflow_docs/nextflow_repo/docs/plugins/plugins.mdx
+[process-shell]: /nextflow_docs/nextflow_repo/docs/process.mdx#shell
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[workflow-outputs-second-preview]: /nextflow_docs/nextflow_repo/docs/migrations/24-10.mdx#workflow-outputs-second-preview
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-publishing-files]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#publishing-files
diff --git a/new-docs/nextflow-docs/migrations/25-10.mdx b/new-docs/nextflow-docs/migrations/25-10.mdx
new file mode 100644
index 0000000000..0b85ca7026
--- /dev/null
+++ b/new-docs/nextflow-docs/migrations/25-10.mdx
@@ -0,0 +1,282 @@
+(migrating-25-10-page)=
+
+# Migrating to 25.10
+
+[Nextflow 25.10](https://github.com/nextflow-io/nextflow/releases/tag/v25.10.0) was released on October 22, 2025.
+
+## New features
+
+<h3>Workflow params</h3>
+
+The `params` block is a new way to declare pipeline parameters in a Nextflow script:
+
+```nextflow
+params {
+    // Path to input data.
+    input: Path
+
+    // Whether to save intermediate files.
+    save_intermeds: Boolean = false
+}
+
+workflow {
+    println "params.input = ${params.input}"
+    println "params.save_intermeds = ${params.save_intermeds}"
+}
+```
+
+This syntax allows you to declare all parameters in one place with explicit type annotations, and it allows Nextflow to validate parameters at runtime.
+
+See [Parameters][workflow-params-def] for details.
+
+(workflow-outputs-final)=
+
+<h3>Workflow outputs (out of preview)</h3>
+
+[Workflow outputs][workflow-output-def], introduced in Nextflow 24.04 as a preview feature, have been brought out of preview and can now be used without the `nextflow.preview.output` feature flag.
+
+The final version adds the ability to specify a type annotation for each output declaration:
+
+```nextflow
+workflow {
+    main:
+    ch_samples = // ...
+
+    publish:
+    samples = ch_samples
+}
+
+output {
+    samples: Channel<Map> {
+        path '.'
+        index {
+            path 'samples.csv'
+        }
+    }
+}
+```
+
+See [Migrating to workflow outputs][migrating-workflow-outputs] to get started.
+
+<h3>Type annotations</h3>
+
+Type annotations are a way to denote the *type* of a variable. They help document and validate pipeline code.
+
+```nextflow
+workflow RNASEQ {
+    take:
+    reads: Channel<Path>
+    index: Value<Path>
+
+    main:
+    samples_ch = QUANT( reads, index )
+
+    emit:
+    samples: Channel<Path> = samples_ch
+}
+
+def isSraId(id: String) -> Boolean {
+    return id.startsWith('SRA')
+}
+
+// feature flag required for typed processes
+nextflow.preview.types = true
+
+process fastqc {
+    input:
+    (id, fastq_1, fastq_2): Tuple<String,Path,Path>
+
+    output:
+    logs = tuple(id, file('fastqc_logs'))
+
+    script:
+    """
+    mkdir fastqc_logs
+    fastqc -o fastqc_logs -f fastq -q ${fastq_1} ${fastq_2}
+    """
+}
+```
+
+The following declarations can be annotated with types:
+
+- Pipeline parameters (the `params` block)
+- Workflow takes and emits
+- Process inputs and outputs
+- Function parameters and returns
+- Local variables
+- Closure parameters
+- Workflow outputs (the `output` block)
+
+Type annotations can refer to any of the [standard types][stdlib-types].
+
+Some types use *generic type parameters* to work with different data types in a type-safe way. For example:
+
+- `List<E>` and `Channel<E>` use the generic type `E` to specify the element type in the list or channel
+- `Map<K,V>` uses the generic types `K` for the key type and `V` for the value type in the map
+
+The following examples show types with type parameters:
+
+```nextflow
+// List<E> where E is String
+def sequences: List<String> = ['ATCG', 'GCTA', 'TTAG']
+
+// List<E> where E is Path
+def fastqs: List<Path> = [file('sample1.fastq'), file('sample2.fastq')]
+
+// Map<K,V> where K is String and V is Integer
+def readCounts: Map<String,Integer> = [sample1: 1000, sample2: 1500]
+
+// Channel<E> where E is Path
+def ch_bams: Channel<Path> = channel.fromPath('*.bam')
+```
+
+Type annotations can be appended with `?` to denote values can be `null`:
+
+```nextflow
+def x_opt: String? = null
+```
+
+In the type system, queue channels are represented as `Channel`, while value channels are represented as `Value`. To make the terminology clearer and more concise, queue channels are now called *dataflow channels* (or simply *channels*), and value channels are now called *dataflow values*. See [Dataflow][dataflow-page] for more information.
+
+:::note
+Nextflow supports Groovy-style type annotations using the `<type> <name>` syntax, but this approach is deprecated in [strict syntax][strict-syntax-page]. While Groovy-style annotations remain valid for functions and local variables, the language server and `nextflow lint` automatically convert them to Nextflow-style annotations during code formatting.
+:::
+
+See [Migrating to static types][migrating-static-types] for details.
+
+<h3>Auth and Launch commands</h3>
+
+The Nextflow CLI has two new commands: `nextflow auth` and `nextflow launch`. Together, they allow you to authenticate with Seqera Platform and launch pipelines from the command line. This approach streamlines the previous workflow of using `nextflow run` with the `-with-tower` option.
+
+```bash
+# Authenticate with Seqera Cloud
+nextflow auth login
+
+# Check authentication status
+nextflow auth status
+
+# Configure Seqera Platform settings
+nextflow auth config
+
+# Launch a pipeline in Seqera Platform
+nextflow launch nextflow-io/hello
+```
+
+See [CLI Auth][cli-auth] and [CLI Launch][cli-launch] for details.
+
+## Enhancements
+
+<h3>Nextflow plugin registry</h3>
+
+Nextflow now uses the [Nextflow plugin registry](https://registry.nextflow.io/) to download plugins in a more efficient and scalable manner.
+
+The legacy plugin index can still be used by setting the `NXF_PLUGINS_REGISTRY_URL` environment variable:
+
+```bash
+export NXF_PLUGINS_REGISTRY_URL="https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json"
+```
+
+:::note
+Plugin developers will not be able to submit PRs to the legacy plugin index once the plugin registry is generally available. Plugins should be updated to publish to the Nextflow plugin registry using the [Nextflow Gradle plugin][gradle-plugin-page] instead. See [plugin registry][plugin-registry-page] for details.
+:::
+
+<h3>New syntax for workflow handlers</h3>
+
+The workflow `onComplete` and `onError` handlers were previously defined by calling `workflow.onComplete` and `workflow.onError` in the pipeline script. You can now define handlers as `onComplete` and `onError` sections in an entry workflow:
+
+```nextflow
+workflow {
+    main:
+    // ...
+
+    onComplete:
+    println "workflow complete"
+
+    onError:
+    println "error: ${workflow.errorMessage}"
+}
+```
+
+This syntax is simpler and easier to use with the [strict syntax][strict-syntax-page]. See [Workflow handlers][workflow-handlers] for details.
+
+<h3>Simpler syntax for dynamic directives</h3>
+
+The [strict syntax][strict-syntax-page] allows dynamic process directives to be specified without a closure:
+
+```nextflow
+process hello {
+    queue (entries > 100 ? 'long' : 'short')
+
+    input:
+    tuple val(entries), path('data.txt')
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Dynamic process settings in configuration files must still be specified with closures.
+
+See [Dynamic directives][dynamic-directives] for details.
+
+<h3>Configurable date formatting</h3>
+
+You can now customize the date and time format used in notifications, reports, and console output using the `NXF_DATE_FORMAT` environment variable:
+
+```bash
+# Default format
+# e.g., 11-Aug-2016 09:40:20
+
+# Use ISO format with timezone
+export NXF_DATE_FORMAT="iso"
+# e.g., 2016-08-11T09:40:20+02:00
+
+# Use custom format
+export NXF_DATE_FORMAT="yyyy-MM-dd HH:mm"
+# e.g., 2016-08-11 09:40
+```
+
+This feature addresses previous inconsistencies in timestamp representations.
+
+## Breaking changes
+
+- The `google-lifesciences` executor is no longer supported because the Google Cloud Life Sciences API was discontinued in July 2025. Use the `google-batch` executor instead.
+
+- The AWS Java SDK used by Nextflow was upgraded from v1 to v2, which introduced some breaking changes to the `aws.client` config options. See [AWS Java SDK v2][aws-java-sdk-v2-page] for details.
+
+- The `nextflow.config.schema` package was renamed to `nextflow.config.spec`. Plugin developers that define custom [configuration scopes][dev-plugins-extension-points-config] will need to update their imports accordingly.
+
+## Deprecations
+
+- The use of workflow handlers in the configuration file has been deprecated. You should define workflow handlers in the pipeline script or a plugin instead. See [Workflow handlers][config-workflow-handlers] for details.
+
+- The legacy type detection of CLI parameters is disabled when using the strict syntax (`NXF_SYNTAX_PARSER=v2`). [Legacy parameters][workflow-params-legacy] in the strict syntax should not rely on legacy type detection. Alternatively, use the new `params` block to convert CLI parameters based on their type annotations. Legacy type detection can be disabled globally by setting the environment variable `NXF_DISABLE_PARAMS_TYPE_DETECTION=true`.
+
+- The `nextflow.enable.configProcessNamesValidation` feature flag is deprecated. It was originally introduced to suppress false warnings for process selectors targeting conditional processes. The [strict syntax][strict-syntax-page] now validates process selectors without producing false warnings.
+
+## Miscellaneous
+
+- New config option: `docker.registryOverride`
+- New config options: `wave.build.compression.*`
+- New executor: Fujitsu Technical Computing Suite (`tcs`)
+- Support Java 25
+
+[aws-java-sdk-v2-page]: /nextflow_docs/nextflow_repo/docs/guides/aws-java-sdk-v2.mdx
+[cli-auth]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#auth
+[cli-launch]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#launch
+[config-workflow-handlers]: /nextflow_docs/nextflow_repo/docs/config.mdx#workflow-handlers
+[dataflow-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[dev-plugins-extension-points-config]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#dev-plugins-extension-points-config
+[dynamic-directives]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-directives
+[gradle-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx
+[migrating-workflow-outputs]: /nextflow_docs/nextflow_repo/docs/tutorials/workflow-outputs.mdx#migrating-workflow-outputs
+[migrating-static-types]: /nextflow_docs/nextflow_repo/docs/tutorials/static-types.mdx
+[plugin-registry-page]: /nextflow_docs/nextflow_repo/docs/plugins/plugin-registry.mdx
+[stdlib-types]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-params-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#parameters
+[workflow-params-legacy]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#legacy-parameters
+[workflow-handlers]: /nextflow_docs/nextflow_repo/docs/notifications.mdx#workflow-handlers
diff --git a/new-docs/nextflow-docs/migrations/dsl1.mdx b/new-docs/nextflow-docs/migrations/dsl1.mdx
new file mode 100644
index 0000000000..a84fd31280
--- /dev/null
+++ b/new-docs/nextflow-docs/migrations/dsl1.mdx
@@ -0,0 +1,209 @@
+# Migrating from DSL1
+
+In Nextflow version `22.03.0-edge`, DSL2 became the default DSL version. In version `22.12.0-edge`, DSL1 support was removed and the Nextflow documentation was updated to use DSL2 by default. Users who are still using DSL1 should migrate their pipelines to DSL2 to use the latest versions of Nextflow. This page describes the differences between DSL1 and DSL2 and how to migrate to DSL2.
+
+## Processes and workflows
+
+In DSL1, a process definition is also the process invocation. Process inputs and outputs are connected to channels using `from` and `into`. You can see a basic Nextflow script written in DSL1 here:
+
+```nextflow
+nextflow.enable.dsl=1
+
+params.str = 'Hello world!'
+
+process split_letters {
+    output:
+    file 'chunk_*' into letters
+
+    script:
+    """
+    printf '${params.str}' | split -b 6 - chunk_
+    """
+}
+
+process convert_to_upper {
+    input:
+    file x from letters.flatten()
+
+    output:
+    stdout result
+
+    script:
+    """
+    cat $x | tr '[a-z]' '[A-Z]'
+    """
+}
+
+result.view { it.trim() }
+```
+
+To migrate this code to DSL2, you need to move all of your channel logic throughout the script into a `workflow` definition. Additionally, you must call each process explicitly, passing any input channels as arguments (instead of `from ...`) and receiving any output channels as return values (instead of `into ...`).
+
+See [Workflows][workflow-page] to learn how to define a workflow.
+
+You can see the DSL1 Nextflow script from above written in DSL2 here:
+
+```nextflow
+params.str = 'Hello world!'
+
+process split_letters {
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf '${params.str}' | split -b 6 - chunk_
+    """
+}
+
+process convert_to_upper {
+    input:
+    path x
+
+    output:
+    stdout
+
+    script:
+    """
+    cat $x | tr '[a-z]' '[A-Z]'
+    """
+}
+
+workflow {
+    split_letters | flatten | convert_to_upper | view { v -> v.trim() }
+}
+```
+
+## Channel forking
+
+In DSL1, a channel can be used as an input only once; to use a channel multiple times, the channel must be forked using the `into` operator. In DSL2, channels are automatically forked when connecting two or more consumers. For example:
+
+```nextflow
+Channel
+    .of('Hello','Hola','Ciao')
+    .set { cheers }
+
+cheers
+    .map { v -> v.toUpperCase() }
+    .view()
+
+cheers
+    .map { v -> v.reverse() }
+    .view()
+```
+
+Similarly, in DSL2, process outputs can be consumed by multiple consumers automatically, which makes workflow scripts much easier to read and write.
+
+## Modules
+
+In DSL1, the entire Nextflow pipeline must be defined in a single file. For example, `main.nf`. This restriction becomes cumbersome as a pipeline grows and hinders the sharing and reuse of pipeline components.
+
+DSL2 introduces the concept of "module scripts" (or "modules" for short), which are Nextflow scripts that can be "included" by other scripts. While modules are not essential to migrating to DSL2, nor are they mandatory in DSL2, modules can help you organize a large pipeline into multiple smaller files and take advantage of modules created by others. See [Modules][module-page] to learn more about modules.
+
+:::note
+DSL2 scripts cannot exceed 64 KB in size. Split large DSL1 scripts into modules to avoid this limit.
+:::
+
+## Deprecations
+
+### Processes
+
+- The `set` process input type is no longer supported, use [tuple][process-input-tuple] instead.
+- The `set` process output type is no longer supported, use [tuple][process-out-tuple] instead.
+- The `mode flatten` option for process outputs is no longer available. Use the [flatten][operator-flatten] operator on the corresponding output channel instead.
+- Unqualified value and file elements in a tuple declaration are no longer allowed. Use an explicit `val` or `path` qualifier. For example:
+
+  ```nextflow
+  process sam2bam {
+      input:
+      tuple X, 'some-file.sam'
+
+      output:
+      tuple X, 'some-file.bam'
+
+      script:
+      """
+      your_command --in $X some-file.sam > some-file.bam
+      """
+  }
+  ```
+
+  Use:
+
+  ```nextflow
+  process sam2bam {
+      input:
+      tuple val(X), path('some-file.sam')
+
+      output:
+      tuple val(X), path('some-file.bam')
+
+      script:
+      """
+      your_command --in $X some-file.sam > some-file.bam
+      """
+  }
+  ```
+
+### Channels
+
+- Channel factories should be accessed through the `channel` namespace instead of the `Channel` type, although they can still be accessed through either method.
+- Channel method `bind` has been deprecated in DSL2.
+- Channel method `<<` has been deprecated in DSL2.
+- Channel factory `create` has been deprecated in DSL2.
+
+### Operators
+
+- Operator `choice` has been deprecated in DSL2. Use [branch][operator-branch] instead.
+- Operator `close` has been deprecated in DSL2.
+- Operator `countBy` has been deprecated in DSL2.
+- Operator `into` has been deprecated in DSL2, as it is no longer needed.
+- Operator `fork` has been renamed to [multiMap][operator-multimap].
+- Operator `groupBy` has been deprecated in DSL2. Use [groupTuple][operator-grouptuple] instead.
+- Operators `print` and `println` have been deprecated in DSL2. Use [view][operator-view] instead.
+- Operator `route` has been deprecated in DSL2.
+- Operator `separate` has been deprecated in DSL2.
+- Operator `spread` has been deprecated in DSL2. Use [combine][operator-combine] instead.
+
+### DSL2 Preview
+
+An early preview of DSL2 was available in 2020. Note that some of that early DSL2 syntax has since changed.
+
+- The `nextflow.preview.dsl=2` (and `nextflow.enable.dsl=1`) feature flags are no longer needed.
+
+- Anonymous and unwrapped includes are no longer supported. Use an explicit module inclusion instead.
+
+  For example:
+
+  ```nextflow
+  include './modules/hello'
+  include bye from './modules/bye'
+
+  workflow {
+      hello()
+      bye()
+  }
+  ```
+
+  Should be replaced with:
+
+  ```nextflow
+  include { hello } from './modules/hello'
+  include { bye } from './modules/bye'
+
+  workflow {
+      hello()
+      bye()
+  }
+  ```
+
+[module-page]: /nextflow_docs/nextflow_repo/docs/module.mdx
+[operator-branch]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#branch
+[operator-combine]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#combine
+[operator-flatten]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#flatten
+[operator-grouptuple]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#grouptuple
+[operator-multimap]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#multimap
+[operator-view]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#view
+[process-input-tuple]: /nextflow_docs/nextflow_repo/docs/process.mdx#input-tuples-tuple
+[process-out-tuple]: /nextflow_docs/nextflow_repo/docs/process.mdx#output-tuples-tuple
+[workflow-page]: /nextflow_docs/nextflow_repo/docs/workflow.mdx
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/migrations/index.mdx b/new-docs/nextflow-docs/migrations/index.mdx
new file mode 100644
index 0000000000..26a297068c
--- /dev/null
+++ b/new-docs/nextflow-docs/migrations/index.mdx
@@ -0,0 +1,7 @@
+import DocCardList from "@theme/DocCardList";
+
+# Migration notes
+
+This section covers important information for migrating between Nextflow versions. It describes new features, enhancements, breaking changes, deprecations, and other miscellaneous updates that may require action during a migration.
+
+<DocCardList />
diff --git a/docs/module.md b/new-docs/nextflow-docs/module.mdx
similarity index 91%
rename from docs/module.md
rename to new-docs/nextflow-docs/module.mdx
index 9820ae5434..d3100891da 100644
--- a/docs/module.md
+++ b/new-docs/nextflow-docs/module.mdx
@@ -1,11 +1,11 @@
-(module-page)=
+
 
 # Modules
 
 Nextflow scripts can include **definitions** (workflows, processes, and functions) from other scripts. When a script is included in this way, it is referred to as a **module**. Modules can be included by other modules or pipeline scripts and can even be shared across workflows.
 
-:::{note}
-Modules were introduced in DSL2. If you are still using DSL1, see the {ref}`dsl1-page` page to learn how to migrate your Nextflow pipelines to DSL2.
+:::note
+Modules were introduced in DSL2. If you are still using DSL1, see [Migrating from DSL1][dsl1-page] to learn how to migrate your Nextflow pipelines to DSL2.
 :::
 
 ## Module inclusion
@@ -32,12 +32,9 @@ Module includes are subject to the following rules:
 - Relative paths must begin with the `./` prefix.
 - Include statements are not allowed from within a workflow. They must occur at the script level.
 
-(module-directory)=
-
 ## Module directory
 
-:::{versionadded} 22.10.0
-:::
+<AddedInVersion version="22.10.0" />
 
 A module can be defined as a directory with the same name as the module and with a script named `main.nf`. For example:
 
@@ -69,8 +66,6 @@ workflow {
 }
 ```
 
-(module-aliases)=
-
 ## Module aliases
 
 When including definition from a module, it's possible to specify an *alias* with the `as` keyword. Aliasing allows you to avoid module name clashes, by assigning them different names in the including context. For example:
@@ -96,13 +91,11 @@ workflow {
 }
 ```
 
-(module-params)=
-
 ## Module parameters
 
-:::{deprecated} 24.07.0-edge
+<DeprecatedInVersion version="24.07.0-edge">
 As a best practice, parameters should be used in the entry workflow and passed to workflows, processes, and functions as explicit inputs.
-:::
+</DeprecatedInVersion>
 
 A module can define parameters using the same syntax as a Nextflow workflow script:
 
@@ -134,11 +127,11 @@ The above snippet prints:
 Hola Mundo
 ```
 
-:::{note}
+:::note
 The module inherits the parameters defined *before* the `include` statement, therefore any parameters set afterwards will not be used by the module.
 :::
 
-:::{tip}
+:::tip
 It is best to define all pipeline parameters *before* any `include` statements.
 :::
 
@@ -180,11 +173,9 @@ The above snippet prints:
 Ciao world!
 ```
 
-(module-templates)=
-
 ## Module templates
 
-Process script {ref}`templates <process-template>` can be included alongside a module in the `templates` directory.
+Process script [templates][process-template] can be included alongside a module in the `templates` directory.
 
 For example, suppose we have a project L with a module that defines two processes, P1 and P2, both of which use templates. The template files can be made available in the local `templates` directory:
 
@@ -244,12 +235,9 @@ baseDir
         └── P7-template.sh
 ```
 
-(module-binaries)=
-
 ## Module binaries
 
-:::{versionadded} 22.10.0
-:::
+<AddedInVersion version="22.10.0" />
 
 Modules can define binary scripts that are locally scoped to the processes defined by the tasks.
 
@@ -273,8 +261,8 @@ The binary scripts must be placed in the module directory names `<module-dir>/re
 
 Those scripts will be made accessible like any other command in the task environment, provided they have been granted the Linux execute permissions.
 
-:::{note}
-This feature requires the use of a local or shared file system for the pipeline work directory, or {ref}`wave-page` when using cloud-based executors.
+:::note
+This feature requires the use of a local or shared file system for the pipeline work directory, or [Wave containers][wave-page] when using cloud-based executors.
 :::
 
 ## Sharing modules
@@ -284,3 +272,7 @@ Modules are designed to be easy to share and re-use across different pipelines,
 - Simply copy the module files into your pipeline repository
 - Use [Git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules) to fetch modules from other Git repositories without maintaining a separate copy
 - Use the [nf-core](https://nf-co.re/tools#modules) CLI to install and update modules with a standard approach used by the nf-core community
+
+[dsl1-page]: /nextflow_docs/nextflow_repo/docs/migrations/dsl1.mdx
+[process-template]: /nextflow_docs/nextflow_repo/docs/process.mdx#template
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
diff --git a/new-docs/nextflow-docs/netlify.toml b/new-docs/nextflow-docs/netlify.toml
new file mode 100644
index 0000000000..419673f57f
--- /dev/null
+++ b/new-docs/nextflow-docs/netlify.toml
@@ -0,0 +1,10 @@
+# No deployment previews unless the docs are edited
+[build]
+  ignore = "git diff --quiet $CACHED_COMMIT_REF $COMMIT_REF ."
+
+# Tell Google not to spider the Netlify staging site
+[[headers]]
+for = "/*"
+
+[headers.values]
+    X-Robots-Tag = "noindex"
diff --git a/docs/notifications.md b/new-docs/nextflow-docs/notifications.mdx
similarity index 75%
rename from docs/notifications.md
rename to new-docs/nextflow-docs/notifications.mdx
index 9828420cf2..d2fc8a5c20 100644
--- a/docs/notifications.md
+++ b/new-docs/nextflow-docs/notifications.mdx
@@ -1,15 +1,11 @@
-(mail-page)=
+
 
 # Notifications
 
 This page documents how to handle workflow events and send notifications.
 
-(workflow-handlers)=
-
 ## Workflow handlers
 
-(metadata-completion-handler)=
-
 ### Completion handler
 
 Due to the asynchronous nature of Nextflow, the termination of a script does not correspond to the termination of the running workflow. Thus some information, only available on execution completion, needs to be accessed by using an asynchronous handler.
@@ -23,8 +19,7 @@ workflow.onComplete {
 }
 ```
 
-:::{versionadded} 25.10.0
-:::
+< AddedInVersion version="25.10.0" />
 
 Entry workflows can define an `onComplete` section instead of using `workflow.onComplete`:
 
@@ -39,8 +34,6 @@ workflow {
 }
 ```
 
-(metadata-error-handler)=
-
 ### Error handler
 
 Nextflow invokes the `onError` event handler when a runtime or process error caused the pipeline execution to stop. For example:
@@ -51,12 +44,11 @@ workflow.onError {
 }
 ```
 
-:::{note}
-Both the `onError` and `onComplete` handlers are invoked when an error condition is encountered. The first is called as soon as the error is raised, while the second is called just before the pipeline execution is about to terminate. When using the `finish` {ref}`process-error-strategy`, there may be a significant gap between the two, depending on the time required to complete any pending job.
+:::note
+Both the `onError` and `onComplete` handlers are invoked when an error condition is encountered. The first is called as soon as the error is raised, while the second is called just before the pipeline execution is about to terminate. When using the `finish` [errorStrategy][process-error-strategy], there may be a significant gap between the two, depending on the time required to complete any pending job.
 :::
 
-:::{versionadded} 25.10.0
-:::
+< AddedInVersion version="25.10.0" />
 
 Entry workflows can define an `onError` section instead of using `workflow.onError`:
 
@@ -74,8 +66,6 @@ workflow {
 
 The built-in function `sendMail` allows you to send a mail message from a workflow script.
 
-(mail-basic)=
-
 ### Basic mail
 
 The mail attributes are specified as named parameters or an equivalent map. For example:
@@ -104,41 +94,54 @@ sendMail(mail)
 
 The following parameters can be specified:
 
-`to`
-: *Multiple email addresses can be specified by separating them with a comma.*
-: The mail target recipients.
 
-`cc`
-: *Multiple email addresses can be specified by separating them with a comma.*
-: The mail CC recipients.
+##### `to`
+
+*Multiple email addresses can be specified by separating them with a comma.*
+
+The mail target recipients.
+
+##### `cc`
+
+*Multiple email addresses can be specified by separating them with a comma.*
+
+The mail CC recipients.
+
+##### `bcc`
+
+*Multiple email addresses can be specified by separating them with a comma.*
+
+The mail BCC recipients.
+
+##### `from`
 
-`bcc`
-: *Multiple email addresses can be specified by separating them with a comma.*
-: The mail BCC recipients.
+*Multiple email addresses can be specified by separating them with a comma.*
 
-`from`
-: *Multiple email addresses can be specified by separating them with a comma.*
-: The mail sender address.
+The mail sender address.
 
-`subject`
-: The mail subject.
+##### `subject`
 
-`charset`
-: The mail content charset (default: `UTF-8`).
+The mail subject.
 
-`text`
-: The mail plain text content.
+##### `charset`
 
-`body`
-: The mail body content. It can be either plain text or HTML content.
+The mail content charset (default: `UTF-8`).
 
-`type`
-: The mail body mime type. If not specified it's automatically detected.
+##### `text`
 
-`attach`
-: Single file or a list of files to be included as mail attachments.
+The mail plain text content.
 
-(mail-advanced)=
+##### `body`
+
+The mail body content. It can be either plain text or HTML content.
+
+##### `type`
+
+The mail body mime type. If not specified it's automatically detected.
+
+##### `attach`
+
+Single file or a list of files to be included as mail attachments.
 
 ### Advanced mail
 
@@ -162,33 +165,35 @@ sendMail {
 
 The same attributes listed in the table in the previous section are allowed.
 
-:::{tip}
+:::tip
 A string expression at the end is implicitly interpreted as the mail body content, therefore the `body` parameter can be omitted as shown above.
 :::
 
-:::{tip}
+:::tip
 To send an email that includes text and HTML content, use both the `text` and `body` attributes. The first is used for the plain text content, while the second is used for the rich HTML content.
 :::
 
-(mail-attachments)=
-
 ### Mail attachments
 
 When using the curly brackets syntax, the `attach` parameter can be repeated two or more times to include multiple attachments in the mail message.
 
 Moreover for each attachment it's possible to specify any of the following options:
 
-`contentId`
-: Defines the `Content-ID` header field for the attachment.
+##### `contentId`
+
+Defines the `Content-ID` header field for the attachment.
+
+##### `disposition`
 
-`disposition`
-: Defines the `Content-Disposition` header field for the attachment.
+Defines the `Content-Disposition` header field for the attachment.
 
-`fileName`
-: Defines the `filename` parameter of the `Content-Disposition` header field.
+##### `fileName`
 
-`description`
-: Defines the `Content-Description` header field for the attachment.
+Defines the `filename` parameter of the `Content-Disposition` header field.
+
+##### `description`
+
+Defines the `Content-Description` header field for the attachment.
 
 For example:
 
@@ -204,8 +209,6 @@ sendMail {
 }
 ```
 
-(mail-config)=
-
 ### Mail configuration
 
 If no mail server configuration is provided, Nextflow tries to send the email using the external mail command eventually provided by the underlying system (e.g. `sendmail` or `mail`).
@@ -220,7 +223,7 @@ mail {
 }
 ```
 
-:::{note}
+:::note
 Some versions of Java (e.g. Java 11 Corretto) do not default to TLS v1.2, and as a result may have issues with 3rd party integrations that enforce TLS v1.2 (e.g. Azure Active Directory OIDC). This problem can be addressed by setting the following config option:
 
 ```groovy
@@ -230,12 +233,11 @@ mail {
 ```
 :::
 
-See the {ref}`mail scope <config-mail>` section to learn more the mail server configuration options.
+See the [mail scope][config-mail] section to learn more the mail server configuration options.
 
 ### AWS SES configuration
 
-:::{versionadded} 23.06.0-edge
-:::
+<AddedInVersion version="23.06.0-edge" />
 
 Nextflow supports the [AWS Simple Email Service](https://aws.amazon.com/ses/) API as an alternative provider to send emails in place of an SMTP server.
 
@@ -267,7 +269,7 @@ mail {
 
 ## Mail notification
 
-You can use the `sendMail` function with a {ref}`workflow completion handler <metadata-completion-handler>` to notify a workflow completion. For example:
+You can use the `sendMail` function with a [workflow completion handler][metadata-completion-handler] to notify a workflow completion. For example:
 
 ```nextflow
 workflow.onComplete {
@@ -299,15 +301,16 @@ To enable simply specify the `-N` option when launching the pipeline execution.
 nextflow run <pipeline name> -N <recipient address>
 ```
 
-It will send a notification mail when the execution completes similar to the one shown below:
+It will send a notification mail when the execution completes.
 
-```{image} _static/workflow-notification-min.png
-```
-
-:::{warning}
+:::warning
 By default the notification message is sent with the `sendmail` system tool, which is assumed to be available in the environment where Nextflow is running. Make sure it's properly installed and configured. Alternatively, you can provide the SMTP server configuration settings to use the Nextflow built-in mail support, which doesn't require any external system tool.
 :::
 
 See the [Mail configuration](#mail-configuration) section to learn about the available mail delivery options and configuration settings.
 
-Read {ref}`Notification scope <config-notification>` section to learn more about the workflow notification configuration details.
+See [Completion handler](#completion-handler) to learn more about the workflow notification configuration details.
+
+[config-mail]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#mail
+[config-notification]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#notification
+[process-error-strategy]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#errorstrategy
diff --git a/new-docs/nextflow-docs/overview.mdx b/new-docs/nextflow-docs/overview.mdx
new file mode 100644
index 0000000000..b56d238636
--- /dev/null
+++ b/new-docs/nextflow-docs/overview.mdx
@@ -0,0 +1,121 @@
+# Overview
+
+## Why Nextflow?
+
+The rise of big data has made it increasingly necessary to be able to analyze and perform experiments on large datasets in a portable and reproducible manner. Parallelization and distributed computing are the best ways to tackle this challenge, but the tools commonly available to computational scientists often lack good support for these techniques, or they provide a model that fits poorly with the needs of computational scientists and often require knowledge of complex tools and APIs. Nextflow was created to address these challenges.
+
+The Nextflow language is inspired by [the Unix philosophy](https://en.wikipedia.org/wiki/Unix_philosophy), in which many simple command line tools can be chained together into increasingly complex tasks. Similarly, a Nextflow script consists of composing many simple processes into increasingly complex pipelines. Each process executes a given tool or scripting language, and by specifying the process inputs and outputs, Nextflow coordinates the execution of tasks for you.
+
+The Nextflow runtime integrates with many popular execution platforms (HPC schedulers, cloud providers) and software tools (Git, Docker, Conda), allowing you to fully describe a computational pipeline with all of its dependencies and run it in nearly any environment - write once, run anywhere.
+
+## Processes and dataflow
+
+In practice a Nextflow pipeline script is made by joining together different processes. Each process can be written in any scripting language that can be executed by the Linux platform (Bash, Perl, Ruby, Python, etc.).
+
+A process can define one or more *inputs* and *outputs*. Data flows from process to process through asynchronous dataflow structures, known as *channels* and *values* in Nextflow. The data dependencies between these processes implicitly determines the flow of execution.
+
+A Nextflow script looks like this:
+
+```nextflow
+// Script parameters
+params.query = "/some/data/sample.fa"
+params.db = "/some/path/pdb"
+
+process blast_search {
+  input:
+  path query
+  path db
+
+  output:
+  path "top_hits.txt"
+
+  script:
+  """
+  blastp -db $db -query $query -outfmt 6 > blast_result
+  cat blast_result | head -n 10 | cut -f 2 > top_hits.txt
+  """
+}
+
+process extract_top_hits {
+  input:
+  path top_hits
+  path db
+
+  output:
+  path "sequences.txt"
+
+  script:
+  """
+  blastdbcmd -db $db -entry_batch $top_hits > sequences.txt
+  """
+}
+
+workflow {
+  def query_ch = channel.fromPath(params.query)
+  blast_search(query_ch, params.db)
+  extract_top_hits(blast_search.out, params.db).view()
+}
+```
+
+The above example defines two processes. Their execution order is not determined by the fact that the `blast_search` process comes before `extract_top_hits` in the script (it could also be written the other way around). Instead, execution order is determined by their _dependencies_ -- `extract_top_hits` depends on the output of `blast_search`, so `blast_search` will be executed first, and then `extract_top_hits`.
+
+When the workflow is executed, it creates two processes (`blast_search` and `extract_top_hits`) connected by the channel `query_ch`. Each process executes a task and emits a value for each input that it receives. Whenever `blast_search` emits a value, `extract_top_hits` receives it through the `query_ch` channel.
+
+Read the [Channels][channels-page] and [Dataflow][dataflow-page] pages to learn more about these features.
+
+## Execution abstraction
+
+While a process defines *what* command or script has to be executed, the *executor* determines *how* that script is actually run on the target system.
+
+If not otherwise specified, processes are executed on the local computer. The local executor is very useful for pipeline development and testing purposes, but for real world computational pipelines an HPC or cloud platform is often required.
+
+In other words, Nextflow provides an abstraction between the pipeline's functional logic and the underlying execution system. Thus it is possible to write a pipeline once and to seamlessly run it on your computer, a grid platform, or the cloud, without modifying it, by simply defining the target execution platform in the configuration file.
+
+The following batch schedulers are supported:
+
+- [Open Grid Engine](http://gridscheduler.sourceforge.net/)
+- [Univa Grid Engine](http://www.univa.com/)
+- [Platform LSF](http://www.ibm.com/systems/technicalcomputing/platformcomputing/products/lsf/)
+- [SLURM](https://computing.llnl.gov/linux/slurm/)
+- [Flux Framework](https://flux-framework.org/)
+- [PBS](http://www.pbsworks.com/gridengine/)
+- [Torque](http://www.adaptivecomputing.com/products/open-source/torque/)
+- [HTCondor](https://research.cs.wisc.edu/htcondor/)
+
+The following cloud platforms are supported:
+
+- [Amazon Web Services (AWS)](https://aws.amazon.com/)
+- [Microsoft Azure](https://azure.microsoft.com/)
+- [Google Cloud Platform (GCP)](https://cloud.google.com/)
+- [Kubernetes](https://kubernetes.io/)
+
+See [Executors][executors-page] to learn more.
+
+## Scripting language
+
+Nextflow is a workflow language based on [Java](https://en.wikipedia.org/wiki/Java_(programming_language)) and [Groovy](https://groovy-lang.org/). It is designed to simplify writing scalable and reproducible pipelines. In most cases, users can leverage their existing programming skills to develop Nextflow pipelines without the steep learning curve that usually comes with a new programming language.
+
+See [Scripts][scripts-page] for more information about the Nextflow scripting language.
+
+## Configuration options
+
+Pipeline configuration properties are defined in a file named `nextflow.config` in the pipeline execution directory.
+
+This file can be used to define which executor to use, the process's environment variables, pipeline parameters etc.
+
+A basic configuration file might look like this:
+
+```groovy
+process {
+  executor = 'sge'
+  queue = 'cn-el6'
+}
+```
+
+See [Configuration][configuration-page] to learn more about the Nextflow configuration file and settings.
+
+[channels-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[configuration-page]: /nextflow_docs/nextflow_repo/docs/config.mdx
+[executors-page]: /nextflow_docs/nextflow_repo/docs/executor.mdx
+[dataflow-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[scripts-page]: /nextflow_docs/nextflow_repo/docs/script.mdx
diff --git a/docs/plugins/developing-plugins.md b/new-docs/nextflow-docs/plugins/developing-plugins.mdx
similarity index 81%
rename from docs/plugins/developing-plugins.md
rename to new-docs/nextflow-docs/plugins/developing-plugins.mdx
index 1c01085e4a..11bb01654a 100644
--- a/docs/plugins/developing-plugins.md
+++ b/new-docs/nextflow-docs/plugins/developing-plugins.mdx
@@ -1,23 +1,19 @@
-(dev-plugins-page)=
+
 
 # Developing plugins
 
 This page describes how to develop plugins for Nextflow.
 
-(dev-plugins-template)=
-
 ## Nextflow plugin template
 
 The [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/) is a scaffold for plugin development. It uses [Gradle](https://gradle.org/), a build automation tool optimized for Java and Groovy projects, as well as the [Nextflow Gradle plugin](https://github.com/nextflow-io/nextflow-plugin-gradle).
 
-You can use the `nextflow plugin create` sub-command to create plugins using the plugin template. See {ref}`gradle-plugin-create` for more information.
+You can use the `nextflow plugin create` sub-command to create plugins using the plugin template. See [Creating a plugin][gradle-plugin-create] for more information.
 
-:::{note}
-The Nextflow Gradle plugin is currently available as a public preview. See {ref}`Migrating to the Nextflow plugin registry <plugin-registry-page>` for more information.
+:::note
+The Nextflow Gradle plugin is currently available as a public preview. See [Migrating to the Nextflow plugin registry][plugin-registry-page>] for more information.
 :::
 
-(dev-plugins-structure)=
-
 ### Structure
 
 The plugin template includes the source directories, build configuration files, and metadata required for development, testing, and publishing. Depending on the developer’s preference, plugins can be written in Java or Groovy.
@@ -98,7 +94,7 @@ plugins {
 }
 ```
 
-:::{note}
+:::note
 You can develop Nextflow plugins without the Gradle plugin. However, this approach is only suggested if you are an advanced developer and your project is incompatible with the Gradle plugin.
 :::
 
@@ -114,19 +110,21 @@ make assemble
 
 The following `make` commands are available:
 
-`assemble`
-: Compiles the Nextflow plugin code and assembles it into a zip archive.
+##### `assemble`
+
+Compiles the Nextflow plugin code and assembles it into a zip archive.
 
-`install`
-: Installs the plugin into the local Nextflow plugins directory.
+##### `install`
 
-`release`
-: Publishes the plugin. See {ref}`gradle-plugin-publish` for more information.
+Installs the plugin into the local Nextflow plugins directory.
 
-`test`
-: Runs plugin unit tests. See {ref}`gradle-plugin-test` for more information.
+##### `release`
 
-(dev-plugins-extension-points)=
+Publishes the plugin. See [Publish a plugin][gradle-plugin-publish] for more information.
+
+##### `test`
+
+Runs plugin unit tests. See [Test a plugin][gradle-plugin-test] for more information.
 
 ## Extension points
 
@@ -168,9 +166,7 @@ The command can be run using the `nextflow plugin` command:
 nextflow plugin my-plugin:hello --alpha --beta
 ```
 
-See the {ref}`cli-plugin` for usage information.
-
-(dev-plugins-extension-points-config)=
+See the [plugin][cli-plugin] for usage information.
 
 ### Configuration
 
@@ -204,12 +200,11 @@ myplugin {
 }
 ```
 
-:::{versionadded} 25.04.0
-:::
+<AddedInVersion version="25.04.0" />
 
-:::{versionchanged} 25.10.0
+<ChangedInVersion version="25.04.0">
 The `nextflow.config.schema` package was renamed to `nextflow.config.spec`.
-:::
+</ChangedInVersion>
 
 Plugins can declare their configuration options by implementing the `ConfigScope` interface and declaring each config option as a field with the `@ConfigOption` annotation. For example:
 
@@ -241,7 +236,7 @@ class MyPluginConfig implements ConfigScope {
 }
 ```
 
-This approach is not required to support plugin config options. However, it allows Nextflow to recognize plugin definitions when validating the configuration. See {ref}`config-scopes-page` for more information.
+This approach is not required to support plugin config options. However, it allows Nextflow to recognize plugin definitions when validating the configuration. See [Configuration scopes][config-scopes-page] for more information.
 
 ### Executors
 
@@ -272,13 +267,13 @@ process hello {
 }
 ```
 
-:::{tip}
+:::tip
 See the source code of Nextflow's built-in executors for examples of how to implement various executor components.
 :::
 
 ### Filesystems
 
-Plugins can define custom filesystems that Nextflow can use to interact with external storage systems using a single interface. For more information about accessing remote files, see {ref}`remote-files`.
+Plugins can define custom filesystems that Nextflow can use to interact with external storage systems using a single interface. For more information about accessing remote files, see [Remote files][remote-files].
 
 To implement a custom filesystem, create a class in your plugin that extends [`FileSystemProvider`](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/nio/file/spi/FileSystemProvider.html). Implement the `getScheme()` method to define the URI scheme for your filesystem. For example:
 
@@ -304,14 +299,13 @@ input = file('myfs://<PATH_TO_INPUT_FILE>')
 
 See [Developing a Custom File System Provider](https://docs.oracle.com/javase/8/docs/technotes/guides/io/fsp/filesystemprovider.html) for more information and the `nf-amazon` plugin (`S3FileSystemProvider`) for an example of a custom filesystem.
 
-:::{tip}
+:::tip
 Custom filesystems are an advanced plugin extension. Before creating a new filesystem, check that your use case cannot already be supported by an existing filesystem such as HTTP or S3.
 :::
 
 ### Functions
 
-:::{versionadded} 22.10.0
-:::
+<AddedInVersion version="22.10.0" />
 
 Plugins can define custom functions that can be included in Nextflow pipelines.
 
@@ -350,8 +344,7 @@ include { reverseString as anotherReverseMethod } from 'plugin/my-plugin'
 
 ### Operators
 
-:::{versionadded} 22.04.0
-:::
+<AddedInVersion version="22.04.0" />
 
 Plugins can define custom channel factories and operators that can then be included in pipelines.
 
@@ -394,19 +387,19 @@ channel
     .sqlInsert(into: 'BAR', columns: 'id', db: 'test')
 ```
 
-:::{note}
+:::note
 The above snippet is based on the [nf-sqldb](https://github.com/nextflow-io/nf-sqldb) plugin. The `fromQuery` factory is included under the alias `fromTable`.
 :::
 
-:::{tip}
+:::tip
 Before creating a custom operator, consider whether the operator can be defined as a [function](#functions) that can be composed with existing operators such as `map` or `subscribe`. Functions are easier to implement and can be used anywhere in your pipeline, not just channel logic.
 :::
 
 ### Process directives
 
-Plugins that implement a custom executor will likely need to access {ref}`process directives <process-directives>` that affect the task execution. When an executor receives a task, the process directives can be accessed through that task’s configuration. Custom executors should try to support all process directives that have executor-specific behavior and are relevant to the executor.
+Plugins that implement a custom executor will likely need to access [process directives][process-directives] that affect the task execution. When an executor receives a task, the process directives can be accessed through that task’s configuration. Custom executors should try to support all process directives that have executor-specific behavior and are relevant to the executor.
 
-Nextflow does not provide the ability to define custom process directives in a plugin. Instead, use the {ref}`process-ext` directive to provide custom process settings to your executor. Use specific names that are not likely to conflict with other plugins or existing pipelines.
+Nextflow does not provide the ability to define custom process directives in a plugin. Instead, use the [`ext`][process-ext] directive directive to provide custom process settings to your executor. Use specific names that are not likely to conflict with other plugins or existing pipelines.
 
 For example, a custom executor can use existing process directives and a custom setting through the `ext` directive:
 
@@ -429,13 +422,11 @@ class MyExecutor extends Executor {
 }
 ```
 
-(plugins-trace-observers)=
-
 ### Trace observers
 
-:::{versionchanged} 25.04.0
+<ChangedInVersion version="25.04.0">
 The `TraceObserver` interface is now deprecated. Use [TraceObserverV2](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserverV2.groovy) and [TraceObserverFactoryV2](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserverFactoryV2.groovy) instead.
-:::
+</ChangedInVersion>
 
 A *trace observer* is an entity that can listen and react to workflow events, such as when a workflow starts, a task is completed, or a file is published. Several components in Nextflow, such as the execution report and DAG visualization, are implemented as trace observers.
 
@@ -449,7 +440,7 @@ import nextflow.trace.TraceObserver
 import nextflow.trace.TraceRecord
 
 class MyObserver implements TraceObserver {
-    
+
     @Override
     void onFlowBegin() {
         println "Okay, let's begin!"
@@ -469,7 +460,7 @@ class MyObserver implements TraceObserver {
     void onFilePublish(Path destination, Path source) {
         println "I published a file! It's located at ${path.toUriString()}"
     }
-    
+
     @Override
     void onFlowError(TaskHandler handler, TraceRecord trace) {
         println "Uh oh, something went wrong..."
@@ -490,39 +481,50 @@ myplugin.enabled = true
 
 See the [`TraceObserver` source code](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy) for descriptions of the available workflow events.
 
-(dev-plugins-env-vars)=
-
 ## Environment variables
 
 The following environment variables are available to develop and test plugins:
 
-`NXF_PLUGINS_MODE`
-: The plugin execution mode. Either `prod` for production or `dev` for development.
+##### `NXF_PLUGINS_MODE`
+
+The plugin execution mode. Either `prod` for production or `dev` for development.
+
+##### `NXF_PLUGINS_DIR`
+
+The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins` in production and `./plugins` in development).
+
+##### `NXF_PLUGINS_DEFAULT`
 
-`NXF_PLUGINS_DIR`
-: The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins` in production and `./plugins` in development).
+Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: true).
 
-`NXF_PLUGINS_DEFAULT`
-: Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: true).
+##### `NXF_PLUGINS_DEV`
 
-`NXF_PLUGINS_DEV`
-: Comma-separated list of development plugin root directories.
+Comma-separated list of development plugin root directories.
 
-`NXF_PLUGINS_TEST_REPOSITORY`
-: :::{versionadded} 23.04.0.
-  :::
-: Comma-separated list of URIs for additional plugin registries or meta files, which will be used in addition to the default registry.
+##### `NXF_PLUGINS_TEST_REPOSITORY`
 
-: The URI should refer to a plugin repository JSON file or a specific plugin JSON meta file. In the latter case, it should match the pattern `https://host.name/some/path/<PLUGIN_NAME>-X.Y.Z-meta.json`. For example:
 
-    ```bash
-    # custom plugin repository at https://github.com/my-org/plugins
-    export NXF_PLUGINS_TEST_REPOSITORY="https://raw.githubusercontent.com/my-org/plugins/main/plugins.json"
+<AddedInVersion version="23.04.0" />
 
-    # custom plugin release
-    export NXF_PLUGINS_TEST_REPOSITORY="https://github.com/nextflow-io/nf-hello/releases/download/0.3.0/nf-hello-0.3.0-meta.json"
+Comma-separated list of URIs for additional plugin registries or meta files, which will be used in addition to the default registry.
+
+The URI should refer to a plugin repository JSON file or a specific plugin JSON meta file. In the latter case, it should match the pattern `https://host.name/some/path/<PLUGIN_NAME>-X.Y.Z-meta.json`. For example:
+
+```bash
+# custom plugin repository at https://github.com/my-org/plugins
+export NXF_PLUGINS_TEST_REPOSITORY="https://raw.githubusercontent.com/my-org/plugins/main/plugins.json"
+
+# custom plugin release
+export NXF_PLUGINS_TEST_REPOSITORY="https://github.com/nextflow-io/nf-hello/releases/download/0.3.0/nf-hello-0.3.0-meta.json"
+
+nextflow run main.nf -plugins nf-hello
+```
 
-    nextflow run main.nf -plugins nf-hello
-    ```
+This variable is useful for testing a plugin release before publishing it to the main registry.
 
-: This variable is useful for testing a plugin release before publishing it to the main registry.
+[cli-plugin]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#plugin
+[config-scopes-page]: /nextflow_docs/nextflow_repo/docs/developer/config-scopes.mdx#config-scopes
+[gradle-plugin-create]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#creating-a-plugin
+[process-directives]: /nextflow_docs/nextflow_repo/docs/process.mdx#directives
+[process-ext]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#ext
+[remote-files]: /nextflow_docs/nextflow_repo/docs/working-with-files.mdx#remote-files
diff --git a/docs/plugins/plugin-registry.md b/new-docs/nextflow-docs/plugins/plugin-registry.mdx
similarity index 82%
rename from docs/plugins/plugin-registry.md
rename to new-docs/nextflow-docs/plugins/plugin-registry.mdx
index 8b24423ec2..8b129a7544 100644
--- a/docs/plugins/plugin-registry.md
+++ b/new-docs/nextflow-docs/plugins/plugin-registry.mdx
@@ -1,17 +1,15 @@
-(plugin-registry-page)=
+
 
 # Nextflow plugin registry
 
 The [Nextflow plugin registry](https://registry.nextflow.io/) is a central repository for Nextflow plugins. It hosts an index of plugin metadata that supports plugin discovery, accessibility, and version tracking.
 
-Nextflow 25.10 and later can use the plugin registry as a drop-in replacement for the [legacy plugin index](https://github.com/nextflow-io/plugins) hosted on GitHub. See {ref}`migrate-plugin-page` for more information about migrating to the Nextflow plugin registry.
+Nextflow 25.10 and later can use the plugin registry as a drop-in replacement for the [legacy plugin index](https://github.com/nextflow-io/plugins) hosted on GitHub. See [Migrating to the Nextflow plugin registry][migrate-plugin-page] for more information about migrating to the Nextflow plugin registry.
 
-:::{note}
+:::note
 The Nextflow plugin registry is currently available as a public preview. Plugin developers can access the registry by contacting [info@nextflow.io](mailto:info@nextflow.io) to obtain access to the registry.
 :::
 
-(plugin-registry-claim)=
-
 ## Claiming a plugin
 
 Ownership of a plugin is required to publish plugins to the Nextflow plugin registry.
@@ -22,7 +20,7 @@ To claim ownership of a plugin:
 
 2. Log in to [Seqera](https://cloud.seqera.io/login) with your GitHub or Google account, or by providing an email address.
 
-    :::{note}
+    :::note
     If you are logging in for the first time, Seqera will send an authentication link to your email address to complete the login process.
     :::
 
@@ -32,7 +30,7 @@ To claim ownership of a plugin:
 
 5. Enter your organization name in the **Provider** field.
 
-    :::{note}
+    :::note
     This organization must match with the organization specified when publishing your plugin.
     :::
 
@@ -40,8 +38,6 @@ To claim ownership of a plugin:
 
 The plugin will show as **PENDING REVIEW** under **Pending Ownership Requests** until an admin approves the claim. Admin approval is required only once.
 
-(plugin-registry-access-token)=
-
 ## Creating an access token
 
 An API access token is required to publish plugins to the Nextflow plugin registry.
@@ -52,7 +48,7 @@ To create an API access token:
 
 2. Log in to [Seqera](https://cloud.seqera.io/login) with your GitHub or Google account, or by providing an email address.
 
-    :::{note}
+    :::note
     If you are logging in for the first time, Seqera will send an authentication link to your email address to complete the login process.
     :::
 
@@ -64,4 +60,7 @@ To create an API access token:
 
 6. Copy and past token somewhere safe, you won't be able to see it again.
 
-Once you have your token, see {ref}`gradle-plugin-publish` for instructions on how to use it.
+Once you have your token, see [Publishing a plugin][gradle-plugin-publish] for instructions on how to use it.
+
+[gradle-plugin-publish]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#publishing-a-plugin
+[migrate-plugin-page]: /nextflow_docs/nextflow_repo/docs/guides/migrate-plugin.mdx
diff --git a/docs/plugins/plugins.md b/new-docs/nextflow-docs/plugins/plugins.mdx
similarity index 81%
rename from docs/plugins/plugins.md
rename to new-docs/nextflow-docs/plugins/plugins.mdx
index 5507005c30..9411220808 100644
--- a/docs/plugins/plugins.md
+++ b/new-docs/nextflow-docs/plugins/plugins.mdx
@@ -1,4 +1,4 @@
-(plugins-page)=
+
 
 # Overview
 
@@ -20,10 +20,10 @@ Core plugins do not require configuration. The latest versions of core plugins a
 * `nf-tower`: Support for [Seqera Platform](https://seqera.io/platform/).
 * `nf-wave`: Support for [Wave containers service](https://seqera.io/wave/).
 
-Specific versions of core plugins can be declared in Nextflow configuration files or by using the `-plugins` option. See {ref}`using-plugins-page` for more information.
+Specific versions of core plugins can be declared in Nextflow configuration files or by using the `-plugins` option. See [Using plugins][using-plugins-page] for more information.
 
-:::{note}
-The automatic retrieval of core plugins can be disabled by setting `NXF_PLUGINS_DEFAULT=false`. See {ref}`dev-plugins-env-vars` for more information.
+:::note
+The automatic retrieval of core plugins can be disabled by setting `NXF_PLUGINS_DEFAULT=false`. See [Environment variables][dev-plugins-env-vars] for more information.
 :::
 
 <h3>Third-party plugins</h3>
@@ -42,7 +42,7 @@ To configure plugins at runtime, use the `-plugins` option. For example:
 nextflow run main.nf -plugins nf-hello@0.5.0
 ```
 
-See {ref}`using-plugins-page` for more information.
+See [Using plugins][using-plugins-page] for more information.
 
 ## Versioning
 
@@ -55,3 +55,6 @@ Semantic versions have the form MAJOR.MINOR.PATCH (e.g., 0.5.0):
 * PATCH: Increment for backward-compatible bug fixes.
 
 Optional pre-release and build metadata can be added (e.g., 1.2.1-alpha+001) as extensions to the base version format.
+
+[dev-plugins-env-vars]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx#environment-variables
+[using-plugins-page]: /nextflow_docs/nextflow_repo/docs/plugins/using-plugins.mdx
diff --git a/docs/plugins/using-plugins.md b/new-docs/nextflow-docs/plugins/using-plugins.mdx
similarity index 78%
rename from docs/plugins/using-plugins.md
rename to new-docs/nextflow-docs/plugins/using-plugins.mdx
index 405789c0d5..49cb8b4f4a 100644
--- a/docs/plugins/using-plugins.md
+++ b/new-docs/nextflow-docs/plugins/using-plugins.mdx
@@ -1,11 +1,9 @@
-(using-plugins-page)=
+
 
 # Using plugins
 
 Nextflow core plugins require no additional configuration. When a pipeline uses a core plugin, Nextflow automatically downloads and uses the latest compatible plugin version. In contrast, third-party plugins must be explicitly declared. When a pipeline uses one or more third-party plugins, Nextflow must be configured to download and use the plugin.
 
-(using-plugins-identifiers)=
-
 ## Identifiers
 
 A plugin identifier consists of the plugin name and version, separated by an `@` symbol:
@@ -16,21 +14,18 @@ nf-hello@0.5.0
 
 The plugin version is optional. If it is not specified, Nextflow will download the latest version of the plugin that meets the minimum Nextflow version requirements specified by the plugin.
 
-:::{note}
-Plugin versions are required for {ref}`offline usage <using-plugins-offline>`.
+:::note
+Plugin versions are required for [offline usage](#offline-usage).
 :::
 
-:::{versionadded} 25.04.0
-:::
+<AddedInVersion version="25.04.0" />
 
 The plugin version can be prefixed with `~` to pin the major and minor versions and allow the latest patch release to be used. For example, `nf-amazon@~2.9.0` will resolve to the latest version matching `2.9.x`. When working offline, Nextflow will resolve version ranges against the local plugin cache defined by `NXF_PLUGINS_DIR`.
 
-:::{tip}
+:::tip
 It is recommended to pin the major and minor version of each plugin to minimize the risk of breaking changes while allowing patch updates to be used automatically.
 :::
 
-(using-plugins-config)=
-
 ## Configuration
 
 Plugins can be configured via Nextflow configuration files or at runtime.
@@ -50,7 +45,7 @@ To configure plugins at runtime, use the `-plugins` option. For example:
 nextflow run main.nf -plugins nf-hello@0.5.0,nf-amazon@2.9.0
 ```
 
-:::{note}
+:::note
 Plugin declarations in Nextflow configuration files are ignored when specifying plugins via the `-plugins` option.
 :::
 
@@ -58,22 +53,25 @@ Plugin declarations in Nextflow configuration files are ignored when specifying
 
 When Nextflow downloads plugins, it caches them in the directory specified by `NXF_PLUGINS_DIR` (`$HOME/.nextflow/plugins` by default).
 
-(using-plugins-offline)=
-
 ## Offline usage
 
 When running Nextflow in an offline environment, any required plugins must be downloaded and moved into the offline environment prior to any runs.
 
 To use Nextflow plugins in an offline environment:
 
-1. Install a self-contained version of Nextflow in an environment with an internet connection. See {ref}`install-standalone` for more information.
+1. Install a self-contained version of Nextflow in an environment with an internet connection. See [Standalone distribution][install-standalone] for more information.
 
 2. Run `nextflow plugin install <PLUGIN_NAME>@<VERSION>` for each required plugin to download it. Alternatively, run the pipeline once, which will automatically download all plugins required by the pipeline.
 
 3. Copy the `nextflow` binary and `$HOME/.nextflow` directory to the offline environment.
 
-4. Specify each plugin and its version in Nextflow configuration files or at runtime. See {ref}`using-plugins-config` for more information.
+4. Specify each plugin and its version in Nextflow configuration files or at runtime. See [Configuration][using-plugins-config] for more information.
 
-    :::{warning}
-    Nextflow will attempt to download newer versions of plugins if their versions are not set. See {ref}`using-plugins-identifiers` for more information.
+    :::warning
+    Nextflow will attempt to download newer versions of plugins if their versions are not set. See [Identifiers][using-plugins-identifiers] for more information.
     :::
+
+[install-standalone]: /nextflow_docs/nextflow_repo/docs/install.mdx#standalone-distribution
+[using-plugins-config]: /nextflow_docs/nextflow_repo/docs/plugins/using-plugins.mdx#configuration
+[using-plugins-identifiers]: /nextflow_docs/nextflow_repo/docs/plugins/using-plugins.mdx#identifiers
+
diff --git a/new-docs/nextflow-docs/process-typed.md b/new-docs/nextflow-docs/process-typed.md
new file mode 100644
index 0000000000..bea15e56e9
--- /dev/null
+++ b/new-docs/nextflow-docs/process-typed.md
@@ -0,0 +1,251 @@
+(process-typed-page)=
+
+# Processes (typed)
+
+:::{versionadded} 25.10.0
+:::
+
+Typed processes use a new syntax for inputs and outputs based on static types.
+
+```nextflow
+nextflow.preview.types = true
+
+process hello {
+    input:
+    message: String
+
+    output:
+    file('hello.txt')
+
+    script:
+    """
+    echo '${message}' > hello.txt
+    """
+}
+```
+
+In order to use this feature, you'll need to:
+
+1. Enable {ref}`strict syntax <strict-syntax-page>` by setting `NXF_SYNTAX_PARSER=v2`.
+2. Set `nextflow.preview.types = true` in every script that uses typed processes.
+
+See {ref}`syntax-process-typed` for the complete syntax reference and {ref}`migrating-static-types` to migrate existing code to static types.
+
+## Inputs
+
+The `input:` section declares process inputs. In typed processes, each input declaration consists of a name and type:
+
+```nextflow
+process fastqc {
+    input:
+    (meta, fastq): Tuple<Map,Path>
+    extra_args: String
+
+    script:
+    """
+    echo 'meta: ${meta}`
+    echo 'fastq: ${fastq}'
+    echo 'extra_args: ${extra_args}'
+    """
+}
+```
+
+All {ref}`standard types <stdlib-types>` except for the dataflow types (`Channel` and `Value`) can be used as type annotations in processes.
+
+### File inputs
+
+Nextflow automatically stages `Path` inputs and `Path` collections (such as `Set<Path>`) into the task directory.
+
+By default, tasks fail if any input receives a `null` value. To allow `null` values, add `?` to the type annotation:
+
+```nextflow
+process cat_opt {
+    input:
+    input: Path?
+
+    stage:
+    stageAs 'input.txt', input
+
+    output:
+    stdout()
+
+    script:
+    '''
+    [[ -f input.txt ]] && cat input.txt || echo 'empty input'
+    '''
+}
+```
+
+### Stage directives
+
+The `stage:` section defines custom staging behavior using *stage directives*.  It should be specified after the `input:` section. These directives serve the same purpose as input qualifiers such as `env` and `stdin` in the legacy syntax. 
+
+The `env` directive declares an environment variable in terms of task inputs:
+
+```nextflow
+process echo_env {
+    input:
+    hello: String
+
+    stage:
+    env 'HELLO', hello
+
+    script:
+    '''
+    echo "$HELLO world!"
+    '''
+}
+```
+
+The `stdin` directive defines the standard input of the task script:
+
+```nextflow
+process cat {
+    input:
+    message: String
+
+    stage:
+    stdin message
+
+    script:
+    """
+    cat -
+    """
+}
+```
+
+The `stageAs` directive stages an input file (or files) under a custom file pattern:
+
+```nextflow
+process blast {
+    input:
+    fasta: Path
+
+    stage:
+    stageAs 'query.fa', fasta
+
+    script:
+    """
+    blastp -query query.fa -db nr
+    """
+}
+```
+
+The file pattern can also reference task inputs:
+
+```nextflow
+process grep {
+    input:
+    id: String
+    fasta: Path
+
+    stage:
+    stageAs "${id}.fa", fasta
+
+    script:
+    """
+    cat ${id}.fa | grep '>'
+    """
+}
+```
+
+See {ref}`process-reference-typed` for available stage directives.
+
+## Outputs
+
+The `output:` section declares the outputs of a typed process. Each output declaration consists of a name, an optional type, and an output value:
+
+```nextflow
+process echo {
+    input:
+    message: String
+
+    output:
+    out_env: String = env('MESSAGE')
+    out_file: Path = file('message.txt')
+    out_std: String = stdout()
+
+    script:
+    """
+    export MESSAGE='${message}'
+
+    echo \$MESSAGE > message.txt
+
+    cat message.txt
+    """
+}
+```
+
+When there is only one output, the name can be omitted:
+
+```nextflow
+process echo {
+    input:
+    message: String
+
+    output:
+    stdout()
+
+    script:
+    """
+    echo '${message}'
+    """
+}
+```
+
+See {ref}`process-reference-typed` for available output functions.
+
+### File outputs
+
+You can use the `file()` and `files()` functions in the `output:` section to get a single file or collection of files from the task directory.
+
+By default, the `file()` function fails if the specified file is not present in the task directory. You can specify `optional: true` to allow missing files. The `file()` function returns `null` for missing files. For example:
+
+```nextflow
+process foo {
+    output:
+    file('output.txt', optional: true)
+
+    script:
+    """
+    exit 0
+    """
+}
+```
+
+## Topics
+
+The `topic:` section emits values to {ref}`topic channels <channel-topic>`. A topic emission consists of an output value and a topic name:
+
+```nextflow
+process cat {
+    input:
+    message: Path
+
+    output:
+    stdout()
+
+    topic:
+    tuple('bash', eval('bash --version')) >> 'versions'
+    tuple('cat', eval('cat --version')) >> 'versions'
+
+    script:
+    """
+    cat ${message}
+    """
+}
+```
+
+Topic emissions can use the same {ref}`output functions <process-reference-typed>` as the `output:` section.
+
+## Script
+
+The `script:` and `exec:` sections behave the same way as {ref}`legacy processes <process-script>`.
+
+## Stub
+
+The `stub:` section behaves the same way as {ref}`legacy processes <process-stub>`.
+
+## Directives
+
+Directives behave the same way as {ref}`legacy processes <process-directives>`.
diff --git a/docs/process.md b/new-docs/nextflow-docs/process.mdx
similarity index 80%
rename from docs/process.md
rename to new-docs/nextflow-docs/process.mdx
index d3c698736c..9dfcf09c40 100644
--- a/docs/process.md
+++ b/new-docs/nextflow-docs/process.mdx
@@ -1,4 +1,4 @@
-(process-page)=
+
 
 # Processes
 
@@ -18,9 +18,7 @@ process hello {
 }
 ```
 
-See {ref}`syntax-process` for a full description of the process syntax.
-
-(process-script)=
+See [Process][syntax-process] for a full description of the process syntax.
 
 ## Script
 
@@ -48,7 +46,7 @@ There is a subtle but important difference between them. Like in Bash, strings d
 
 In the above code fragment, the `$db` variable is replaced by the actual value defined elsewhere in the pipeline script.
 
-:::{warning}
+:::warning
 Since Nextflow uses the same Bash syntax for variable substitutions in strings, you must manage them carefully depending on whether you want to evaluate a *Nextflow* variable or a *Bash* variable.
 :::
 
@@ -113,7 +111,7 @@ workflow {
 }
 ```
 
-:::{tip}
+:::tip
 Since the actual location of the interpreter binary file can differ across platforms, it is wise to use the `env` command followed by the interpreter name, e.g. `#!/usr/bin/env perl`, instead of the absolute path, in order to make your script more portable.
 :::
 
@@ -153,8 +151,6 @@ process align {
 
 In the above example, the process will execute one of several scripts depending on the value of the `mode` parameter. By default it will execute the `tcoffee` command.
 
-(process-template)=
-
 ### Template
 
 Process scripts can be externalized to **template** files, which allows them to be reused across different processes and tested independently from the pipeline execution.
@@ -200,19 +196,17 @@ The following caveats should be considered:
 
 - Template variables are evaluated even if they are commented out in the template script. If a template variable is missing, it will cause the pipeline to fail regardless of where it occurs in the template.
 
-:::{tip}
+:::tip
 Template scripts are generally discouraged due to the caveats described above. The best practice for using a custom script is to embed it in the process definition at first and move it to a separate file with its own command line interface once the code matures.
 :::
 
-(process-shell)=
-
 ### Shell
 
-:::{deprecated} 24.11.0-edge
-Use the `script` section instead. Consider using the {ref}`strict syntax <strict-syntax-page>`, which provides error checking to help distinguish between Nextflow variables and Bash variables in the process script.
-:::
+<DeprecatedInVersion version="24.11.0-edge">
+Use the `script` section instead. Consider using the [strict syntax][strict-syntax-page], which provides error checking to help distinguish between Nextflow variables and Bash variables in the process script.
+</DeprecatedInVersion>
 
-The `shell` section is a string expression that defines the script that is executed by the process. It is an alternative to the {ref}`process-script` definition with one important difference: it uses the exclamation mark `!` character, instead of the usual dollar `$` character, to denote Nextflow variables.
+The `shell` section is a string expression that defines the script that is executed by the process. It is an alternative to the [Script][process-script] definition with one important difference: it uses the exclamation mark `!` character, instead of the usual dollar `$` character, to denote Nextflow variables.
 
 This way, it is possible to use both Nextflow and Bash variables in the same script without having to escape the latter, which makes process scripts easier to read and maintain. For example:
 
@@ -234,14 +228,12 @@ workflow {
 
 In the above example, `$USER` is treated as a Bash variable, while `!{str}` is treated as a Nextflow variable.
 
-:::{note}
-- Shell script definitions require the use of single-quote `'` delimited strings. When using double-quote `"` delimited strings, dollar variables are interpreted as Nextflow variables as usual. See {ref}`string-interpolation`.
+:::note
+- Shell script definitions require the use of single-quote `'` delimited strings. When using double-quote `"` delimited strings, dollar variables are interpreted as Nextflow variables as usual. See [String interpolation][string-interpolation] for more information.
 - Variables prefixed with `!` must always be enclosed in curly brackets, i.e. `!{str}` is a valid variable whereas `!str` is ignored.
-- Shell scripts support the use of the {ref}`process-template` mechanism. The same rules are applied to the variables defined in the template script.
+- Shell scripts support the use of the [Template][process-template] mechanism. The same rules are applied to the variables defined in the template script.
 :::
 
-(process-native)=
-
 ### Native execution
 
 The `exec` section executes the given code without launching a job.
@@ -270,14 +262,11 @@ Hello Mr. a
 Hello Mr. c
 ```
 
-A native process is very similar to a {ref}`function <syntax-function>`. However, it provides additional capabilities such as parallelism, caching, and progress logging.
-
-(process-stub)=
+A native process is very similar to a [function][syntax-function]. However, it provides additional capabilities such as parallelism, caching, and progress logging.
 
 ## Stub
 
-:::{versionadded} 20.11.0-edge
-:::
+<AddedInVersion version="20.11.0-edge" />
 
 You can define a command *stub*, which replaces the actual process command when the `-stub-run` or `-stub` command-line option is enabled:
 
@@ -308,8 +297,6 @@ The `stub` section can be defined before or after the `script` section. When the
 
 This feature makes it easier to quickly prototype the workflow logic without using the real commands. The developer can use it to provide a dummy script that mimics the execution of the real one in a quicker manner. In other words, it is a way to perform a dry-run.
 
-(process-input)=
-
 ## Inputs
 
 The `input` section defines the input of a process, similar to function arguments. A process may have at most one input section, which must contain at least one input declaration.
@@ -334,7 +321,7 @@ The following input qualifiers are available:
 - `tuple`: Handle a group of input values having any of the above qualifiers.
 - `each`: Execute the process for each element in the input collection.
 
-See {ref}`process reference <process-reference-inputs>` for the full list of input methods and options.
+See [process reference][process-reference-inputs] for the full list of input methods and options.
 
 ### Input variables (`val`)
 
@@ -365,11 +352,11 @@ process job 1
 process job 2
 ```
 
-:::{note}
+:::note
 Processes do not necessarily process items in the order that they are received. In the above example, the value `3` was processed before the others.
 :::
 
-:::{note}
+:::note
 When the process declares exactly one input, the pipe `|` operator can be used to provide inputs to the process, instead of passing it as a parameter. Both methods have identical semantics:
 
 ```nextflow
@@ -389,8 +376,6 @@ workflow {
 ```
 :::
 
-(process-input-path)=
-
 ### Input files (`path`)
 
 The `path` qualifier allows you to provide input files to the process execution context. Nextflow will stage the files into the process execution directory, and they can be accessed in the script by using the specified input name. For example:
@@ -451,7 +436,7 @@ workflow {
 
 In this example, each file received by the process is staged with the name `query.fa` in a different execution context (i.e. the folder where a task is executed).
 
-:::{tip}
+:::tip
 This feature allows you to execute the process command multiple times without worrying about the file names changing. In other words, Nextflow helps you write pipeline tasks that are self-contained and decoupled from the execution environment. As a best practice, you should avoid referencing files in your process script other than those defined in your input section.
 :::
 
@@ -473,8 +458,8 @@ workflow {
 }
 ```
 
-:::{note}
-Process `path` inputs have nearly the same interface as described in {ref}`stdlib-types-path`, with one difference which is relevant when files are staged into a subdirectory. Given the following input:
+:::note
+Process `path` inputs have nearly the same interface as described in [Path][stdlib-types-path], with one difference which is relevant when files are staged into a subdirectory. Given the following input:
 
 ```nextflow
 path x, name: 'my-dir/file.txt'
@@ -548,12 +533,11 @@ workflow {
 }
 ```
 
-:::{note}
-Rewriting input file names according to a named pattern is an extra feature and not at all required. The normal file input syntax introduced in the {ref}`process-input-path` section is valid for collections of multiple files as well. To handle multiple input files while preserving the original file names, use a variable identifier or the `*` wildcard.
+:::note
+Rewriting input file names according to a named pattern is an extra feature and not at all required. The normal file input syntax introduced in the [Input files (`path`)][process-input-path] section is valid for collections of multiple files as well. To handle multiple input files while preserving the original file names, use a variable identifier or the `*` wildcard.
 :::
 
-:::{versionadded} 23.09.0-edge
-:::
+<AddedInVersion version="23.09.0-edge" />
 
 The `arity` option can be used to enforce the expected number of files, either as a number or a range.
 
@@ -589,7 +573,7 @@ In the above example, the input file name is determined by the current value of
 
 This approach allows input files to be staged in the task directory with a name that is coherent with the current execution context.
 
-:::{tip}
+:::tip
 In most cases, you won't need to use dynamic file names, because each task is executed in its own directory, and input files are automatically staged into this directory by Nextflow. This behavior guarantees that input files with the same name won't overwrite each other. The above example is useful specifically when there are potential file name conflicts within a single task.
 :::
 
@@ -651,8 +635,6 @@ ciao
 hello
 ```
 
-(process-input-tuple)=
-
 ### Input tuples (`tuple`)
 
 The `tuple` qualifier groups multiple values into a single input definition. Each element in the tuple is associated with a corresponding element in the `tuple` definition. For example:
@@ -730,22 +712,20 @@ workflow {
 
 In the above example, each sequence input file emitted by the `sequences` channel triggers six alignment tasks, three with the `regular` method against each library file, and three with the `espresso` method.
 
-:::{note}
+:::note
 When multiple repeaters are defined, the process is executed for each *combination* of them.
 :::
 
-:::{note}
-Input repeaters do not support tuples. Use the {ref}`operator-combine` or {ref}`operator-cross` operator to combine the repeated input with the other inputs to produce all of the desired input combinations.
+:::note
+Input repeaters do not support tuples. Use the [`combine`][operator-combine] or [`cross`][operator-cross] operator to combine the repeated input with the other inputs to produce all of the desired input combinations.
 :::
 
-(process-multiple-inputs)=
-
 ### Multiple inputs
 
 A process can declare multiple inputs, which allows it to accept inputs from multiple dataflow sources.
 
-:::{warning}
-Do not supply more than one channel when calling a process with multiple inputs. Invoking a process with multiple channels can lead to {ref}`non-deterministic behavior <cache-nondeterministic-inputs>`. All additional inputs should be dataflow values. 
+:::warning
+Do not supply more than one channel when calling a process with multiple inputs. Invoking a process with multiple channels can lead to [non-deterministic behavior][cache-nondeterministic-inputs]. All additional inputs should be dataflow values.
 :::
 
 When a process is defined with multiple inputs, it waits for a value from each input and launches a new task with the combined values. When one of the inputs is a channel, the process repeats until all values in the channel are consumed. If the channel is empty, the process will not launch any tasks.
@@ -779,9 +759,11 @@ The above example executes the `echo` process three times. The dataflow value `x
 1 and c
 ```
 
-See also: {ref}`process-out-singleton`.
+:::note
+In general, multiple input channels should be used to process *combinations* of different inputs, using the `each` qualifier or value channels. Having multiple queue channels as inputs is equivalent to using the [`merge`][operator-merge] operator, which is not recommended as it may lead to [non-deterministic process inputs][cache-nondeterministic-inputs].
+:::
 
-(process-output)=
+See also: [Singleton outputs](#singleton-outputs).
 
 ## Outputs
 
@@ -796,7 +778,7 @@ output:
 
 An output declaration consists of a *qualifier* and a *name*. Some optional attributes can also be specified.
 
-When a process is invoked, each process output is returned as a channel (except under {ref}`certain conditions <process-out-singleton>`). The examples provided in the following sections demonstrate how to access the outputs of a process.
+When a process is invoked, each process output is returned as a channel (except under [certain conditions][process-out-singleton]). The examples provided in the following sections demonstrate how to access the outputs of a process.
 
 The following output qualifiers are available:
 
@@ -807,7 +789,7 @@ The following output qualifiers are available:
 - `tuple`: Emit multiple values.
 - `eval`: Emit the result of a script or command evaluated in the task execution context.
 
-Refer to the {ref}`process reference <process-reference-outputs>` for the full list of available output methods and options.
+Refer to the [process reference][process-reference-outputs] for the full list of available output methods and options.
 
 ### Output variables (`val`)
 
@@ -887,7 +869,7 @@ workflow {
 
 In the above example, the `random_number` process creates a file named `result.txt` which contains a random number. Since a `path` output with the same name is declared, that file is emitted by the corresponding process output. A downstream process or operator with a compatible input will be able to receive it.
 
-Refer to the {ref}`process reference <process-reference-outputs>` for the list of available options for `path` outputs.
+Refer to the [process reference][process-reference-outputs] for the list of available options for `path` outputs.
 
 ### Multiple output files
 
@@ -920,21 +902,20 @@ File: chunk_ac => l
 File: chunk_ad => a
 ```
 
-By default, all the files matching the specified glob pattern are emitted as a single list. However, as the above example demonstrates, the {ref}`operator-flatten` operator can be used to transform the list of files into a channel that emits each file individually.
+By default, all the files matching the specified glob pattern are emitted as a single list. However, as the above example demonstrates, the [`flatten`][operator-flatten] operator can be used to transform the list of files into a channel that emits each file individually.
 
 Some caveats on glob pattern behavior:
 
 - Input files are not included (unless `includeInputs` is `true`)
 - Directories are included, unless the `**` pattern is used to recurse through directories
 
-:::{warning}
+:::warning
 Although the input files matching an output glob pattern are not included in the resulting output, these files may still be transferred from the task scratch directory to the original task work directory. Therefore, to avoid unnecessary file copies, avoid using loose wildcards when defining output files, e.g. `path '*'`. Instead, use a prefix or a suffix to restrict the set of matching files to only the expected ones, e.g. `path 'prefix_*.sorted.bam'`.
 :::
 
 Read more about glob syntax at the following link [What is a glob?][glob]
 
-:::{versionadded} 23.09.0-edge
-:::
+<AddedInVersion version="23.09.0-edge" />
 
 The `arity` option can be used to enforce the expected number of files, either as a number or a range.
 
@@ -971,60 +952,48 @@ process align {
 
 In the above example, each process execution produces an alignment file whose name depends on the actual value of the `species` input.
 
-:::{tip}
+:::tip
 The management of output files in Nextflow is often misunderstood.
 
 With other tools it is generally necessary to organize the output files into some kind of directory structure or to guarantee a unique file name scheme, so that result files don't overwrite each other and so they can be referenced unequivocally by downstream tasks.
 
-With Nextflow, in most cases, you don't need to manage the naming of output files, because each task is executed in its own unique directory, so files produced by different tasks can't overwrite each other. Also, metadata can be associated with outputs by using the {ref}`tuple output <process-out-tuple>` qualifier, instead of including them in the output file name.
+With Nextflow, in most cases, you don't need to manage the naming of output files, because each task is executed in its own unique directory, so files produced by different tasks can't overwrite each other. Also, metadata can be associated with outputs by using the [tuple output][process-out-tuple] qualifier, instead of including them in the output file name.
 
 One example in which you'd need to manage the naming of output files is when you use the `publishDir` directive to have output files also in a specific path of your choice. If two tasks have the same filename for their output and you want them to be in the same path specified by `publishDir`, the last task to finish will overwrite the output of the task that finished before. You can dynamically change that by adding the `saveAs` option to your `publishDir` directive.
 
 To sum up, the use of output files with static names over dynamic ones is preferable whenever possible, because it will result in simpler and more portable code.
 :::
 
-(process-env)=
-
 ### Output environment variables (`env`)
 
 The `env` qualifier allows you to output a variable defined in the process execution environment:
 
-```{literalinclude} snippets/process-out-env.nf
-:language: nextflow
+```nextflow file=./snippets/process-out-env.nf
 ```
 
-(process-stdout)=
-
 ### Standard output (`stdout`)
 
 The `stdout` qualifier allows you to output the `stdout` of the executed process:
 
-```{literalinclude} snippets/process-stdout.nf
-:language: nextflow
+```nextflow file=./snippets/process-stdout.nf
 ```
 
-(process-out-eval)=
-
 ### Eval output (`eval`)
 
-:::{versionadded} 24.02.0-edge
-:::
+<AddedInVersion version="24.02.0-edge" />
 
 The `eval` qualifier allows you to capture the standard output of an arbitrary command evaluated the task shell interpreter context:
 
-```{literalinclude} snippets/process-out-eval.nf
-:language: nextflow
+```nextflow file=./snippets/process-out-eval.nf
 ```
 
 Only one-line Bash commands are supported. You can use a semi-colon `;` to specify multiple Bash commands on a single line, and many interpreters can execute arbitrary code on the command line, e.g. `python -c 'print("Hello world!")'`.
 
 If the command fails, the task will also fail. In Bash, you can append `|| true` to a command to suppress any command failure.
 
-(process-out-tuple)=
-
 ### Output tuples (`tuple`)
 
-The `tuple` qualifier outputs multiple values in a single output as a {ref}`tuple <script-tuples>`. For example:
+The `tuple` qualifier outputs multiple values in a single output as a [tuple][script-tuples]. For example:
 
 ```nextflow
 process blast {
@@ -1053,7 +1022,7 @@ In the above example, a `blast` task is executed for each pair of `species` and
 
 A `tuple` definition may contain any of the following qualifiers, as previously described: `val`, `path`, `env` and `stdout`. Files specified with the `path` qualifier are treated exactly the same as standalone `path` inputs.
 
-:::{note}
+:::note
 While parentheses for input and output qualifiers are generally optional, they are required when specifying elements in an input/output tuple.
 
 Here's an example with a single path output (parentheses optional):
@@ -1086,8 +1055,6 @@ process hello {
 ```
 :::
 
-(process-naming-outputs)=
-
 ### Naming outputs
 
 The `emit` option is used to define the name of a process output, which can be used to access the output by name in the calling workflow. For example:
@@ -1111,7 +1078,7 @@ workflow {
 }
 ```
 
-See {ref}`workflow-process-invocation` for more details.
+See [Calling processes and workflows][workflow-process-invocation] for more details.
 
 ### Optional outputs
 
@@ -1124,32 +1091,28 @@ path("output.txt"), optional: true
 
 In this example, the process is normally expected to produce an `output.txt` file, but in this case, if the file is missing, the task will not fail. The output channel will only contain values for those tasks that produced `output.txt`.
 
-:::{note}
+:::note
 While this option can be used with any process output, it cannot be applied to individual elements of a [tuple](#output-tuples-tuple) output. The entire tuple must be optional or not optional.
 :::
 
-(process-out-singleton)=
-
 ### Singleton outputs
 
 When a process is only supplied with dataflow values, regular values, or no inputs, it returns outputs as dataflow values. For example:
 
-```{literalinclude} snippets/process-out-singleton.nf
-:language: nextflow
+```nextflow
+file=./snippets/process-out-singleton.nf
 ```
 
 In the above example, the `echo` process is invoked with a regular value that is wrapped in a dataflow value. As a result, `echo` returns a dataflow value and `greet` is executed three times.
 
 If the call to `echo` was changed to `echo( channel.of('hello') )`, the process would instead return a channel, and `greet` would be executed only once.
 
-See also: {ref}`process-multiple-inputs`.
-
-(process-when)=
+See also: [Multiple inputs][process-multiple-inputs].
 
 ## When
 
-:::{note}
-As a best practice, conditional logic should be implemented in the calling workflow (e.g. using an `if` statement or {ref}`operator-filter` operator) instead of the process definition.
+:::note
+As a best practice, conditional logic should be implemented in the calling workflow (e.g. using an `if` statement or [`filter`][operator-filter] operator) instead of the process definition.
 :::
 
 The `when` section allows you to define a condition that must be satisfied in order to execute the process. The condition can be any expression that returns a boolean value.
@@ -1172,33 +1135,29 @@ process blast_search {
 }
 ```
 
-(process-directives)=
-
 ## Directives
 
 Directives are optional settings that affect the execution of the current process.
 
 By default, directives are evaluated when the process is defined. However, if the value is a dynamic string or closure, it will be evaluated separately for each task, which allows task-specific variables like `task` and `val` inputs to be used.
 
-Some directives are only supported by specific executors. Refer to the {ref}`executor-page` page for more information about each executor.
+Some directives are only supported by specific executors. See [Executors][executor-page] for more information about each executor.
 
-Refer to the {ref}`process reference <process-reference-directives>` for the full list of process directives. If you are new to Nextflow, here are some commonly-used operators to learn first:
+Refer to the [process reference][process-reference-directives] for the full list of process directives. If you are new to Nextflow, here are some commonly-used operators to learn first:
 
 General:
-- {ref}`process-error-strategy`: strategy for handling task failures
-- {ref}`process-executor`: the {ref}`executor <executor-page>` with which to execute tasks
-- {ref}`process-tag`: a semantic name used to differentiate between task executions of the same process
+- [errorStrategy][process-error-strategy]]: strategy for handling task failures
+- [tag][process-executor]: the [executor][executor-page] to execute tasks
+- [executor][process-tag]: a semantic name used to differentiate between task executions of the same process
 
 Resource requirements:
-- {ref}`process-cpus`: the number of CPUs to request for each task
-- {ref}`process-memory`: the amount of memory to request for each task
-- {ref}`process-time`: the amount of walltime to request for each task
+- [cpus][process-cpus]: the number of CPUs to request for each task
+- [memory][process-memory]: the amount of memory to request for each task
+- [time][process-time]: the amount of walltime to request for each task
 
 Software dependencies:
-- {ref}`process-conda`: list of conda packages to provision for tasks
-- {ref}`process-container`: container image to use for tasks
-
-(task-directive-values)=
+- [conda][process-conda]: list of conda packages to provision for tasks
+- [container][process-container]: container image to use for tasks
 
 ### Using task directive values
 
@@ -1213,15 +1172,13 @@ process hello {
 }
 ```
 
-In the above snippet, `task.cpus` and `task.memory` hold the values for the {ref}`cpus directive<process-cpus>` and {ref}`memory directive<process-memory>` directives, respectively, which were resolved for this task based on the process configuration.
-
-(dynamic-directives)=
+In the above snippet, `task.cpus` and `task.memory` hold the values for the [cpus directive][process-cpus] and [memory directive][process-memory] directives, respectively, which were resolved for this task based on the process configuration.
 
 ### Dynamic directives
 
 A directive can be assigned *dynamically*, during the process execution, so that its actual value can be evaluated based on the process inputs.
 
-To be defined dynamically, the directive's value needs to be expressed using a {ref}`closure <script-closure>`. For example:
+To be defined dynamically, the directive's value needs to be expressed using a [closure][script-closure]. For example:
 
 ```nextflow
 process hello {
@@ -1238,18 +1195,17 @@ process hello {
 }
 ```
 
-In the above example, the {ref}`process-queue` directive is evaluated dynamically, depending on the input value `entries`. When it is larger than 100, jobs will be submitted to the `long` queue, otherwise the `short` queue will be used.
+In the above example, the [queue][process-queue] directive is evaluated dynamically, depending on the input value `entries`. When it is larger than 100, jobs will be submitted to the `long` queue, otherwise the `short` queue will be used.
 
 All directives can be assigned a dynamic value except the following:
 
-- {ref}`process-executor`
-- {ref}`process-label`
-- {ref}`process-maxforks`
+- [executor][process-executor]
+- [label][process-label]
+- [maxForks][process-maxforks]
 
-:::{versionadded} 25.10
-:::
+<AddedInVersion version="25.10.0" />
 
-Dynamic directives can be specified without a closure when using the {ref}`strict syntax <strict-syntax-page>`:
+Dynamic directives can be specified without a closure when using the [strict syntax][strict-syntax-page]:
 
 ```nextflow
 queue (entries > 100 ? 'long' : 'short')
@@ -1257,8 +1213,6 @@ queue (entries > 100 ? 'long' : 'short')
 
 Directives will be evaluated dynamically if they reference task inputs. Process configuration options must still be specified with a closure to be dynamic.
 
-(dynamic-task-resources)=
-
 ### Dynamic task resources
 
 It's a very common scenario that different instances of the same process may have very different needs in terms of computing resources. In such situations requesting, for example, an amount of memory too low will cause some tasks to fail. Instead, using a higher limit that fits all the tasks in your execution could significantly decrease the execution priority of your jobs.
@@ -1280,13 +1234,13 @@ process hello {
 }
 ```
 
-In the above example the {ref}`process-memory` and execution {ref}`process-time` limits are defined dynamically. The first time the process is executed the `task.attempt` is set to `1`, thus it will request 2 GB of memory and 1 hour of walltime.
+In the above example the [memory][process-memory] and execution [time][process-time] limits are defined dynamically. The first time the process is executed the `task.attempt` is set to `1`, thus it will request 2 GB of memory and 1 hour of wall time.
 
-If the task execution fails with an exit status between 137 and 140, the task is re-executed; otherwise, the run is terminated immediately. The re-executed task will have `task.attempt` set to `2`, and will request 4 GB of memory and 2 hours of walltime.
+If the task execution fails with an exit status between 137 and 140, the task is re-executed; otherwise, the run is terminated immediately. The re-executed task will have `task.attempt` set to `2`, and will request 4 GB of memory and 2 hours of wall time.
 
-The {ref}`process-maxretries` directive sets the maximum number of times the same task can be re-executed.
+The [ maxRetries][process-maxretries] directive sets the maximum number of times the same task can be re-executed.
 
-:::{tip}
+:::tip
 Directives with named arguments, such as `accelerator` and `disk`, must use a more verbose syntax when they are dynamic. For example:
 
 ```nextflow
@@ -1316,14 +1270,11 @@ process hello {
 
 In this example, each task requests 8 GB of memory, plus the size of the input file rounded up to the next GB. This way, each task requests only as much memory as it needs based on the size of the inputs. The specific function that you use should be tuned for each process.
 
-(task-previous-execution-trace)=
-
 ### Dynamic task resources with previous execution trace
 
-:::{versionadded} 24.10.0
-:::
+<AddedInVersion version="24.10.0" />
 
-Task resource requests can be updated relative to the {ref}`trace record <trace-report>` metrics of the previous task attempt. The metrics can be accessed through the `task.previousTrace` variable. For example:
+Task resource requests can be updated relative to the [trace file][trace-report] metrics of the previous task attempt. The metrics can be accessed through the `task.previousTrace` variable. For example:
 
 ```nextflow
 process hello {
@@ -1338,7 +1289,7 @@ process hello {
 }
 ```
 
-In the above example, the {ref}`process-memory` is set according to previous trace record metrics. In the first attempt, when no trace metrics are available, it is set to 1 GB. In each subsequent attempt, the requested memory is doubled. See {ref}`trace-report` for more information about trace records.
+In the above example, the [memory][process-memory] is set according to previous trace record metrics. In the first attempt, when no trace metrics are available, it is set to 1 GB. In each subsequent attempt, the requested memory is doubled. See [Trace file][trace-report] for more information about trace records.
 
 ### Dynamic retry with backoff
 
@@ -1356,4 +1307,44 @@ process hello {
 }
 ```
 
-[glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+[cache-nondeterministic-inputs]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#non-deterministic-process-inputs
+[channel-types]: /nextflow_docs/nextflow_repo/docs/channel.mdx#channel-types
+[channel-type-value]: /nextflow_docs/nextflow_repo/docs/channel.mdx#value-channel
+[channel-value]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#value
+[executor-page]: /nextflow_docs/nextflow_repo/docs/executor.mdx
+[glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html.mdx#glob
+[operator-combine]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#combine
+[operator-filter]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#filter
+[operator-flatten]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#flatten
+[operator-cross]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#cross
+[operator-merge]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#merge
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
+[process-container]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#container
+[process-cpus]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cpus
+[process-error-strategy]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#errorstrategy
+[process-executor]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#executor
+[process-input-path]: /nextflow_docs/nextflow_repo/docs/process.mdx#input-files-path
+[process-label]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#label
+[process-maxforks]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#maxforks
+[process-maxretries]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#maxretries
+[process-memory]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#memory
+[process-out-singleton]: /nextflow_docs/nextflow_repo/docs/process.mdx#singleton-outputs
+[process-out-tuple]: /nextflow_docs/nextflow_repo/docs/process.mdx#output-tuples-tuple
+[process-queue]: nextflow_docs/nextflow_repo/docs/reference/process.mdx#queue
+[process-tag]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#tag
+[process-time]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#time
+[process-script]: /nextflow_docs/nextflow_repo/docs/process.mdx#script
+[process-multiple-inputs]: /nextflow_docs/nextflow_repo/docs/process.mdx#multiple-inputs
+[process-reference-directives]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#directives
+[process-reference-inputs]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#inputs
+[process-reference-outputs]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#outputs
+[process-template]: /nextflow_docs/nextflow_repo/docs/process.mdx#template
+[script-closure]: /nextflow_docs/nextflow_repo/docs/script.mdx#closures
+[script-tuples]: /nextflow_docs/nextflow_repo/docs/script.mdx#tuples
+[stdlib-types-path]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#path
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[string-interpolation]: /nextflow_docs/nextflow_repo/docs/script.mdx#string-interpolation
+[syntax-function]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx#function
+[syntax-process]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx#process
+[trace-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
+[workflow-process-invocation]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#calling-processes-and-workflows
diff --git a/docs/reference/channel.md b/new-docs/nextflow-docs/reference/channel.mdx
similarity index 79%
rename from docs/reference/channel.md
rename to new-docs/nextflow-docs/reference/channel.mdx
index 52aab69422..a3a8964cb1 100644
--- a/docs/reference/channel.md
+++ b/new-docs/nextflow-docs/reference/channel.mdx
@@ -1,22 +1,18 @@
-(channel-factory)=
 
-# Channel factories
 
-(channel-empty)=
+# Channel factories
 
 ## empty
 
 The `channel.empty` factory method, by definition, creates a channel that doesn't emit any value.
 
-See also: {ref}`operator-ifempty`.
-
-(channel-from)=
+See also: [ifEmpty]operator-ifempty].
 
 ## from
 
-:::{deprecated} 19.09.0-edge
+<DeprecatedInVersion version="19.09.0-edge">
 Use [channel.of](#of) or [channel.fromList](#fromlist) instead.
-:::
+</DeprecatedInVersion>
 
 The `channel.from` method allows you to create a channel emitting any sequence of values that are specified as the method argument, for example:
 
@@ -41,7 +37,7 @@ zeroToNine = channel.from( 0..9 )
 strings = channel.from( 'A'..'Z' )
 ```
 
-:::{note}
+:::note
 When the `channel.from` argument is an object implementing the (Java) [Collection](http://docs.oracle.com/javase/7/docs/api/java/util/Collection.html) interface, the resulting channel emits the collection entries as individual items.
 :::
 
@@ -58,17 +54,14 @@ But when more than one argument is provided, they are always managed as *single*
 channel.from( [1, 2], [5,6], [7,9] )
 ```
 
-(channel-from-lineage)=
-
 ## fromLineage
 
-:::{versionadded} 25.04.0
-:::
+<AddedInVersion version="25.04.0" />
 
-:::{warning} *Experimental: may change in a future release.*
+:::warning *Experimental: may change in a future release.*
 :::
 
-The `channel.fromLineage` factory creates a channel that emits files from the {ref}`cli-lineage` store that match the given key-value params:
+The `channel.fromLineage` factory creates a channel that emits files from the [lineage][cli-lineage] store that match the given key-value params:
 
 ```nextflow
 channel
@@ -80,21 +73,21 @@ The above snippet emits files published by the given workflow run that are label
 
 Available options:
 
-`label`
-: List of labels associated with the desired files.
+##### `label`
+
+List of labels associated with the desired files.
+
+##### `taskRun`
 
-`taskRun`
-: LID of the task run that produced the desired files.
+LID of the task run that produced the desired files.
 
-`workflowRun`
-: LID of the workflow run that produced the desired files.
+##### `workflowRun`
 
-(channel-fromlist)=
+LID of the workflow run that produced the desired files.
 
 ## fromList
 
-:::{versionadded} 19.10.0
-:::
+<AddedInVersion version="19.10.0" />
 
 The `channel.fromList` method allows you to create a channel emitting the values provided as a list of elements, for example:
 
@@ -115,8 +108,6 @@ value: d
 
 See also: [channel.of](#of) factory method.
 
-(channel-path)=
-
 ## fromPath
 
 You can create a channel emitting one or more file paths by using the `channel.fromPath` method and specifying a path
@@ -129,7 +120,7 @@ myFileChannel = channel.fromPath( '/data/some/bigfile.txt' )
 The above line creates a channel and binds it to a [Path](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Path.html)
 object for the specified file.
 
-:::{note}
+:::note
 `channel.fromPath` does not check whether the file exists.
 :::
 
@@ -142,7 +133,7 @@ myFileChannel = channel.fromPath( '/data/big/*.txt' )
 
 This example creates a channel and emits as many `Path` items as there are files with `txt` extension in the `/data/big` folder.
 
-:::{tip}
+:::tip
 Two asterisks, i.e. `**`, works like `*` but crosses directory boundaries. This syntax is generally used for matching complete paths. Curly brackets specify a collection of sub-patterns.
 :::
 
@@ -156,7 +147,7 @@ pairFiles = channel.fromPath( 'data/file_{1,2}.fq' )
 
 The first line returns a channel emitting the files ending with the suffix `.fa` in the `data` folder *and* recursively in all its sub-folders. While the second one only emits the files which have the same suffix in *any* sub-folder in the `data` path. Finally the last example emits two files: `data/file_1.fq` and `data/file_2.fq`.
 
-:::{note}
+:::note
 As in Linux Bash, the `*` wildcard does not catch hidden files (i.e. files whose name starts with a `.` character).
 :::
 
@@ -189,28 +180,33 @@ The first example will return all *directory* paths ending with the `b` suffix,
 
 Available options:
 
-`checkIfExists`
-: When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
+##### `checkIfExists`
 
-`followLinks`
-: When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
+When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
 
-`glob`
-: When `true` interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
+##### `followLinks`
 
-`hidden`
-: When `true` includes hidden files in the resulting paths (default: `false`)
+When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
 
-`maxDepth`
-: Maximum number of directory levels to visit (default: no limit)
+##### `glob`
 
-`relative`
-: When `true` returned paths are relative to the top-most common directory (default: `false`)
+When `true` interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
 
-`type`
-: Type of paths returned, either `file`, `dir` or `any` (default: `file`)
+##### `hidden`
 
-(channel-filepairs)=
+When `true` includes hidden files in the resulting paths (default: `false`)
+
+##### `maxDepth`
+
+Maximum number of directory levels to visit (default: no limit)
+
+##### `relative`
+
+When `true` returned paths are relative to the top-most common directory (default: `false`)
+
+##### `type`
+
+Type of paths returned, either `file`, `dir` or `any` (default: `file`)
 
 ## fromFilePairs
 
@@ -234,7 +230,7 @@ It will produce an output similar to the following:
 [SRR493371, [/my/data/SRR493371_1.fastq, /my/data/SRR493371_2.fastq]]
 ```
 
-:::{note}
+:::note
 The glob pattern must contain at least one `*` wildcard character.
 :::
 
@@ -254,33 +250,37 @@ channel
 
 Available options:
 
-`checkIfExists`
-: When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
+##### `checkIfExists`
+
+When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
+
+##### `followLinks`
+
+When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
+
+##### `flat`
 
-`followLinks`
-: When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
+When `true` the matching files are produced as sole elements in the emitted tuples (default: `false`).
 
-`flat`
-: When `true` the matching files are produced as sole elements in the emitted tuples (default: `false`).
+##### `hidden`
 
-`hidden`
-: When `true` includes hidden files in the resulting paths (default: `false`)
+When `true` includes hidden files in the resulting paths (default: `false`)
 
-`maxDepth`
-: Maximum number of directory levels to visit (default: no limit)
+##### `maxDepth`
 
-`size`
-: Defines the number of files each emitted item is expected to hold (default: 2). Set to `-1` for any.
+Maximum number of directory levels to visit (default: no limit)
 
-`type`
-: Type of paths returned, either `file`, `dir` or `any` (default: `file`)
+##### `size`
 
-(channel-fromsra)=
+Defines the number of files each emitted item is expected to hold (default: 2). Set to `-1` for any.
+
+##### `type`
+
+Type of paths returned, either `file`, `dir` or `any` (default: `file`)
 
 ## fromSRA
 
-:::{versionadded} 19.04.0
-:::
+<AddedInVersion version="19.04.0" />
 
 The `channel.fromSRA` method queries the [NCBI SRA](https://www.ncbi.nlm.nih.gov/sra) database and returns a channel emitting the FASTQ files matching the specified criteria i.e project or accession number(s). For example:
 
@@ -317,7 +317,7 @@ channel
 [ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]
 ```
 
-:::{note}
+:::note
 Each read pair is implicitly managed and returned as a list of files.
 :::
 
@@ -337,20 +337,25 @@ To access the ESearch API, you must provide your [NCBI API keys](https://ncbiins
 
 Available options:
 
-`apiKey`
-: NCBI user API key.
+##### `apiKey`
+
+NCBI user API key.
+
+##### `cache`
 
-`cache`
-: Enable/disable the caching API requests (default: `true`).
+Enable/disable the caching API requests (default: `true`).
 
-`max`
-: Maximum number of entries that can be retried (default: unlimited) .
+##### `max`
 
-`protocol`
-: Allow choosing the protocol for the resulting remote URLs. Available choices: `ftp`, `http`, `https` (default: `ftp`).
+Maximum number of entries that can be retried (default: unlimited) .
 
-`retryPolicy`
-: Set a retry policy in case the SRA request fails with a retriable error.
+##### `protocol`
+
+Allow choosing the protocol for the resulting remote URLs. Available choices: `ftp`, `http`, `https` (default: `ftp`).
+
+##### `retryPolicy`
+
+Set a retry policy in case the SRA request fails with a retriable error.
 The retry policy is set as a Map specifying the different policy properties.
 
 Available retry policy properties:
@@ -364,11 +369,9 @@ Available retry policy properties:
 
 The following code snippet shows an example for using the `channel.fromSRA` factory method with a custom `retryPolicy`.
 
-  ```nextflow
-  channel.fromSRA(ids, retryPolicy: [delay: '250ms', maxAttempts: 5])
-  ```
-
-(channel-interval)=
+```nextflow
+channel.fromSRA(ids, retryPolicy: [delay: '250ms', maxAttempts: 5])
+```
 
 ## interval
 
@@ -378,7 +381,7 @@ The `interval` method emits an incrementing index (starting from zero) at a peri
 channel.interval('1s').view()
 ```
 
-The above snippet will emit 0, 1, 2, and so on, every second, forever. You can use an operator such as {ref}`operator-take` or {ref}`operator-until` to close the channel based on a stopping condition.
+The above snippet will emit 0, 1, 2, and so on, every second, forever. You can use an operator such as [take][operator-take] or [until][operator-until] to close the channel based on a stopping condition.
 
 An optional closure can be used to transform the index. Additionally, returning `channel.STOP` will close the channel. For example:
 
@@ -389,12 +392,9 @@ ch = channel.interval('1s') { i ->
 ch.view()
 ```
 
-(channel-of)=
-
 ## of
 
-:::{versionadded} 19.10.0
-:::
+<AddedInVersion version="19.10.0" />
 
 The `channel.of` method allows you to create a channel that emits the arguments provided to it, for example:
 
@@ -436,20 +436,17 @@ Y
 
 See also: [channel.fromList](#fromlist) factory method.
 
-(channel-topic)=
-
 ## topic
 
-:::{versionadded} 23.11.0-edge
-:::
+<AddedInVersion version="23.11.0-edge" />
 
-:::{note}
+:::note
 In versions of Nextflow prior to 25.04, this feature requires the `nextflow.preview.topic` feature flag to be enabled.
 :::
 
 A *topic channel* is a channel that can receive values from many sources *implicitly* based on a matching *topic name*.
 
-:::{tip}
+:::tip
 You can think of it as a channel that is shared across many different processes using the same topic name.
 :::
 
@@ -457,17 +454,17 @@ A process output can be assigned to a topic using the `topic` option on an outpu
 
 ```nextflow
 process hello {
-  output:
-  val('hello'), topic: my_topic
+    output:
+    val('hello'), topic: my_topic
 
-  // ...
+    // ...
 }
 
 process bye {
-  output:
-  val('bye'), topic: my_topic
+    output:
+    val('bye'), topic: my_topic
 
-  // ...
+    // ...
 }
 ```
 
@@ -479,13 +476,11 @@ channel.topic('my-topic').view()
 
 This approach is a convenient way to collect related items from many different sources without explicitly connecting them (e.g. using the `mix` operator).
 
-:::{warning}
+:::warning
 Any process that consumes a topic channel (directly or indirectly) should not send any outputs to that topic, or else the pipeline will hang forever.
 :::
 
-See also: {ref}`process-additional-options` for process outputs.
-
-(channel-value)=
+See also: [Options][process-additional-options] for process outputs.
 
 ## value
 
@@ -498,8 +493,6 @@ v2 = channel.value( [1,2,3,4,5] )
 
 The first line creates a dataflow value bound to the string `'Hello there'`. The second line creates a dataflow value bound to the list `[1,2,3,4,5]`, which is treated as a single value in dataflow logic.
 
-(channel-watchpath)=
-
 ## watchPath
 
 The `channel.watchPath` method watches a folder for one or more files matching a specified pattern. As soon as there
@@ -529,16 +522,21 @@ channel
     .subscribe { fa -> println "File created or modified: $fa" }
 ```
 
-:::{warning}
+:::warning
 The `channel.watchPath` factory waits endlessly for files that match the specified pattern and event(s), which means
 that it will cause your pipeline to run forever. Consider using the `take` or `until` operator to close the channel when
 a certain condition is met (e.g. after receiving 10 files, receiving a file named `DONE`).
 :::
 
-:::{note}
+:::note
 The `channel.watchPath` factory only works with local and shared filesystems. It does not support object storage such as S3.
 :::
 
 See also: [channel.fromPath](#frompath) factory method.
 
+[cli-lineage]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lineage
 [glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+[operator-ifempty]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#ifempty
+[process-additional-options]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#options
+[operator-take]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#take
+[operator-until]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#until
diff --git a/docs/reference/cli.md b/new-docs/nextflow-docs/reference/cli.mdx
similarity index 58%
rename from docs/reference/cli.md
rename to new-docs/nextflow-docs/reference/cli.mdx
index c30afa4963..990ee65c05 100644
--- a/docs/reference/cli.md
+++ b/new-docs/nextflow-docs/reference/cli.mdx
@@ -1,10 +1,8 @@
-(cli-reference)=
 
-# CLI reference
 
-This page lists all of the available options and subcommands for the {ref}`Nextflow CLI <cli-page>`.
+# CLI reference
 
-(cli-options)=
+This page lists all of the available options and subcommands for the [Nextflow CLI][cli-page].
 
 ## Options
 
@@ -12,52 +10,66 @@ The top-level options are meant to be invoked in relation to the core Nextflow a
 
 Available options:
 
-`-C`
-: Comma-separated list of configuration files which are used as the configuration set. Any other default configuration files are ignored.
+##### `-C`
 
-`-D`
-: Set JVM properties.
+Comma-separated list of configuration files which are used as the configuration set. Any other default configuration files are ignored.
 
-`-bg`
-: Execute nextflow in background.
+##### `-D`
 
-`-c, -config`
-: Comma-separated list of configuration files which are added to the configuration set.
+Set JVM properties.
 
-`-d, -dockerize`
-: :::{deprecated} 23.09.0-edge
-  :::
-: Launch nextflow via Docker (experimental).
+##### `-bg`
 
-`-h`
-: Print this help.
+Execute nextflow in background.
 
-`-log`
-: Set nextflow log file path.
+##### `-c, -config`
 
-`-q, -quiet`
-: Do not print information messages.
+Comma-separated list of configuration files which are added to the configuration set.
 
-`-remote-debug`
-: Enable JVM interactive remote debugging (experimental).
+##### `-d, -dockerize`
 
-`-syslog`
-: Send logs to syslog server (e.g. localhost:514).
+<DeprecatedInVersion version="23.09.0-edge">
+</DeprecatedInVersion>
 
-`-trace`
-: Enable trace level logging for the specified packages. Multiple packages can be provided separating them with a comma, e.g. `-trace nextflow,io.seqera`.
+Launch nextflow via Docker (experimental).
 
-`-v, -version`
-: Print the program version.
+##### `-h`
 
-## Commands
+Print this help.
+
+##### `-log`
+
+Set nextflow log file path.
+
+##### `-q, -quiet`
+
+Do not print information messages.
+
+##### `-remote-debug`
+
+Enable JVM interactive remote debugging (experimental).
+
+##### `-syslog`
+
+Send logs to syslog server (e.g. localhost:514).
+
+##### `-trace`
+
+Enable trace level logging for the specified packages. Multiple packages can be provided separating them with a comma, e.g. `-trace nextflow,io.seqera`.
+
+##### `-v, -version`
 
-(cli-auth)=
+Print the program version.
+
+##### `-E`
+
+Exports all current system environment.
+
+## Commands
 
 ### `auth`
 
-:::{versionadded} 25.09.0-edge
-:::
+<AddedInVersion version="25.09.0-edge" />
 
 Manage Seqera Platform authentication.
 
@@ -73,26 +85,37 @@ The `auth` command provides authentication and configuration management for Seqe
 
 **Options**
 
-`-h, -help`
-: Prints the command usage information.
+##### `-h, -help`
+
+Prints the command usage information.
+
+#
 
 **Subcommands**
 
-`login`
-: Authenticates with Seqera and saves credentials. Sets Seqera primary compute environment, monitoring, and workspace.
-: The following options are available:
+##### `login`
+
+Authenticates with Seqera and saves credentials. Sets Seqera primary compute environment, monitoring, and workspace.
+
+The following options are available:
+
+######  `-u, -url`
+
+Specifies your Seqera API endpoint (default: `https://api.cloud.seqera.io`)
+
+##### `logout`
+
+Removes Seqera authentication and revokes the Seqera Cloud access token (if applicable).
+
+##### `config`
 
-  `-u, -url`
-  : Specifies your Seqera API endpoint (default: `https://api.cloud.seqera.io`)
+Sets Seqera primary compute environment, monitoring, and workspace.
 
-`logout`
-: Removes Seqera authentication and revokes the Seqera Cloud access token (if applicable).
+##### `status`
 
-`config`
-: Sets Seqera primary compute environment, monitoring, and workspace.
+Shows Seqera authentication status and configuration.
 
-`status`
-: Shows Seqera authentication status and configuration.
+#
 
 **Examples**
 
@@ -126,8 +149,6 @@ Remove authentication:
 $ nextflow auth logout
 ```
 
-(cli-clean)=
-
 ### `clean`
 
 Clean up *cache* and *work* directories.
@@ -146,29 +167,40 @@ If no run name or session id is provided, it will clean the latest run.
 
 **Options**
 
-`-after`
-: Clean up runs executed *after* the specified one.
+##### `-after`
+
+Clean up runs executed *after* the specified one.
+
+##### `-before`
+
+Clean up runs executed *before* the specified one.
+
+##### `-but`
+
+Clean up all runs *except* the specified one.
+
+##### `-n, -dry-run`
 
-`-before`
-: Clean up runs executed *before* the specified one.
+Print names of files to be removed without deleting them.
 
-`-but`
-: Clean up all runs *except* the specified one.
+##### `-f, -force`
 
-`-n, -dry-run`
-: Print names of files to be removed without deleting them.
+Force clean command.
 
-`-f, -force`
-: Force clean command.
+##### `-h, -help`
 
-`-h, -help`
-: Print the command usage.
+Print the command usage.
 
-`-k, -keep-logs`
-: Removes only temporary files but retains execution log entries and metadata.
+##### `-k, -keep-logs`
 
-`-q, -quiet`
-: Do not print names of files removed.
+Removes only temporary files but retains execution log entries and metadata.
+
+##### `-q, -quiet`
+
+Do not print names of files removed.
+
+
+#
 
 **Examples**
 
@@ -249,20 +281,27 @@ The `clone` command downloads a pipeline from a Git-hosting platform into the *c
 
 **Options**
 
-`-d, -deep`
-: Create a shallow clone of the specified depth.
+##### `-d, -deep`
+
+Create a shallow clone of the specified depth.
+
+##### `-h, -help`
+
+Print the command usage.
 
-`-h, -help`
-: Print the command usage.
+##### `-hub` (`github`)
 
-`-hub` (`github`)
-: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`.
+Service hub where the project is hosted. Options: `gitlab` or `bitbucket`.
 
-`-r` (`master`)
-: Revision to clone - It can be a git branch, tag, or revision number.
+##### `-r` (`master`)
 
-`-user`
-: Private repository user name.
+Revision to clone - It can be a git branch, tag, or revision number.
+
+##### `-user`
+
+Private repository user name.
+
+#
 
 **Examples**
 
@@ -292,32 +331,40 @@ $ nextflow config [options] [project name or path]
 
 **Description**
 
-The `config` command is used for printing the project's configuration i.e. the `nextflow.config` and is especially useful for understanding the resolved profiles and parameters that Nextflow will use run a pipeline. For in-depth information, please refer the {ref}`config-profiles` section.
+The `config` command is used for printing the project's configuration i.e. the `nextflow.config` and is especially useful for understanding the resolved profiles and parameters that Nextflow will use run a pipeline. For in-depth information, please refer the [Config profiles][config-profiles] section.
 
 **Options**
 
-`-flat`
-: Print config using flat notation.
+##### `-flat`
+
+Print config using flat notation.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-profile`
 
-`-h, -help`
-: Print the command usage.
+Choose a configuration profile.
 
-`-profile`
-: Choose a configuration profile.
+##### `-properties`
+Print config using Java properties notation.
 
-`-properties`
-: Print config using Java properties notation.
+##### `-a, -show-profiles`
 
-`-a, -show-profiles`
-: Show all configuration profiles.
+Show all configuration profiles.
 
-`-sort`
-: Sort config attributes.
+##### `-sort`
 
-`-value`
-: :::{versionadded} 23.08.0-edge
-  :::
-: Print the value of a config option, or fail if the option is not defined.
+Sort config attributes.
+
+##### `-value`
+
+<AddedInVersion version="23.08.0-edge" />
+
+Print the value of a config option, or fail if the option is not defined.
+
+#
 
 **Examples**
 
@@ -384,8 +431,6 @@ profiles {
 }
 ```
 
-(cli-console)=
-
 ### `console`
 
 Launch the Nextflow interactive console.
@@ -428,11 +473,15 @@ The `drop` command is used to remove the projects which have been downloaded int
 
 **Options**
 
-`-f`
-: Delete the repository without taking care of local changes.
+##### `-f`
+
+Delete the repository without taking care of local changes.
 
-`-h, -help`
-: Print the command usage.
+##### `-h, -help`
+
+Print the command usage.
+
+#
 
 **Examples**
 
@@ -464,8 +513,11 @@ The `fs` command is used to perform filesystem operations like copy, move, delet
 
 **Options**
 
-`-h, -help`
-: Print the command usage.
+##### `-h, -help`
+
+Print the command usage.
+
+#
 
 **Examples**
 
@@ -499,8 +551,7 @@ Delete a file or directory.
 $ nextflow fs rm <path>
 ```
 
-:::{versionadded} 23.10.0
-:::
+<AddedInVersion version="23.10.0" />
 
 Print file or directory attributes.
 
@@ -524,8 +575,11 @@ The `help` command prints out the overview of the CLI interface and enumerates t
 
 **Options**
 
-`-h, -help`
-: Print the command usage.
+##### `-h, -help`
+
+Print the command usage.
+
+#
 
 **Examples**
 
@@ -563,17 +617,23 @@ If no run name or session id is provided, it will clean the latest run.
 
 **Options**
 
-`-u, -check-updates`
-: Check for remote updates.
+##### `-u, -check-updates`
 
-`-d`
-: Show detailed information.
+Check for remote updates.
 
-`-h, -help`
-: Print the command usage.
+##### `-d`
 
-`-o` (`text`)
-: Output format, either `text`, `json` or `yaml`.
+Show detailed information.
+
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-o` (`text`)
+
+Output format, either `text`, `json` or `yaml`.
+
+#
 
 **Examples**
 
@@ -606,12 +666,9 @@ $ nextflow info nextflow-io/hello
     v1.2 [t]
 ```
 
-(cli-inspect)=
-
 ### `inspect`
 
-:::{versionadded} 23.09.0-edge
-:::
+<AddedInVersion version="23.09.0-edge" />
 
 Inspect process settings in a pipeline project. Currently only supports the `container` directive.
 
@@ -627,23 +684,31 @@ The `inspect` command allows you to determine the container for each process in
 
 **Options**
 
-`-concretize`
-: Build the container images resolved by the inspect command.
+##### `-concretize`
 
-`-format` (`json`)
-: Inspect output format. Can be `json` or `config`.
+Build the container images resolved by the inspect command.
 
-`-i, -ignore-errors`
-: Ignore errors while inspecting the pipeline.
+##### `-format` (`json`)
 
-`-params-file`
-: Load script parameters from a JSON/YAML file.
+Inspect output format. Can be `json` or `config`.
 
-`-profile`
-: Use the given configuration profile(s).
+##### `-i, -ignore-errors`
 
-`-r, revision`
-: Revision of the project to inspect (either a git branch, tag or commit SHA number).
+Ignore errors while inspecting the pipeline.
+
+##### `-params-file`
+
+Load script parameters from a JSON/YAML file.
+
+##### `-profile`
+
+Use the given configuration profile(s).
+
+##### `-r, revision`
+
+Revision of the project to inspect (either a git branch, tag or commit SHA number).
+
+#
 
 **Examples**
 
@@ -671,7 +736,7 @@ $ nextflow kuberun [options] [project]
 
 **Description**
 
-The `kuberun` command builds upon the `run` command and offers a deep integration with the Kubernetes execution environment. This command deploys the Nextflow runtime as a Kubernetes pod and assumes that you've already installed the `kubectl` CLI. The `kuberun` command does not allow the execution of local Nextflow scripts. See {ref}`k8s-page` for more information.
+The `kuberun` command builds upon the `run` command and offers a deep integration with the Kubernetes execution environment. This command deploys the Nextflow runtime as a Kubernetes pod and assumes that you've already installed the `kubectl` CLI. The `kuberun` command does not allow the execution of local Nextflow scripts. See [kubernetes][k8s-page] for more information.
 
 **Options**
 
@@ -717,37 +782,39 @@ The `kuberun` command supports the following options from [`run`](#run):
 
 The following new options are also available:
 
-`-head-cpus`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specify number of CPUs requested for the Nextflow pod.
+##### `-head-cpus`
+
+Specify number of CPUs requested for the Nextflow pod.
+
+##### `-head-image`
+
+Specify the container image for the Nextflow driver pod.
+
+##### `-head-memory`
+
+Specify amount of memory requested for the Nextflow pod.
+
+##### `-head-prescript`
 
-`-head-image`
-: :::{versionadded} 22.07.1-edge
-  :::
-: Specify the container image for the Nextflow driver pod.
+Specify script to be run before the Nextflow pod starts.
 
-`-head-memory`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specify amount of memory requested for the Nextflow pod.
+##### `-n, -namespace`
 
-`-head-prescript`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Specify script to be run before the Nextflow pod starts.
+Specify the K8s namespace to use.
 
-`-n, -namespace`
-: Specify the K8s namespace to use.
+##### `-remoteConfig`
 
-`-remoteConfig`
-: Add the specified file from the K8s cluster to configuration set.
+Add the specified file from the K8s cluster to configuration set.
 
-`-remoteProfile`
-: Choose a configuration profile in the remoteConfig.
+##### `-remoteProfile`
 
-`-v, -volume-mount`
-: Volume claim mounts, e.g. `my-pvc:/mnt/path`.
+Choose a configuration profile in the remoteConfig.
+
+##### `-v, -volume-mount`
+
+Volume claim mounts, e.g. `my-pvc:/mnt/path`.
+
+#
 
 **Examples**
 
@@ -757,12 +824,9 @@ Execute a pipeline into a Kubernetes cluster.
 $ nextflow kuberun nextflow-io/hello
 ```
 
-(cli-launch)=
-
 ### `launch`
 
-:::{versionadded} 25.10.0
-:::
+<AddedInVersion version="25.10.0" />
 
 Launch a workflow in [Seqera Platform](https://seqera.io/platform/).
 
@@ -778,47 +842,61 @@ The `launch` command launches a pipeline run in Seqera Platform. To log in and c
 
 **Options**
 
-`-compute-env`
-: The compute environment for workflow execution.
+##### `-compute-env`
+
+The compute environment for workflow execution.
+
+##### `-c, -config`
+
+A configuration file to add to the configuration set.
+
+##### `-entry`
+
+The entry workflow to be executed.
+
+##### `-h, -help`
+
+Prints command usage information.
+
+##### `-latest`
+
+Whether to pull the latest changes before execution.
 
-`-c, -config`
-: A configuration file to add to the configuration set.
+##### `-name`
 
-`-entry`
-: The entry workflow to be executed.
+A mnemonic name to assign to the run.
 
-`-h, -help`
-: Prints command usage information.
+##### `-main-script`
 
-`-latest`
-: Whether to pull the latest changes before execution.
+The script file to be executed when launching a project directory or repository.
 
-`-name`
-: A mnemonic name to assign to the run.
+##### `-params-file`
 
-`-main-script`
-: The script file to be executed when launching a project directory or repository.
+A JSON or YAML file to load parameters from.
 
-`-params-file`
-: A JSON or YAML file to load parameters from.
+##### `-profile`
 
-`-profile`
-: A configuration profile.
+A configuration profile.
 
-`-resume`
-: Whether to resume an execution using cached results from a previous run.
+##### `-resume`
 
-`-r, -revision`
-: The project revision to run. Can be a git branch, tag, or commit hash.
+Whether to resume an execution using cached results from a previous run.
 
-`-stub-run, -stub`
-: Whether to replace scripts with command stubs when executing the run.
+##### `-r, -revision`
 
-`-w, -work-dir`
-: The directory where intermediate result files are stored.
+The project revision to run. Can be a git branch, tag, or commit hash.
 
-`-workspace`
-: The Seqera Platform workspace name.
+##### `-stub-run, -stub`
+
+Whether to replace scripts with command stubs when executing the run.
+
+##### `-w, -work-dir`
+
+The directory where intermediate result files are stored.
+
+##### `-workspace`
+
+The Seqera Platform workspace name.
 
 **Examples**
 
@@ -828,14 +906,11 @@ Execute a pipeline in Seqera Platform.
 $ nextflow launch nextflow-io/hello
 ```
 
-(cli-lineage)=
-
 ### `lineage`
 
-:::{versionadded} 25.04.0
-:::
+<AddedInVersion version="25.04.0" />
 
-:::{warning} *Experimental: may change in a future release.*
+:::warning{title="Experimental: may change in a future release."}
 :::
 
 Inspect lineage metadata for Nextflow runs.
@@ -850,35 +925,41 @@ $ nextflow lineage SUBCOMMAND [arg ..]
 
 The `lineage` command is used to inspect lineage metadata.
 
-See the {ref}`data-lineage-page` guide to learn how to get started with data lineage.
+See the [Data lineage][data-lineage-page] guide to learn how to get started with data lineage.
 
 **Options**
 
-`-h, -help`
-: Print the command usage.
+##### `-h, -help`
+
+Print the command usage.
 
 **Subcommands**
 
-`check <lid>`
-: Validate the checksum of output lineage record.
+##### `check <lid>`
+
+Validate the checksum of output lineage record.
+
+##### `diff <lid-1> <lid-2>`
+
+Display a git-style diff between two lineage records.
+
+##### `find <field-1>=<value-1> [<field-2>=<value-2> ...]`
+
+Find all lineage records that match the given field values.
 
-`diff <lid-1> <lid-2>`
-: Display a git-style diff between two lineage records.
+##### `list`
 
-`find <field-1>=<value-1> [<field-2>=<value-2> ...]`
-: Find all lineage records that match the given field values.
+List the Nextflow runs with lineage enabled, printing the corresponding lineage ID (LID) for each run.
 
-`list`
-: List the Nextflow runs with lineage enabled, printing the corresponding lineage ID (LID) for each run.
+##### `render <lid> [path]`
 
-`render <lid> [path]`
-: Render the lineage graph for a lineage record as an HTML file (default output path: `./lineage.html`).
-: The lineage record should be of type `FileOutput`, `TaskRun`, or `WorkflowRun`.
+Render the lineage graph for a lineage record as an HTML file (default output path: `./lineage.html`).
 
-`view <lid>`
-: View a lineage record.
+The lineage record should be of type `FileOutput`, `TaskRun`, or `WorkflowRun`.
 
-(cli-lint)=
+##### `view <lid>`
+
+View a lineage record.
 
 ### `lint`
 
@@ -896,23 +977,31 @@ The `lint` command parses and analyzes the given Nextflow scripts and config fil
 
 **Options**
 
-`-exclude`
-: File pattern to exclude from linting. Can be specified multiple times (default: `.git, .nf-test, work`).
+##### `-exclude`
+
+File pattern to exclude from linting. Can be specified multiple times (default: `.git, .nf-test, work`).
+
+##### `-format`
+
+Format scripts and config files that have no errors.
+
+##### `-o, -output`
+
+Output mode for reporting errors: `full`, `extended`, `concise`, `json` (default: `full`).
+
+##### `-sort-declarations`
 
-`-format`
-: Format scripts and config files that have no errors.
+Sort script declarations in Nextflow scripts (default: `false`).
 
-`-o, -output`
-: Output mode for reporting errors: `full`, `extended`, `concise`, `json` (default: `full`).
+##### `-spaces`
 
-`-sort-declarations`
-: Sort script declarations in Nextflow scripts (default: `false`).
+Number of spaces to indent (default: `4`).
 
-`-spaces`
-: Number of spaces to indent (default: `4`).
+##### `-tabs`
 
-`-tabs`
-: Indent with tabs (default: `false`).
+Indent with tabs (default: `false`).
+
+#
 
 **Examples**
 
@@ -950,8 +1039,11 @@ The `list` commands prints a list of the projects which are already downloaded i
 
 **Options**
 
-`-h, -help`
-: Print the command usage.
+##### `-h, -help`
+
+Print the command usage.
+
+#
 
 **Examples**
 
@@ -964,8 +1056,6 @@ nextflow-io/hello
 nextflow-hub/fastqc
 ```
 
-(cli-log)=
-
 ### `log`
 
 Print the execution history and log information.
@@ -982,35 +1072,47 @@ The `log` command is used to query the execution metadata associated with pipeli
 
 **Options**
 
-`-after`
-: Show log entries for runs executed *after* the specified one.
+##### `-after`
+
+Show log entries for runs executed *after* the specified one.
+
+##### `-before`
+
+Show log entries for runs executed *before* the specified one.
 
-`-before`
-: Show log entries for runs executed *before* the specified one.
+##### `-but`
 
-`-but`
-: Show log entries for runs executed *but* the specified one.
+Show log entries for runs executed *but* the specified one.
 
-`-f, -fields`
-: Comma-separated list of fields to include in the printed log. Use the `-l` option to see the list of available fields.
+##### `-f, -fields`
 
-`-F, -filter`
-: Filter log entries by a custom expression, e.g. `process =~ /hello.*/ && status == 'COMPLETED'`.
+Comma-separated list of fields to include in the printed log. Use the `-l` option to see the list of available fields.
 
-`-h, -help`
-: Print the command usage.
+##### `-F, -filter`
 
-`-l, -list-fields`
-: Show all available fields.
+Filter log entries by a custom expression, e.g. `process =~ /hello.*/ && status == 'COMPLETED'`.
 
-`-quiet`
-: Show only run names.
+##### `-h, -help`
 
-`-s`
-: Character used to separate column values.
+Print the command usage.
 
-`-t, -template`
-: Text template used to each record in the log.
+##### `-l, -list-fields`
+
+Show all available fields.
+
+##### `-quiet`
+
+Show only run names.
+
+##### `-s`
+
+Character used to separate column values.
+
+##### `-t, -template`
+
+Text template used to each record in the log.
+
+#
 
 **Examples**
 
@@ -1095,8 +1197,6 @@ $ nextflow log tiny_leavitt -F 'process =~ /split_letters/'
 work/1f/f1ea9158fb23b53d5083953121d6b6
 ```
 
-(cli-plugin)=
-
 ### `plugin`
 
 Manage plugins and run plugin-specific commands.
@@ -1105,19 +1205,19 @@ Manage plugins and run plugin-specific commands.
 $ nextflow plugin <subcommand> [options]
 ```
 
-`create`
+##### `create`
 
-: :::{versionadded} 25.04.0
-  :::
-: Create a plugin scaffold using the [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/). See {ref}`gradle-plugin-create` for more information.
+<AddedInVersion version="25.04.0" />
 
-`install <plugin[@version],..>`
+Create a plugin scaffold using the [Nextflow plugin template](https://github.com/nextflow-io/nf-plugin-template/). See [Creating a plugin][gradle-plugin-create] for more information.
 
-: Install a plugin. Multiple plugins can be specified as a comma-separated list. Each plugin id consists of a name and optional version separated by a `@`.
+##### `install <plugin[@version],..>`
 
-`<plugin>:<subcommand> [options]`
+Install a plugin. Multiple plugins can be specified as a comma-separated list. Each plugin id consists of a name and optional version separated by a `@`.
 
-: Execute a plugin-specific command.
+##### `<plugin>:<subcommand> [options]`
+
+Execute a plugin-specific command.
 
 ### `pull`
 
@@ -1135,24 +1235,33 @@ The `pull` command downloads a pipeline from a Git-hosting platform into the glo
 
 **Options**
 
-`-all`
-: Update all downloaded projects.
+##### `-all`
+
+Update all downloaded projects.
+
+##### `-d, -deep`
+
+Create a shallow clone of the specified depth.
+
+##### `-h, -help`
 
-`-d, -deep`
-: Create a shallow clone of the specified depth.
+Print the command usage.
 
-`-h, -help`
-: Print the command usage.
+##### `-hub` (`github`)
 
-`-hub` (`github`)
-: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
+Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
 
-`-r, -revision`
-: Revision of the project to run (either a git branch, tag or commit hash).
-: When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
+##### `-r, -revision`
 
-`-user`
-: Private repository user name.
+Revision of the project to run (either a git branch, tag or commit hash).
+
+When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
+
+##### `-user`
+
+Private repository user name.
+
+#
 
 **Examples**
 
@@ -1185,8 +1294,6 @@ Checking nextflow-io/hello ...
 checkout-out at AnyObjectId[1c3e9e7404127514d69369cd87f8036830f5cf64] - revision: 1c3e9e7404 [v1.1]
 ```
 
-(cli-run)=
-
 ### `run`
 
 Execute a pipeline.
@@ -1203,184 +1310,247 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 
 **Options**
 
-`-E`
-: Exports all current system environment.
+##### `-E`
+
+Exports all current system environment.
+
+##### `-ansi-log`
+
+Enable/disable ANSI console logging.
+
+##### `-bucket-dir`
+
+Remote bucket where intermediate result files are stored. When running a hybrid workflow, `-bucket-dir` and `-work-dir` should define separate work directories for remote tasks and local tasks, respectively.
+
+##### `-cache`
+
+Enable/disable processes caching.
+
+##### `-d, -deep`
+
+Create a shallow clone of the specified depth.
+
+##### `-disable-jobs-cancellation`
+
+Prevent the cancellation of child jobs on execution termination
+
+##### `-dsl1`
+
+<DeprecatedInVersion version="23.09.0-edge">
+</DeprecatedInVersion>
+
+Execute the workflow using DSL1 syntax.
+
+##### `-dsl2`
+
+<DeprecatedInVersion version="23.09.0-edge">
+</DeprecatedInVersion>
+
+Execute the workflow using DSL2 syntax.
+
+##### `-dump-channels`
+
+Dump channels for debugging purpose.
+
+##### `-dump-hashes`
+Dump task hash keys for debugging purposes.
+
+<AddedInVersion version="23.10.0">
+You can use `-dump-hashes json` to dump the task hash keys as JSON for easier post-processing. See the [caching and resuming tip][cache-compare-hashes] for more details.
+</AddedInVersion>
+
+##### `-e.<key>=<value>`
 
-`-ansi-log`
-: Enable/disable ANSI console logging.
+Add the specified variable to execution environment.
 
-`-bucket-dir`
-: Remote bucket where intermediate result files are stored. When running a hybrid workflow, `-bucket-dir` and `-work-dir` should define separate work directories for remote tasks and local tasks, respectively.
+##### `-entry`
 
-`-cache`
-: Enable/disable processes caching.
+<DeprecatedInVersion version="24.10.0">
+Use params in the entry workflow to call different workflows from the command line.
+</DeprecatedInVersion>
 
-`-d, -deep`
-: Create a shallow clone of the specified depth.
+Entry workflow to be executed.
 
-`-disable-jobs-cancellation`
-: Prevent the cancellation of child jobs on execution termination
+##### `-h, -help`
 
-`-dsl1`
-: :::{deprecated} 23.09.0-edge
-  :::
-: Execute the workflow using DSL1 syntax.
+Print the command usage.
 
-`-dsl2`
-: :::{deprecated} 23.09.0-edge
-  :::
-: Execute the workflow using DSL2 syntax.
+##### `-hub` (`github`)
 
-`-dump-channels`
-: Dump channels for debugging purpose.
+Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
 
-`-dump-hashes`
-: Dump task hash keys for debugging purposes.
-: :::{versionadded} 23.10.0
-  You can use `-dump-hashes json` to dump the task hash keys as JSON for easier post-processing. See the {ref}`caching and resuming tips <cache-compare-hashes>` for more details.
-  :::
+##### `-latest`
 
-`-e.<key>=<value>`
-: Add the specified variable to execution environment.
+Pull latest changes before run.
 
-`-entry`
-: :::{deprecated} 24.10.0
-  Use params in the entry workflow to call different workflows from the command line.
-  :::
-: Entry workflow to be executed.
+##### `-lib`
 
-`-h, -help`
-: Print the command usage.
+Library extension path.
 
-`-hub` (`github`)
-: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
+##### `-main-script` (`main.nf`)
 
-`-latest`
-: Pull latest changes before run.
+<AddedInVersion version="20.09.1-edge" />
 
-`-lib`
-: Library extension path.
+The script file to be executed when launching a project directory or repository.
 
-`-main-script` (`main.nf`)
-: :::{versionadded} 20.09.1-edge
-  :::
-: The script file to be executed when launching a project directory or repository.
 
-`-name`
-: Assign a mnemonic name to the a pipeline run.
+##### `-name`
 
-`-offline`
-: Do not check for remote project updates.
+Assign a mnemonic name to the a pipeline run.
 
-`-o, -output-dir` (`results`)
-: :::{versionadded} 24.10.0
-  :::
-: Directory where workflow outputs are stored.
+##### `-offline`
 
-`-params-file`
-: Load script parameters from a JSON/YAML file.
+Do not check for remote project updates.
 
-`-plugins`
-: Comma separated list of plugin ids to be applied in the pipeline execution.
+##### `-o, -output-dir` (`results`)
 
-`-preview`
-: :::{versionadded} 22.06.0-edge
-  :::
-: Run the workflow script skipping the execution of all processes.
+<AddedInVersion version="24.10.0" />
 
-`-process.<key>=<value>`
-: Set process config options.
+Directory where workflow outputs are stored.
 
-`-profile`
-: Choose a configuration profile.
+##### `-params-file`
 
-`-qs, -queue-size`
-: Max number of processes that can be executed in parallel by each executor.
+Load script parameters from a JSON/YAML file.
 
-`-resume`
-: Execute the script using the cached results, useful to continue executions that was stopped by an error.
+##### `-plugins`
 
-`-r, -revision`
-: Revision of the project to run (either a git branch, tag or commit hash).
-: When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
+Comma separated list of plugin ids to be applied in the pipeline execution.
 
-`-stub-run, -stub`
-: Execute the workflow replacing process scripts with command stubs
+##### `-preview`
 
-`-test`
-: Test a script function with the name specified.
+<AddedInVersion version="22.06.0-edge" />
 
-`-user`
-: Private repository user name.
+Run the workflow script skipping the execution of all processes.
 
-`-with-apptainer`
-: Enable process execution in an Apptainer container.
+##### `-process.<key>=<value>`
 
-`-with-charliecloud`
-: Enable process execution in a Charliecloud container.
+Set process config options.
 
-`-with-cloudcache`
-: Enable the use of the Cloud cache plugin for storing cache metadata to an object storage bucket.
+##### `-profile`
 
-`-with-conda`
-: Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
+Choose a configuration profile.
 
-`-with-dag` (`dag-<timestamp>.html`)
-: Create pipeline DAG file.
-: :::{versionchanged} 23.10.0
-  The default format was changed from `dot` to `html`.
-  :::
+##### `-qs, -queue-size`
 
-`-with-docker`
-: Enable process execution in a Docker container.
+Max number of processes that can be executed in parallel by each executor.
 
-`-N, -with-notification`
-: Send a notification email on workflow completion to the specified recipients.
+##### `-resume`
 
-`-with-podman`
-: Enable process execution in a Podman container.
+Execute the script using the cached results, useful to continue executions that was stopped by an error.
 
-`-with-report` (`report-<timestamp>.html`)
-: Create workflow execution HTML report.
+##### `-r, -revision`
 
-`-with-singularity`
-: Enable process execution in a Singularity container.
+Revision of the project to run (either a git branch, tag or commit hash).
 
-`-with-spack`
-: Use the specified Spack environment package or file (must end with `.yaml`)
+When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
 
-`-with-timeline` (`timeline-<timestamp>.html`)
-: Create workflow execution timeline.
+##### `-stub-run, -stub`
 
-`-with-tower` (`https://api.cloud.seqera.io`)
-: Monitor workflow execution with [Seqera Platform](https://seqera.io/) (formerly Tower Cloud).
+Execute the workflow replacing process scripts with command stubs
 
-`-with-trace` (`trace-<timestamp>.txt`)
-: Create workflow execution trace file.
+##### `-test`
 
-`-with-wave` (`https://wave.seqera.io`)
-: Enable the use of Wave containers.
+Test a script function with the name specified.
 
-`-with-weblog` (`http://localhost`)
-: Send workflow status messages via HTTP to target URL.
+##### `-user`
 
-`-without-conda`
-: Disable process execution with Conda.
+Private repository user name.
 
-`-without-docker`
-: Disable process execution with Docker.
+##### `-with-apptainer`
 
-`-without-podman`
-: Disable process execution in a Podman container.
+Enable process execution in an Apptainer container.
 
-`-without-spack`
-: Disable process execution with Spack.
+##### `-with-charliecloud`
 
-`-without-wave`
-: Disable the use of Wave containers.
+Enable process execution in a Charliecloud container.
 
-`-w, -work-dir` (`work`)
-: Directory where intermediate result files are stored.
+##### `-with-cloudcache`
+
+Enable the use of the Cloud cache plugin for storing cache metadata to an object storage bucket.
+
+##### `-with-conda`
+
+Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
+
+##### `-with-dag` (`dag-<timestamp>.html`)
+
+Create pipeline DAG file.
+
+Create pipeline DAG file.
+
+<ChangedInVersion version="23.10.0">
+The default format was changed from `dot` to `html`.
+</ChangedInVersion>
+
+##### `-with-docker`
+
+Enable process execution in a Docker container.
+
+##### `-N, -with-notification`
+
+Send a notification email on workflow completion to the specified recipients.
+
+##### `-with-podman`
+
+Enable process execution in a Podman container.
+
+##### `-with-report` (`report-<timestamp>.html`)
+
+Create workflow execution HTML report.
+
+##### `-with-singularity`
+
+Enable process execution in a Singularity container.
+
+##### `-with-spack`
+
+Use the specified Spack environment package or file (must end with `.yaml`)
+
+##### `-with-timeline` (`timeline-<timestamp>.html`)
+
+Create workflow execution timeline.
+
+##### `-with-tower` (`https://api.cloud.seqera.io`)
+
+Monitor workflow execution with [Seqera Platform](https://seqera.io/) (formerly Tower Cloud).
+
+##### `-with-trace` (`trace-<timestamp>.txt`)
+
+Create workflow execution trace file.
+
+##### `-with-wave` (`https://wave.seqera.io`)
+
+Enable the use of Wave containers.
+
+##### `-with-weblog` (`http://localhost`)
+
+Send workflow status messages via HTTP to target URL.
+
+##### `-without-conda`
+
+Disable process execution with Conda.
+
+##### `-without-docker`
+
+Disable process execution with Docker.
+
+##### `-without-podman`
+
+Disable process execution in a Podman container.
+
+##### `-without-spack`
+
+Disable process execution with Spack.
+
+##### `-without-wave`
+
+Disable the use of Wave containers.
+
+##### `-w, -work-dir` (`work`)
+
+Directory where intermediate result files are stored.
+
+#
 
 **Examples**
 
@@ -1399,7 +1569,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
   $ nextflow run main.nf -profile docker
   ```
 
-- Execute a pipeline and generate the summary HTML report. For more information on the metrics, please refer the {ref}`tracing-page` section:
+- Execute a pipeline and generate the summary HTML report. See [Reports][tracing-page] for more information:
 
   ```console
   $ nextflow run main.nf -with-report
@@ -1429,13 +1599,11 @@ The `run` command is used to execute a local pipeline script or remote pipeline
   $ nextflow run main.nf -params-file pipeline_params.yml
   ```
 
-  See {ref}`cli-params` for more information about writing custom parameters files.
-
-(cli-secrets)=
+See [Pipeline parameters][cli-params] for more information about writing custom parameters files.
 
 ### `secrets`
 
-Manage {ref}`pipeline secrets <secrets-page>`.
+Manage [pipeline secrets][secrets-page].
 
 **Usage**
 
@@ -1445,22 +1613,29 @@ $ nextflow secrets <SUBCOMMAND> [OPTIONS]
 
 **Options**
 
-`-h, -help`
-: Print the command usage.
+##### `-h, -help`
+
+Print the command usage.
 
 **Subcommands**
 
-`list`
-: List secrets available in the current store.
+##### `list`
+
+List secrets available in the current store.
+
+##### `get <secret>`
+
+Retrieve a secret value.
+
+##### `set <secret> <value> `
 
-`get <secret>`
-: Retrieve a secret value.
+Create or update a secret.
 
-`set <secret> <value> `
-: Create or update a secret.
+##### `delete <secret>`
 
-`delete <secret>`
-: Delete a secret.
+Delete a secret.
+
+#
 
 **Examples**
 
@@ -1536,14 +1711,19 @@ The `view` command is used to inspect the pipelines that are already stored in t
 
 **Options**
 
-`-h, -help`
-: Print the command usage.
+##### `-h, -help`
+
+Print the command usage.
+
+##### `-l`
 
-`-l`
-: List repository content.
+List repository content.
 
-`-q`
-: Hide header line.
+##### `-q`
+
+Hide header line.
+
+#
 
 **Examples**
 
@@ -1607,3 +1787,13 @@ workflow {
   channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
 }
 ```
+
+[cache-compare-hashes]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#comparing-the-hashes-of-two-runs
+[config-profiles]: /nextflow_docs/nextflow_repo/docs/config.mdx#config-profiles
+[gradle-plugin-create]: /nextflow_docs/nextflow_repo/docs/guides/gradle-plugin.mdx#creating-a-plugin
+[cli-page]: /nextflow_docs/nextflow_repo/docs/cli.mdx
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[data-lineage-page]: /nextflow_docs/nextflow_repo/docs/tutorials/data-lineage.mdx
+[k8s-page]: /nextflow_docs/nextflow_repo/docs/kubernetes.mdx
+[secrets-page]: /nextflow_docs/nextflow_repo/docs/secrets.mdx
+[tracing-page]: /nextflow_docs/nextflow_repo/docs/reports.mdx
diff --git a/new-docs/nextflow-docs/reference/config.mdx b/new-docs/nextflow-docs/reference/config.mdx
new file mode 100644
index 0000000000..29fc91a8b4
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/config.mdx
@@ -0,0 +1,2214 @@
+
+
+# Configuration options
+
+This page lists all of the available settings in the [Nextflow configuration][config-page].
+
+## Unscoped options
+
+The following settings are available:
+
+##### `bucketDir`
+
+The remote work directory used by hybrid workflows. Equivalent to the `-bucket-dir` option of the `run` command.
+
+##### `cleanup`
+
+Delete all files associated with a run in the work directory when the run completes successfully (default: `false`).
+
+:::warning
+This option will prevent the use of the *resume* feature on subsequent executions of that pipeline run.
+:::
+
+:::warning
+This option is not supported for remote work directories, such as Amazon S3, Google Cloud Storage, and Azure Blob Storage.
+:::
+
+##### `dumpHashes`
+
+If `true`, dump task hash keys in the log file, for debugging purposes. Equivalent to the `-dump-hashes` option of the `run` command.
+
+##### `outputDir`
+
+<AddedInVersion version="24.10.0">
+</AddedInVersion>
+
+The pipeline output directory. Equivalent to the `-output-dir` option of the `run` command.
+
+##### `resume`
+
+Enable the use of previously cached task executions. Equivalent to the `-resume` option of the `run` command.
+
+##### `workDir`
+
+The pipeline work directory. Equivalent to the `-work-dir` option of the `run` command.
+
+## `apptainer`
+
+The `apptainer` scope controls how [Apptainer](https://apptainer.org) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `apptainer.autoMounts`
+
+Automatically mount host paths in the executed container (default: `true`). It requires the `user bind control` feature to be enabled in your Apptainer installation.
+
+##### `apptainer.cacheDir`
+
+The directory where remote Apptainer images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+##### `apptainer.enabled`
+
+Execute tasks with Apptainer containers (default: `false`).
+
+##### `apptainer.engineOptions`
+
+Specify additional options supported by the Apptainer engine i.e. `apptainer [OPTIONS]`.
+
+##### `apptainer.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `apptainer.libraryDir`
+
+Directory where remote Apptainer images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+##### `apptainer.noHttps`
+
+Pull the Apptainer image with http protocol (default: `false`).
+
+##### `apptainer.ociAutoPull`
+
+<AddedInVersion version="23.12.0-edge">
+</AddedInVersion>
+
+When enabled, OCI (and Docker) container images are pulled and converted to the SIF format by the Apptainer run command, instead of Nextflow (default: `false`).
+
+:::note
+Leave `ociAutoPull` disabled if you are willing to build a Singularity/Apptainer native image with Wave (see the [Singularity][wave-singularity] section).
+:::
+
+
+##### `apptainer.pullTimeout`
+
+The amount of time the Apptainer pull can last, exceeding which the process is terminated (default: `20 min`).
+
+##### `apptainer.registry`
+
+The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `apptainer.runOptions`
+
+Specify extra command line options supported by `apptainer exec`.
+
+See the [Apptainer][container-apptainer] page to learn more about how to use Apptainer containers with Nextflow.
+
+## `aws`
+
+The `aws` scope controls the interactions with AWS, including AWS Batch and S3.
+
+The following settings are available:
+
+##### `aws.accessKey`
+
+AWS account access key.
+
+##### `aws.profile`
+
+<AddedInVersion version="22.12.0-edge">
+</AddedInVersion>
+
+AWS profile from `~/.aws/credentials`.
+
+##### `aws.region`
+
+AWS region (e.g. `us-east-1`).
+
+##### `aws.secretKey`
+
+AWS account secret key.
+
+##### `aws.batch.cliPath`
+
+The path where the AWS command line tool is installed in the host AMI.
+
+##### `aws.batch.delayBetweenAttempts`
+
+Delay between download attempts from S3 (default: `10 sec`).
+
+##### `aws.batch.executionRole`
+
+The AWS Batch [Execution Role](https://docs.aws.amazon.com/batch/latest/userguide/execution-IAM-role.html) ARN that needs to be used to execute the Batch Job. It is mandatory when using AWS Fargate.
+
+##### `aws.batch.jobRole`
+
+The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
+
+##### `aws.batch.logsGroup`
+
+<AddedInVersion version="22.09.0-edge">
+</AddedInVersion>
+
+The name of the logs group used by Batch Jobs (default: `/aws/batch/job`).
+
+##### `aws.batch.maxParallelTransfers`
+
+Max parallel upload/download transfer operations *per job* (default: `4`).
+
+##### `aws.batch.maxSpotAttempts`
+
+<AddedInVersion version="22.04.0">
+</AddedInVersion>
+
+<ChangedInVersion version="24.08.0-edge">
+The default value was changed from `5` to `0`.
+</ChangedInVersion>
+
+Max number of execution attempts of a job interrupted by a EC2 Spot reclaim event (default: `0`)
+
+##### `aws.batch.maxTransferAttempts`
+
+Max number of downloads attempts from S3 (default: `1`).
+
+##### `aws.batch.platformType`
+
+The compute platform type used by AWS Batch. Can be either `ec2` or `fargate`. Set to `fargate` to use [AWS Fargate](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html).
+
+##### `aws.batch.retryMode`
+
+The [retry mode](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-retries.html) used to handle rate-limiting by AWS APIs. Can be one of `standard`, `legacy`, `adaptive`, or `built-in` (default: `standard`).
+
+##### `aws.batch.schedulingPriority`
+
+<AddedInVersion version="23.01.0-edge">
+</AddedInVersion>
+
+The scheduling priority for all tasks when using [fair-share scheduling](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/) (default: `0`).
+
+##### `aws.batch.shareIdentifier`
+
+<AddedInVersion version="22.09.0-edge">
+</AddedInVersion>
+
+The share identifier for all tasks when using [fair-share scheduling](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/).
+
+##### `aws.batch.terminateUnschedulableJobs`
+
+<AddedInVersion version="25.03.0-edge">
+</AddedInVersion>
+
+When `true`, jobs that cannot be scheduled due to lack of resources or misconfiguration are terminated and handled as task failures (default: `false`).
+
+##### `aws.batch.volumes`
+
+List of container mounts. Mounts can be specified as simple e.g. `/some/path` or canonical format e.g. `/host/path:/mount/path[:ro|rw]`.
+
+##### `aws.client.anonymous`
+
+Allow the access of public S3 buckets without providing AWS credentials (default: `false`). Any service that does not accept unsigned requests will return a service access error.
+
+##### `aws.client.connectionTimeout`
+
+The amount of time to wait (in milliseconds) when initially establishing a connection before timing out (default: `10000`).
+
+##### `aws.client.endpoint`
+
+The AWS S3 API entry point e.g. `https://s3-us-west-1.amazonaws.com`. The endpoint must include the protocol prefix e.g. `https://`.
+
+##### `aws.client.maxConcurrency`
+
+<AddedInVersion version="25.06.0-edge" />
+
+The maximum number of concurrent S3 transfers used by the S3 transfer manager. By default, this setting is determined by `aws.client.targetThroughputInGbps`. Modifying this value can affect the amount of memory used for S3 transfers.
+
+##### `aws.client.maxConnections`
+
+The maximum number of open HTTP connections used by the S3 client (default: `50`).
+
+##### `aws.client.maxDownloadHeapMemory`
+
+The maximum size for the heap memory buffer used by concurrent downloads. It must be at least 10 times the `minimumPartSize` (default:`400 MB`).
+
+##### `aws.client.maxErrorRetry`
+
+The maximum number of retry attempts for failed retryable requests (default: `-1`).
+
+##### `aws.client.maxNativeMemory`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The maximum native memory used by the S3 transfer manager. By default, this setting is determined by `aws.client.targetThroughputInGbps`.
+
+##### `aws.client.minimumPartSize`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The minimum part size used for multipart S3 transfers (default: `8 MB`).
+
+##### `aws.client.multipartThreshold`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The object size threshold used for multipart S3 transfers (default: same as `aws.cllient.minimumPartSize`).
+
+##### `aws.client.protocol`
+
+<AddedInVersion version="25.06.0-edge" />
+
+The protocol to use when connecting to AWS. Can be `http` or `https` (default: `'https'`).
+
+##### `aws.client.proxyHost`
+
+The proxy host to connect through.
+
+##### `aws.client.proxyPassword`
+
+The password to use when connecting through a proxy.
+
+##### `aws.client.proxyPort`
+
+The port to use when connecting through a proxy.
+
+##### `aws.client.proxyScheme`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The protocol scheme to use when connecting through a proxy. Can be `http` or `https` (default: `'http'`).
+
+##### `aws.client.proxyUsername`
+
+The user name to use when connecting through a proxy.
+
+##### `aws.client.requesterPays`
+
+<AddedInVersion version="24.05.0-edge">
+</AddedInVersion>
+
+Use [Requester Pays](https://docs.aws.amazon.com/AmazonS3/latest/userguide/RequesterPaysBuckets.html) for S3 buckets (default: `false`).
+
+##### `aws.client.s3Acl`
+
+Specify predefined bucket permissions, also known as [canned ACL](https://docs.aws.amazon.com/AmazonS3/latest/userguide/acl-overview.html#canned-acl). Can be one of `Private`, `PublicRead`, `PublicReadWrite`, `AuthenticatedRead`, `LogDeliveryWrite`, `BucketOwnerRead`, `BucketOwnerFullControl`, or `AwsExecRead`.
+
+##### `aws.client.s3PathStyleAccess`
+
+Use the path-based access model to access objects in S3-compatible storage systems (default: `false`).
+
+##### `aws.client.signerOverride`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The name of the signature algorithm to use for signing requests made by the client.
+
+##### `aws.client.socketSendBufferSizeHint`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The Size hint (in bytes) for the low level TCP send buffer (default: `0`).
+
+##### `aws.client.socketRecvBufferSizeHint`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The Size hint (in bytes) for the low level TCP receive buffer (default: `0`).
+
+##### `aws.client.socketTimeout`
+
+The amount of time to wait (in milliseconds) for data to be transferred over an established, open connection before the connection is timed out (default: `50000`).
+
+##### `aws.client.storageClass`
+
+The S3 storage class applied to stored objects, one of \[`STANDARD`, `STANDARD_IA`, `ONEZONE_IA`, `INTELLIGENT_TIERING`\] (default: `STANDARD`).
+
+##### `aws.client.storageEncryption`
+
+The S3 server side encryption to be used when saving objects on S3. Can be `AES256` or `aws:kms` (default: none).
+
+##### `aws.client.storageKmsKeyId`
+
+<AddedInVersion version="25.05.0-edge">
+</AddedInVersion>
+
+The AWS KMS key Id to be used to encrypt files stored in the target S3 bucket.
+
+##### `aws.client.targetThroughputInGbps`
+
+<AddedInVersion version="25.06.0-edge">
+</AddedInVersion>
+
+The target network throughput (in Gbps) used for S3 uploads and downloads (default: `10`).
+
+The number of threads used by the S3 transfer manager (default: `10`).
+
+##### `aws.client.userAgent`
+
+<DeprecatedInVersion version="25.06.0-edge">
+</DeprecatedInVersion>
+
+The HTTP user agent header passed with all HTTP requests.
+
+##### `aws.client.uploadChunkSize`
+
+<DeprecatedInVersion version="25.06.0-edge">
+</DeprecatedInVersion>
+
+The size of a single part in a multipart upload (default: `100 MB`).
+
+##### `aws.client.uploadMaxAttempts`
+
+<DeprecatedInVersion version="25.06.0-edge">
+</DeprecatedInVersion>
+
+The maximum number of upload attempts after which a multipart upload returns an error (default: `5`).
+
+##### `aws.client.uploadMaxThreads`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The maximum number of threads used for multipart upload (default: `10`).
+
+##### `aws.client.uploadRetrySleep`
+
+<DeprecatedInVersion version="24.06.0-edge" />
+
+The time to wait after a failed upload attempt to retry the part upload (default: `500ms`).
+
+##### `aws.client.uploadStorageClass`
+
+The S3 storage class applied to stored objects. Can be `STANDARD`, `STANDARD_IA`, `ONEZONE_IA`, or `INTELLIGENT_TIERING` (default: `STANDARD`).
+
+## `azure`
+
+The `azure` scope allows you to configure the interactions with Azure, including Azure Batch and Azure Blob Storage.
+
+The following settings are available:
+
+##### `azure.activeDirectory.servicePrincipalId`
+
+The service principal client ID. Defaults to environment variable `AZURE_CLIENT_ID`.
+
+##### `azure.activeDirectory.servicePrincipalSecret`
+
+The service principal client secret. Defaults to environment variable `AZURE_CLIENT_SECRET`.
+
+##### `azure.activeDirectory.tenantId`
+
+The Azure tenant ID. Defaults to environment variable `AZURE_TENANT_ID`.
+
+##### `azure.azcopy.blobTier`
+
+The blob [access tier](https://learn.microsoft.com/en-us/azure/storage/blobs/access-tiers-overview) used by `azcopy` to upload files to Azure Blob Storage. Valid options are `None`, `Hot`, or `Cool` (default: `None`).
+
+##### `azure.azcopy.blockSize`
+
+The block size (in MB) used by `azcopy` to transfer files between Azure Blob Storage and compute nodes (default: `4`).
+
+##### `azure.batch.accountKey`
+
+The batch service account key. Defaults to environment variable `AZURE_BATCH_ACCOUNT_KEY`.
+
+##### `azure.batch.accountName`
+
+The batch service account name. Defaults to environment variable `AZURE_BATCH_ACCOUNT_NAME`.
+
+##### `azure.batch.allowPoolCreation`
+
+Enable the automatic creation of batch pools specified in the Nextflow configuration file (default: `false`).
+
+##### `azure.batch.autoPoolMode`
+
+Enable the automatic creation of batch pools depending on the pipeline resources demand (default: `true`).
+
+##### `azure.batch.copyToolInstallMode`
+
+The mode in which the `azcopy` tool is installed by Nextflow (default: `'node'`).
+
+The following options are available:
+
+###### `'node'`
+
+The `azcopy` tool is installed once during the pool creation.
+
+###### `'task'`
+
+The `azcopy` tool is installed for each task execution.
+
+###### `'off'`
+
+The `azcopy` tool is not installed.
+
+##### `azure.batch.deleteJobsOnCompletion`
+
+<ChangedInVersion version="24.08.0-edge">
+Default value was changed from `true` to `false`.
+</ChangedInVersion>
+
+Delete all jobs when the workflow completes (default: `false`).
+
+##### `azure.batch.deletePoolsOnCompletion`
+
+Delete all compute node pools when the workflow completes (default: `false`).
+
+##### `azure.batch.deleteTasksOnCompletion`
+
+<AddedInVersion version="23.08.0-edge">
+</AddedInVersion>
+
+Delete each task when it completes (default: `true`).
+Although this setting is enabled by default, failed tasks will not be deleted unless it is explicitly enabled. This way, the default behavior is that successful tasks are deleted while failed tasks are preserved for debugging purposes.
+
+##### `azure.batch.endpoint`
+
+The batch service endpoint e.g. `https://nfbatch1.westeurope.batch.azure.com`.
+
+##### `azure.batch.jobMaxWallClockTime`
+
+<AddedInVersion version="25.04.0">
+</AddedInVersion>
+
+The maximum elapsed time that jobs may run, measured from the time they are created (default: `30d`).
+
+If jobs do not complete within this time limit, the Batch service terminates them and any tasks still running.
+
+##### `azure.batch.location`
+
+The name of the batch service region, e.g. `westeurope` or `eastus2`. Not needed when the endpoint is specified.
+
+#####`azure.batch.poolIdentityClientId`
+
+<AddedInVersion version="25.05.0-edge" />
+
+The client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) that is available on all Azure Batch node pools. This identity is used by Fusion to authenticate to Azure storage. If set to `'auto'`, Fusion will use the first available managed identity.
+
+##### `azure.batch.pools.<name>.autoScale`
+
+Enable autoscaling feature for the pool identified with `<name>`.
+
+##### `azure.batch.pools.<name>.fileShareRootPath`
+
+The internal root mount point when mounting File Shares. Must be `/mnt/resource/batch/tasks/fsmounts` for CentOS nodes or `/mnt/batch/tasks/fsmounts` for Ubuntu nodes (default: CentOS).
+
+##### `azure.batch.pools.<name>.lowPriority`
+
+Enable the use of low-priority VMs (default: `false`).
+
+:::warning
+As of September 30, 2025, Low Priority VMs will no longer be supported in Azure Batch accounts that use Batch Managed mode for pool allocation.
+You may continue to use this setting to configure Spot VMs in Batch accounts configured with User Subscription mode.
+:::
+
+##### `azure.batch.pools.<name>.maxVmCount`
+
+The max number of virtual machines when using auto scaling.
+
+##### `azure.batch.pools.<name>.mountOptions`
+
+The mount options for mounting the file shares (default: `-o vers=3.0,dir_mode=0777,file_mode=0777,sec=ntlmssp`).
+
+##### `azure.batch.pools.<name>.offer`
+
+The offer type of the virtual machine type used by the pool identified with `<name>` (default: `centos-container`).
+
+##### `azure.batch.pools.<name>.privileged`
+
+Enable the task to run with elevated access. Ignored if `runAs` is set (default: `false`).
+
+##### `azure.batch.pools.<name>.publisher`
+
+The publisher of virtual machine type used by the pool identified with `<name>` (default: `microsoft-azure-batch`).
+
+##### `azure.batch.pools.<name>.runAs`
+
+The username under which the task is run. The user must already exist on each node of the pool.
+
+##### `azure.batch.pools.<name>.scaleFormula`
+
+The [scale formula](https://docs.microsoft.com/en-us/azure/batch/batch-automatic-scaling) for the pool identified with `<name>`.
+
+##### `azure.batch.pools.<name>.scaleInterval`
+
+The interval at which to automatically adjust the Pool size according to the autoscale formula. Must be at least 5 minutes and at most 168 hours (default: `10 mins`).
+
+##### `azure.batch.pools.<name>.schedulePolicy`
+
+The scheduling policy for the pool identified with `<name>`. Can be either `spread` or `pack` (default: `spread`).
+
+##### `azure.batch.pools.<name>.sku`
+
+The ID of the Compute Node agent SKU which the pool identified with `<name>` supports (default: `batch.node.centos 8`).
+
+##### `azure.batch.pools.<name>.startTask.privileged`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+Enable the `startTask` to run with elevated access (default: `false`).
+
+##### `azure.batch.pools.<name>.startTask.script`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+The `startTask` that is executed as the node joins the Azure Batch node pool.
+
+##### `azure.batch.pools.<name>.virtualNetwork`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+The subnet ID of a virtual network in which to create the pool.
+
+##### `azure.batch.pools.<name>.vmCount`
+
+The number of virtual machines provisioned by the pool identified with `<name>`.
+
+##### `azure.batch.pools.<name>.vmType`
+
+Specify the virtual machine type used by the pool identified with `<name>`.
+
+##### `azure.batch.terminateJobsOnCompletion`
+
+<AddedInVersion version="23.05.0-edge">
+</AddedInVersion>
+
+When the workflow completes, set all jobs to terminate on task completion (default: `true`).
+
+##### `azure.managedIdentity.clientId`
+
+The client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview). Defaults to environment variable `AZURE_MANAGED_IDENTITY_USER`.
+
+##### `azure.managedIdentity.system`
+
+ When `true`, use the system-assigned [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) to authenticate Azure resources. Defaults to environment variable `AZURE_MANAGED_IDENTITY_SYSTEM`.
+
+##### `azure.registry.password`
+
+The password to connect to a private container registry.
+
+##### `azure.registry.server`
+
+The container registry from which to pull the Docker images (default: `docker.io`).
+
+##### `azure.registry.userName`
+
+The username to connect to a private container registry.
+
+##### `azure.retryPolicy.delay`
+
+Delay when retrying failed API requests (default: `250ms`).
+
+##### `azure.retryPolicy.jitter`
+
+Jitter value when retrying failed API requests (default: `0.25`).
+
+##### `azure.retryPolicy.maxAttempts`
+
+Max attempts when retrying failed API requests (default: `10`).
+
+##### `azure.retryPolicy.maxDelay`
+
+Max delay when retrying failed API requests (default: `90s`).
+
+##### `azure.storage.accountKey`
+
+The blob storage account key. Defaults to environment variable `AZURE_STORAGE_ACCOUNT_KEY`.
+
+##### `azure.storage.accountName`
+
+The blob storage account name. Defaults to environment variable `AZURE_STORAGE_ACCOUNT_NAME`.
+
+##### `azure.storage.fileShares.<name>.mountOptions`
+
+The file share mount options.
+
+##### `azure storage.fileShares.<name>.mountPath`
+
+The file share mount path.
+
+##### `azure.storage.sasToken`
+
+The blob storage shared access signature (SAS) token, which can be provided instead of an account key. Defaults to environment variable `AZURE_STORAGE_SAS_TOKEN`.
+
+##### `azure.storage.tokenDuration`
+
+The duration of the SAS token generated by Nextflow when the `sasToken` option is *not* specified (default: `48h`).
+
+## `charliecloud`
+
+The `charliecloud` scope controls how [Charliecloud](https://hpc.github.io/charliecloud/) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `charliecloud.cacheDir`
+
+The directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+##### `charliecloud.enabled`
+
+Execute tasks with Charliecloud containers (default: `false`).
+
+##### `charliecloud.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `charliecloud.pullTimeout`
+
+The amount of time the Charliecloud pull can last, exceeding which the process is terminated (default: `20 min`).
+
+##### `charliecloud.registry`
+
+The registry from where images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `charliecloud.runOptions`
+
+Specify extra command line options supported by the `ch-run` command.
+
+##### `charliecloud.temp`
+
+Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
+
+##### `charliecloud.writableInputMounts`
+
+When `false`, mount input directories as read-only (default: `true`).
+
+##### `charliecloud.writeFake`
+
+Run containers from storage in writeable mode using overlayfs (default: `true`).
+
+This option requires unprivileged `overlayfs` (Linux kernel >= 5.11). For full support, tempfs with xattrs in the user namespace (Linux kernel >= 6.6) is required. See [charliecloud documentation](https://hpc.github.io/charliecloud/ch-run.html#ch-run-overlay) for details.
+
+## `conda`
+
+The `conda` scope controls the creation of Conda environments by the Conda package manager.
+
+The following settings are available:
+
+##### `conda.cacheDir`
+
+The path where Conda environments are stored. It should be accessible from all compute nodes when using a shared file system.
+
+##### `conda.channels`
+
+The list of Conda channels that can be used to resolve Conda packages. Channel priority decreases from left to right.
+
+##### `conda.createOptions`
+
+Extra command line options for the `conda create` command. See the [Conda documentation](https://docs.conda.io/projects/conda/en/latest/commands/create.html) for more information.
+
+##### `conda.createTimeout`
+
+The amount of time to wait for the Conda environment to be created before failing (default: `20 min`).
+
+##### `conda.enabled`
+
+Execute tasks with Conda environments (default: `false`).
+
+##### `conda.useMamba`
+
+Use [Mamba](https://github.com/mamba-org/mamba) instead of `conda` to create Conda environments (default: `false`).
+
+<AddedInVersion version="25.05.0-edge">
+</AddedInVersion>
+
+Use [Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) instead of `conda` to create Conda environments (default: `false`).
+
+See [Conda][conda-page] for more information about using Conda environments with Nextflow.
+
+## `dag`
+
+The `dag` scope controls the workflow diagram generated by Nextflow.
+
+The following settings are available:
+
+##### `dag.enabled`
+
+When `true` enables the generation of the DAG file (default: `false`).
+
+##### `dag.depth`
+
+<AddedInVersion version="23.10.0">
+</AddedInVersion>
+
+*Supported by the HTML and Mermaid renderers.*
+
+Controls the maximum depth at which to render sub-workflows (default: no limit).
+
+##### `dag.direction`
+
+<AddedInVersion version="23.10.0">
+</AddedInVersion>
+
+*Supported by Graphviz, DOT, HTML and Mermaid renderers.*
+
+Controls the direction of the DAG, can be `'LR'` (left-to-right) or `'TB'` (top-to-bottom) (default: `'TB'`).
+
+##### `dag.enabled`
+
+When `true` enables the generation of the DAG file (default: `false`).
+
+##### `dag.file`
+
+Graph file name (default: `'dag-<timestamp>.html'`).
+
+##### `dag.overwrite`
+
+When `true` overwrites any existing DAG file with the same name (default: `false`).
+
+##### `dag.verbose`
+
+<AddedInVersion version="23.10.0">
+</AddedInVersion>
+
+*Only supported by the HTML and Mermaid renderers.*
+
+When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`).
+
+## `docker`
+
+The `docker` scope controls how [Docker](https://www.docker.com) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `docker.enabled`
+
+Enable Docker execution (default: `false`).
+
+##### `docker.engineOptions`
+
+Specify additional options supported by the Docker engine i.e. `docker [OPTIONS]`.
+
+##### `docker.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `docker.fixOwnership`
+
+Fix ownership of files created by the Docker container (default: `false`).
+
+##### `docker.legacy`
+
+Use command line options removed since Docker 1.10.0 (default: `false`).
+
+##### `docker.mountFlags`
+
+Add the specified flags to the volume mounts e.g. `'ro,Z'`.
+
+##### `docker.registry`
+
+The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `docker.registryOverride`
+
+<AddedInVersion version="25.06.0-edge" />
+
+When `true`, forces the override of the registry name in fully qualified container image names with the registry specified by `docker.registry` (default: `false`).
+
+This setting allows you to redirect container image pulls from their original registry to a different registry, such as a private mirror or proxy.
+
+##### `docker.remove`
+
+Clean up the container after the execution (default: `true`). See the [Docker documentation](https://docs.docker.com/engine/reference/run/#clean-up---rm) for details.
+
+##### `docker.runOptions`
+
+Specify extra command line options supported by the `docker run` command. See the [Docker documentation](https://docs.docker.com/engine/reference/run/) for details.
+
+##### `docker.sudo`
+
+Executes Docker run command as `sudo` (default: `false`).
+
+##### `docker.temp`
+
+Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
+
+##### `docker.tty`
+
+Allocates a pseudo-tty (default: `false`).
+
+##### `docker.writableInputMounts`
+
+When `false`, mount input directories as read-only (default: `true`).
+
+## `env`
+
+The `env` scope allows the definition one or more variables that will be exported into the environment where workflow tasks are executed.
+
+Simply prefix your variable names with the `env` scope or surround them by curly brackets, as shown below:
+
+```groovy
+env.ALPHA = 'some value'
+env.BETA = "$HOME/some/path"
+
+env {
+     DELTA = 'one more'
+     GAMMA = "/my/path:$PATH"
+}
+```
+
+:::note
+In the above example, variables like `$HOME` and `$PATH` are evaluated when the workflow is launched. If you want these variables to be evaluated during task execution, escape them with `\$`. This difference is important for variables like `$PATH`, which may be different in the workflow environment versus the task environment.
+:::
+
+:::warning
+The `env` scope provides environment variables to *tasks*, not Nextflow itself. Nextflow environment variables such as `NXF_VER` should be set in the environment in which Nextflow is launched.
+:::
+
+## `executor`
+
+The `executor` scope controls various executor behaviors.
+
+The following settings are available:
+
+##### `executor.account`
+
+<AddedInVersion version="24.04.0">
+</AddedInVersion>
+
+*Used only by the [SLURM][slurm-executor], [LSF][lsf-executor], [PBS][pbs-executor] and [PBS Pro][pbspro-executor] executors.*
+The project or organization account that should be charged for running the pipeline jobs.
+
+##### `executor.cpus`
+
+*Used only by the local executor.*
+
+The maximum number of CPUs made available by the underlying system.
+
+##### `executor.dumpInterval`
+
+Determines how often to log the executor status (default: `5 min`).
+
+##### `executor.exitReadTimeout`
+
+*Used only by grid executors.*
+
+Determines how long to wait for the `.exitcode` file to be created after the task has completed, before returning an error status (default: `270 sec`).
+
+##### `executor.jobName`
+
+*Used only by grid executors and Google Batch.*
+
+Determines the name of jobs submitted to the underlying cluster executor:
+
+```groovy
+executor.jobName = { "$task.name - $task.hash" }
+```
+
+The job name should satisfy the validation constraints of the underlying scheduler.
+
+##### `executor.killBatchSize`
+
+Determines the number of jobs that can be killed in a single command execution (default: `100`).
+
+##### `executor.memory`
+
+*Used only by the local executor.*
+
+The maximum amount of memory made available by the underlying system.
+
+##### `executor.name`
+
+The name of the executor to be used (default: `local`).
+
+##### `executor.perCpuMemAllocation`
+
+<AddedInVersion version="23.07.0-edge">
+</AddedInVersion>
+
+*Used only by the [SLURM][slurm-executor] executor.*
+
+When `true`, memory allocations for SLURM jobs are specified as `--mem-per-cpu <task.memory / task.cpus>` instead of `--mem <task.memory>`.
+
+##### `executor.perJobMemLimit`
+
+*Used only by the [LSF][lsf-executor] executor.*
+
+Specifies Platform LSF *per-job* memory limit mode (default: `false`).
+
+##### `executor.perTaskReserve`
+
+*Used only by the [LSF][lsf-executor] executor.*
+
+Enables the *per-task* memory reserve mode for LSF jobs.
+
+##### `executor.pollInterval`
+
+Determines how often to check for process termination. Default varies for each executor.
+
+##### `executor.queueGlobalStatus`
+
+<AddedInVersion version="23.01.0-edge">
+</AddedInVersion>
+
+Determines how job status is retrieved. When `false` only the queue associated with the job execution is queried. When `true` the job status is queried globally i.e. irrespective of the submission queue (default: `false`).
+
+##### `executor.queueSize`
+
+The number of tasks the executor will handle in a parallel manner. A queue size of zero corresponds to no limit. Default varies for each executor.
+
+##### `executor.queueStatInterval`
+
+*Used only by grid executors.*
+
+Determines how often to fetch the queue status from the scheduler (default: `1 min`).
+
+##### `executor.submitRateLimit`
+
+Determines the max rate of job submission per time unit, for example `'10sec'` (10 jobs per second) or `'50/2min'` (50 jobs every 2 minutes) (default: unlimited).
+
+##### `executor.retry.delay`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+*Used only by grid executors.*
+
+Delay when retrying failed job submissions (default: `500ms`).
+
+##### `executor.retry.jitter`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+*Used only by grid executors.*
+
+Jitter value when retrying failed job submissions (default: `0.25`).
+
+##### `executor.retry.maxAttempt`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+*Used only by grid executors.*
+
+Max attempts when retrying failed job submissions (default: `3`).
+
+##### `executor.retry.maxDelay`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+*Used only by grid executors.*
+
+Max delay when retrying failed job submissions (default: `30s`).
+
+##### `executor.retry.reason`
+
+<AddedInVersion version="23.03.0-edge">
+</AddedInVersion>
+
+<ChangedInVersion version="23.03.0-edge">
+This option was renamed from `executor.submit.retry.reason` to `executor.retry.reason`.
+</ChangedInVersion>
+
+*Used only by grid executors.*
+
+Regex pattern that when verified causes a failed submit operation to be re-tried (default: `Socket timed out`).
+
+### Executor-specific defaults
+
+Some executor settings have different default values depending on the executor.
+
+| Executor       | `queueSize` | `pollInterval` |
+| -------------- | ----------- | -------------- |
+| AWS Batch      | `1000`      | `10s`          |
+| Azure Batch    | `1000`      | `10s`          |
+| Google Batch   | `1000`      | `10s`          |
+| Grid Executors | `100`       | `5s`           |
+| Kubernetes     | `100`       | `5s`           |
+| Local          | N/A         | `100ms`        |
+
+### Executor-specific configuration
+
+Executor config settings can be applied to specific executors by prefixing the executor name with the symbol `$` and using it as special scope. For example:
+
+```groovy
+// block syntax
+executor {
+  $sge {
+      queueSize = 100
+      pollInterval = '30sec'
+  }
+
+  $local {
+      cpus = 8
+      memory = '32 GB'
+  }
+}
+
+// dot syntax
+executor.$sge.queueSize = 100
+executor.$sge.pollInterval = '30sec'
+executor.$local.cpus = 8
+executor.$local.memory = '32 GB'
+```
+
+## `fusion`
+
+The `fusion` scope provides advanced configuration for the use of the [Fusion file system][fusion-page].
+
+The following settings are available:
+
+##### `fusion.cacheSize`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+The maximum size of the local cache used by the Fusion client.
+
+##### `fusion.containerConfigUrl`
+
+The URL of the container layer that provides the Fusion client.
+
+##### `fusion.enabled`
+
+Enable the Fusion file system (default: `false`).
+
+##### `fusion.exportStorageCredentials`
+
+Export access credentials required by the underlying object storage as environment variables (e.g., `AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY`, and `AWS_SESSION_TOKEN` for AWS S3) to task execution environments (default: `false`).
+
+:::note
+This configuration does not mount or provide access to credential files. For example, AWS credentials like `~/.aws/credentials`, `~/.aws/config`, and SSO cache files are not mounted. AWS SSO users must export credentials to environment variables:
+
+```bash
+eval "$(aws configure export-credentials --format env)"
+```
+:::
+
+:::warning
+This option leaks credentials is the task launcher script. It should only be used for testing and development purposes.
+:::
+
+##### `fusion.logLevel`
+
+The log level of the Fusion client.
+
+##### `fusion.logOutput`
+
+The output location of the Fusion log.
+
+##### `fusion.privileged`
+
+<AddedInVersion version="23.10.0-edge">
+</AddedInVersion>
+
+Enable privileged containers for Fusion (default: `true`)
+Non-privileged use is supported only on Kubernetes with the [k8s-fuse-plugin](https://github.com/nextflow-io/k8s-fuse-plugin) or a similar FUSE device plugin
+
+##### `fusion.snapshots`
+
+<AddedInVersion version="25.03.0-edge">
+</AddedInVersion>
+
+*Currently only supported for AWS Batch*
+
+Enable Fusion snapshotting (preview, default: `false`). This feature allows Fusion to automatically restore a job when it is interrupted by a spot reclamation.
+
+##### `fusion.tags`
+
+The pattern that determines how tags are applied to files created via the Fusion client (default: `[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`). Set to `false` to disable tags.
+
+## `google`
+
+The `google` scope allows you to configure the interactions with Google Cloud, including Google Cloud Batch and Google Cloud Storage.
+
+The following settings are available:
+
+##### `google.enableRequesterPaysBuckets`
+
+Use the given Google Cloud project ID as the billing project for storage access (default: `false`). Required when accessing data from [requester pays](https://cloud.google.com/storage/docs/requester-pays) buckets.
+
+##### `google.httpConnectTimeout`
+
+<AddedInVersion version="23.06.0-edge">
+</AddedInVersion>
+
+The HTTP connection timeout for Cloud Storage API requests (default: `'60s'`).
+
+##### `google.httpReadTimeout`
+
+<AddedInVersion version="23.06.0-edge">
+</AddedInVersion>
+
+The HTTP read timeout for Cloud Storage API requests (default: `'60s'`).
+
+##### `google.location`
+
+The Google Cloud location where jobs are executed (default: `us-central1`).
+
+##### `google.project`
+
+The Google Cloud project ID to use for pipeline execution.
+
+##### `google.batch.allowedLocations`
+
+<AddedInVersion version="22.12.0-edge">
+</AddedInVersion>
+
+The set of [allowed locations](https://cloud.google.com/batch/docs/reference/rest/v1/projects.locations.jobs#locationpolicy) for VMs to be provisioned (default: no restriction).
+
+##### `google.batch.autoRetryExitCodes`
+
+<AddedInVersion version="24.07.0-edge">
+</AddedInVersion>
+
+The list of exit codes that should be automatically retried by Google Batch when `google.batch.maxSpotAttempts` is greater than 0 (default: `[50001]`).
+See [Google Batch documentation](https://cloud.google.com/batch/docs/troubleshooting#reserved-exit-codes) for the complete list of exit codes.
+
+##### `google.batch.bootDiskImage`
+
+<AddedInVersion version="24.08.0-edge">
+</AddedInVersion>
+
+The image URI of the virtual machine boot disk, e.g `batch-debian` (default: none).
+See [Google documentation](https://cloud.google.com/batch/docs/vm-os-environment-overview#vm-os-image-options) for details.
+
+##### `google.batch.bootDiskSize`
+
+The size of the virtual machine boot disk, e.g `50.GB` (default: none).
+
+##### `google.batch.cpuPlatform`
+
+The [minimum CPU Platform](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications), e.g. `'Intel Skylake'` (default: none).
+
+##### `google.batch.gcsfuseOptions`
+
+<AddedInVersion version="25.03.0-edg">
+</AddedInVersion>
+
+List of custom mount options for `gcsfuse` (default: `['-o rw', '-implicit-dirs']`).
+
+##### `google.batch.maxSpotAttempts`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+<ChangedInVersion version="24.08.0-edge">
+The default value was changed from `5` to `0`.
+</ChangedInVersion>
+
+Max number of execution attempts of a job interrupted by a Compute Engine Spot reclaim event (default: `0`).
+See also: `google.batch.autoRetryExitCodes`
+
+##### `google.batch.network`
+
+The URL of an existing network resource to which the VM will be attached.
+
+Specify the network as a full or partial URL. For example, the following are all valid URLs:
+
+- `https://www.googleapis.com/compute/v1/projects/\{project\}/global/networks/\{network\}`
+- `projects/\{project\}/global/networks/\{network\}`
+- `global/networks/\{network\}`
+
+##### `google.batch.networkTags`
+
+The [network tags](https://cloud.google.com/vpc/docs/add-remove-network-tags) to be applied to the instances created by Google Batch jobs (e.g., `['allow-ssh', 'allow-http']`).
+
+Network tags are ignored when using instance templates.
+
+##### `google.batch.serviceAccountEmail`
+
+The Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
+
+This service account will only be used for tasks submitted by Nextflow, not for Nextflow itself. See [Credentials][google-credentials] for more information on Google Cloud credentials.
+
+##### `google.batch.spot`
+
+Enable the use of spot virtual machines (default: `false`).
+
+##### `google.batch.subnetwork`
+
+The URL of an existing subnetwork resource in the network to which the VM will be attached.
+
+You can specify the subnetwork as a full or partial URL. For example, the following are all valid URLs:
+
+- `https://www.googleapis.com/compute/v1/projects/\{project\}/regions/\{region\}/subnetworks/\{subnetwork\}`
+- `projects/\{project\}/regions/\{region}/subnetworks/\{subnetwork\}`
+- `regions/\{regio\n}/subnetworks/\{subnetwork\}`
+
+##### `google.batch.usePrivateAddress`
+
+Do not provision public IP addresses for VMs, such that they only have an internal IP address (default: `false`).
+
+When this option is enabled, jobs can only load Docker images from Google Container Registry, and cannot use external services other than Google APIs.
+
+##### `google.storage.retryPolicy.maxAttempts`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+Max attempts when retrying failed API requests to Cloud Storage (default: `10`).
+
+##### `google.storage.retryPolicy.maxDelay`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+Max delay when retrying failed API requests to Cloud Storage (default: `'90s'`).
+
+##### `google.storage.retryPolicy.multiplier`
+
+<AddedInVersion version="23.11.0-edge">
+</AddedInVersion>
+
+Delay multiplier when retrying failed API requests to Cloud Storage (default: `2.0`).
+
+## `k8s`
+
+The `k8s` scope controls the deployment and execution of workflow applications in a Kubernetes cluster.
+
+The following settings are available:
+
+##### `k8s.autoMountHostPaths`
+
+Automatically mount host paths into the task pods (default: `false`). Only intended for development purposes when using a single node.
+
+##### `k8s.cleanup`
+
+When `true`, successful pods are automatically deleted (default: `true`).
+
+##### `k8s.client`
+
+Map of options for the Kubernetes HTTP client.
+If this option is specified, it will be used instead of `.kube/config`.
+
+The following options are available:
+
+- `server`
+- `token`
+- `tokenFile`
+- `verifySsl`
+- `sslCert`
+- `sslCertFile`
+- `clientCert`
+- `clientCertFile`
+- `clientKey`
+- `clientKeyFile`
+
+##### `k8s.computeResourceType`
+
+<AddedInVersion version="22.05.0-edge">
+</AddedInVersion>
+
+Whether to use Kubernetes `Pod` or `Job` resource type to carry out Nextflow tasks (default: `Pod`).
+
+##### `k8s.context`
+
+The Kubernetes [configuration context](https://kubernetes.io/docs/tasks/access-application-cluster/configure-access-multiple-clusters/) to use.
+
+##### `k8s.cpuLimits`
+
+<AddedInVersion version="24.04.0-edge">
+</AddedInVersion>
+
+When `true`, set both the pod CPUs `request` and `limit` to the value specified by the `cpus` directive, otherwise set only the `request` (default: `false`).
+
+This setting is useful when a K8s cluster requires a CPU limit to be defined through a [LimitRange](https://kubernetes.io/docs/concepts/policy/limit-range/).
+
+##### `k8s.fetchNodeName`
+
+<AddedInVersion version="22.05.0-edge">
+</AddedInVersion>
+
+Include the hostname of each task in the execution trace (default: `false`).
+
+##### `k8s.fuseDevicePlugin`
+
+<AddedInVersion version="24.01.0-edge">
+</AddedInVersion>
+
+The FUSE device plugin to be used when enabling Fusion in unprivileged mode (default: `['nextflow.io/fuse': 1]`).
+
+##### `k8s.httpConnectTimeout`
+
+<AddedInVersion version="22.10.0">
+</AddedInVersion>
+
+The Kubernetes HTTP client request connection timeout e.g. `'60s'`.
+
+##### `k8s.httpReadTimeout`
+
+<AddedInVersion version="22.10.0">
+</AddedInVersion>
+
+The Kubernetes HTTP client request connection read timeout e.g. `'60s'`.
+
+##### `k8s.imagePullPolicy`
+
+The strategy for pulling container images. Can be `IfNotPresent`, `Always`, `Never`.
+
+##### `k8s.launchDir`
+
+The path where the workflow is launched and the user data is stored (default: `<volume-claim-mount-path>/<user-name>`). Must be a path in a shared K8s persistent volume.
+
+##### `k8s.namespace`
+
+The Kubernetes namespace to use (default: `default`).
+
+##### `k8s.pod`
+
+Additional pod configuration options such as environment variables, config maps, secrets, etc. Allows the same settings as the [pod][process-pod] process directive.
+
+When using the `kuberun` command, this setting also applies to the submitter pod.
+
+##### `k8s.projectDir`
+
+The path where Nextflow projects are downloaded (default: `<volume-claim-mount-path>/projects`). Must be a path in a shared K8s persistent volume.
+
+##### `k8s.runAsUser`
+
+The user ID to be used to run the containers. Shortcut for the `securityContext` option.
+
+##### `k8s.securityContext`
+
+The [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) to use for all pods.
+
+##### `k8s.serviceAccount`
+
+The Kubernetes [service account name](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/) to use.
+
+##### `k8s.storageClaimName`
+
+The name of the persistent volume claim where the shared work directory is stored.
+
+##### `k8s.storageMountPath`
+
+The mount path for the persistent volume claim (default: `/workspace`).
+
+##### `k8s.storageSubPath`
+
+The path in the persistent volume to be mounted (default: `/`).
+
+##### `k8s.workDir`
+
+The path of the shared work directory (default: `<user-dir>/work`). Must be a path in a shared K8s persistent volume.
+
+##### `k8s.debug.yaml`
+
+Save the pod spec for each task to `.command.yaml` in the task directory (default: `false`).
+
+##### `k8s.retryPolicy.delay`
+
+Delay when retrying failed API requests (default: `250ms`).
+
+##### `k8s.retryPolicy.jitter`
+
+Jitter value when retrying failed API requests (default: `0.25`).
+
+##### `k8s.retryPolicy.maxAttempts`
+
+Max attempts when retrying failed API requests (default: `4`).
+
+##### `k8s.retryPolicy.maxDelay`
+
+Max delay when retrying failed API requests (default: `90s`).
+
+## `lineage`
+
+The `lineage` scope controls the generation of [lineage][cli-lineage] metadata.
+
+The following settings are available:
+
+##### `lineage.enabled`
+
+Enable generation of lineage metadata (default: `false`).
+
+##### `lineage.store.location`
+
+The location of the lineage metadata store (default: `./.lineage`).
+
+## `mail`
+
+The `mail` scope controls the mail server used to send email notifications.
+
+The following settings are available:
+
+##### `mail.debug`
+
+Enable Java Mail logging for debugging purposes (default: `false`).
+
+##### `mail.from`
+
+Default email sender address.
+
+##### `mail.smtp.host`
+
+Host name of the mail server.
+
+##### `mail.smtp.password`
+
+User password to connect to the mail server.
+
+##### `mail.smtp.port`
+
+Port number of the mail server.
+
+##### `mail.smtp.user`
+
+User name to connect to the mail server.
+
+##### `mail.smtp.proxy.host`
+
+Host name of an HTTP web proxy server that will be used for connections to the mail server.
+
+##### `mail.smtp.proxy.port`
+
+Port number for the HTTP web proxy server.
+
+##### `mail.smtp.*`
+
+Any SMTP configuration property supported by the [Java Mail API](https://javaee.github.io/javamail/), which Nextflow uses to send emails. See the table of available properties [here](https://javaee.github.io/javamail/docs/api/com/sun/mail/smtp/package-summary.html#properties).
+
+## `manifest`
+
+The `manifest` scope allows you to define some metadata that is useful when publishing or running your pipeline.
+
+The following settings are available:
+
+##### `manifest.author`
+
+<DeprecatedInVersion version="24.09.0-edge">
+Use `manifest.contributors` instead.
+</DeprecatedInVersion>
+
+Project author name (use a comma to separate multiple names).
+
+##### `manifest.contributors`
+
+<AddedInVersion version="24.09.0-edge">
+</AddedInVersion>
+
+List of project contributors. Should be a list of maps.
+
+The following fields are supported in the contributor map:
+
+###### `name`
+
+The contributor's name.
+
+###### `affiliation`
+
+The contributor's affiliated organization.
+
+###### `email`
+
+The contributor's email address.
+
+###### `github`
+
+The contributor's GitHub URL.
+
+###### `contribution`
+
+List of contribution types, each element can be one of `'author'`, `'maintainer'`, or `'contributor'`.
+
+###### `orcid`
+
+The contributor's [ORCID](https://orcid.org/) URL.
+
+##### `manifest.defaultBranch`
+
+Git repository default branch (default: `master`).
+
+##### `manifest.description`
+
+Free text describing the workflow project.
+
+##### `manifest.docsUrl`
+
+Project documentation URL.
+
+##### `manifest.doi`
+
+Project related publication DOI identifier.
+
+##### `manifest.gitmodules`
+
+Controls whether git sub-modules should be cloned with the main repository.
+Can be either a boolean value, a list of submodule names, or a comma-separated string of submodule names.
+
+##### `manifest.homePage`
+
+Project home page URL.
+
+##### `manifest.icon`
+
+Project related icon location (Relative path or URL).
+
+##### `manifest.license`
+
+Project license.
+
+##### `manifest.mainScript`
+
+Project main script (default: `main.nf`).
+
+##### `manifest.name`
+
+Project short name.
+
+##### `manifest.nextflowVersion`
+
+Minimum required Nextflow version.
+
+This setting may be useful to ensure that a specific version is used:
+
+```groovy
+manifest.nextflowVersion = '1.2.3'        // exact match
+manifest.nextflowVersion = '1.2+'         // 1.2 or later (excluding 2 and later)
+manifest.nextflowVersion = '>=1.2'        // 1.2 or later
+manifest.nextflowVersion = '>=1.2, <=1.5' // any version in the 1.2 .. 1.5 range
+manifest.nextflowVersion = '!>=1.2'       // with ! prefix, stop execution if current version does not match required version.
+```
+
+##### `manifest.organization`
+
+Project organization.
+
+##### `manifest.recurseSubmodules`
+
+Pull submodules recursively from the Git repository.
+
+##### `manifest.version`
+
+Project version number.
+
+## `nextflow`
+
+<ChangedInVersion version="24.10.0">
+The `nextflow.publish.retryPolicy` settings were moved to `workflow.output.retryPolicy`.
+</ChangedInVersion>
+
+<ChangedInVersion version="25.06.0-edge">
+The `workflow.output.retryPolicy` settings were moved to `nextflow.retryPolicy`.
+</ChangedInVersion>
+
+##### `retryPolicy.delay`
+
+Delay used for retryable operations (default: `350ms`).
+
+##### `retryPolicy.jitter`
+
+Jitter value used for retryable operations (default: `0.25`).
+
+##### `retryPolicy.maxAttempts`
+
+Max attempts used for retryable operations (default: `5`).
+
+##### `retryPolicy.maxDelay`
+
+Max delay used for retryable operations (default: `90s`).
+
+## `notification`
+
+The `notification` scope controls the automatic sending of an email notification on workflow completion.
+
+The following settings are available:
+
+##### `notification.attributes`
+
+Map of variables that can be used in the template file.
+
+##### `notification.enabled`
+
+Send an email notification when the workflow execution completes (default: `false`).
+
+##### `notification.from`
+
+Sender address for the email notification.
+
+##### `notification.template`
+
+Path of a template file containing the contents of the email notification.
+
+##### `notification.to`
+
+Recipient address for the email notification. Multiple addresses can be specified as a comma-separated list.
+
+## `podman`
+
+The `podman` scope controls how [Podman](https://podman.io/) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `podman.enabled`
+
+Execute tasks with Podman containers (default: `false`).
+
+##### `podman.engineOptions`
+
+Specify additional options supported by the Podman engine i.e. `podman [OPTIONS]`.
+
+##### `podman.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `podman.mountFlags`
+
+Add the specified flags to the volume mounts e.g. `'ro,Z'`.
+
+##### `podman.registry`
+
+The registry from where container images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `podman.remove`
+
+Clean-up the container after the execution (default: `true`).
+
+##### `podman.runOptions`
+
+Specify extra command line options supported by the `podman run` command.
+
+##### `podman.temp`
+
+Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `'auto'` to create a temporary directory each time a container is created.
+
+## `report`
+The `report` scope allows you to configure the workflow [Execution report][execution-report].
+
+The following settings are available:
+
+##### `report.enabled`
+
+Create the execution report on workflow completion (default: `false`).
+
+##### `report.file`
+
+The path of the created execution report file (default: `'report-<timestamp>.html'`).
+
+##### `report.overwrite`
+
+Overwrite any existing report file with the same name (default: `false`).
+
+## `sarus`
+
+The `sarus` scope controls how [Sarus](https://sarus.readthedocs.io) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `sarus.enabled`
+
+Execute tasks with Sarus containers (default: `false`).
+
+##### `sarus.envWhitelist`
+
+Comma-separated list of environment variable names to be included in the container environment.
+
+##### `sarus.runOptions`
+
+Specify extra command line options supported by the `sarus run` command.
+
+For details see the [Sarus user guide](https://sarus.readthedocs.io/en/stable/user/user_guide.html).
+
+##### `sarus.tty`
+
+Allocates a pseudo-tty (default: `false`).
+
+See the [Sarus][container-sarus] page to learn more about how to use Sarus containers with Nextflow.
+
+## `shifter`
+
+The `shifter` scope controls how [Shifter](https://docs.nersc.gov/programming/shifter/overview/) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `shifter.enabled`
+
+Execute tasks with Shifter containers (default: `false`).
+
+##### `shifter.envWhitelist`
+
+Comma-separated list of environment variable names to be included in the container environment.
+
+## `singularity`
+
+The `singularity` scope controls how [Singularity](https://sylabs.io/singularity/) containers are executed by Nextflow.
+
+The following settings are available:
+
+##### `singularity.autoMounts`
+
+<ChangedInVersion version="23.09.0-edge">
+Default value was changed from `false` to `true`.
+</ChangedInVersion>
+
+Automatically mount host paths in the executed container (default: `true`). It requires the `user bind control` feature to be enabled in your Singularity installation.
+
+##### `singularity.cacheDir`
+
+The directory where remote Singularity images are stored. When using a compute cluster, it must be a shared folder accessible to all compute nodes.
+
+##### `singularity.enabled`
+
+Execute tasks with Singularity containers (default: `false`).
+
+##### `singularity.engineOptions`
+
+Specify additional options supported by the Singularity engine i.e. `singularity [OPTIONS]`.
+
+##### `singularity.envWhitelist`
+
+Comma separated list of environment variable names to be included in the container environment.
+
+##### `singularity.libraryDir`
+
+Directory where remote Singularity images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+##### `singularity.noHttps`
+
+Pull the Singularity image with http protocol (default: `false`).
+
+##### `singularity.ociAutoPull`
+
+<AddedInVersion version="23.12.0-edge">
+</AddedInVersion>
+
+*Requires Singularity 3.11 or later*
+
+When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow (default: `false`).
+
+:::note
+Leave `ociAutoPull` disabled if willing to build a Singularity native image with Wave. See [Build Singularity native images][wave-singularity] for more information.
+:::
+
+##### `singularity.ociMode`
+
+<AddedInVersion version="23.12.0-edge">
+</AddedInVersion>
+
+*Requires Singularity 4 or later*
+
+nable OCI-mode, that allows running native OCI compliant container image with Singularity using `crun` or `runc` as low-level runtime (default: `false`). See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
+
+:::note
+Leave `ociMode` disabled if you are willing to build a Singularity native image with Wave. See the [Build Singularity native images][wave-singularit] section for more information.
+:::
+
+##### `singularity.pullTimeout`
+
+The amount of time the Singularity pull can last, after which the process is terminated (default: `20 min`).
+
+##### `singularity.registry`
+
+<AddedInVersion version="22.12.0-edge">
+</AddedInVersion>
+
+The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+##### `singularity.runOptions`
+
+Specify extra command line options supported by `singularity exec`.
+
+## `spack`
+
+The `spack` scope controls the creation of a Spack environment by the Spack package manager.
+
+The following settings are available:
+
+##### `spack.cacheDir`
+
+The path where Spack environments are stored. It should be accessible from all compute nodes when using a shared file system.
+
+##### `spack.checksum`
+
+Enable checksum verification of source tarballs (default: `true`).
+Only disable when requesting a package version not yet encoded in the corresponding Spack recipe.
+
+##### `spack.createTimeout`
+
+The amount of time to wait for the Spack environment to be created before failing (default: `60 min`).
+
+##### `spack.enabled`
+
+Execute tasks with Spack environments (default: `false`).
+
+##### `spack.parallelBuilds`
+
+The maximum number of parallel package builds (default: the number of available CPUs).
+
+## `timeline`
+
+The `timeline` scope controls the execution timeline report generated by Nextflow.
+
+The following settings are available:
+
+##### `timeline.enabled`
+
+Create the timeline report on workflow completion file (default: `false`).
+
+##### `timeline.file`
+
+Timeline file name (default: `'timeline-<timestamp>.html'`).
+
+##### `timeline.overwrite`
+
+Overwrite any existing timeline file with the same name (default: `false`).
+
+## `tower`
+
+The `tower` scope controls the settings for [Seqera Platform](https://seqera.io) (formerly Tower Cloud).
+
+The following settings are available:
+
+##### `tower.accessToken`
+
+The unique access token for your Seqera Platform account.
+
+Your `accessToken` can be obtained from your Seqera Platform instance in the [Tokens page](https://cloud.seqera.io/tokens).
+
+##### `tower.computeEnvId`
+
+The compute environment ID in your Seqera Platform account used to launch pipelines (default: the primary compute environment in the selected workspace).
+
+##### `tower.enabled`
+
+Enable workflow monitoring with Seqera Platform (default: `false`).
+
+##### `tower.endpoint`
+
+The endpoint of your Seqera Platform instance (default: `https://api.cloud.seqera.io`).
+
+##### `tower.workspaceId`
+
+The workspace ID in Seqera Platform in which to save the run (default: the launching user's personal workspace).
+
+The workspace ID can also be specified using the environment variable `TOWER_WORKSPACE_ID` (config file has priority over the environment variable).
+
+## `trace`
+
+The `trace` scope controls the layout of the execution trace file generated by Nextflow.
+
+The following settings are available:
+
+##### `trace.enabled`
+
+Create the execution trace file on workflow completion (default: `false`).
+
+##### `trace.fields`
+
+Comma-separated list of [trace fields][trace-fields] to include in the report.
+
+##### `trace.file`
+
+Trace file name (default: `'trace-<timestamp>.txt'`).
+
+##### `trace.overwrite`
+Overwrite any existing trace file with the same name (default: `false`).
+
+##### `trace.raw`
+
+Report trace metrics as raw numbers where applicable, i.e. report duration values in milliseconds and memory values in bytes (default: `false`).
+
+##### `trace.sep`
+
+Character used to separate values in each row (default: `\t`).
+
+## `wave`
+
+The `wave` scope provides advanced configuration for the use of [Wave containers][wave-page].
+
+The following settings are available:
+
+##### `wave.enabled`
+
+Enable the use of Wave containers (default: `false`).
+
+##### `wave.endpoint`
+
+The Wave service endpoint (default: `https://wave.seqera.io`).
+
+##### `wave.freeze`
+
+<AddedInVersion version="23.07.0-edge" />
+
+Enable Wave container freezing (default: `false`). Wave will provision a non-ephemeral container image that will be pushed to a container repository of your choice.
+
+The target registry must be specified using the `wave.build.repository` setting. It is also recommended to specify a custom cache repository using `wave.build.cacheRepository`.
+
+:::note
+The container registry authentication must be managed by the underlying infrastructure.
+:::
+
+##### `wave.mirror`
+
+<AddedInVersion version="23.07.0-edge" />
+
+Enable Wave container mirroring (default: `false`). Wave will mirror (i.e. copy) the containers in your pipeline to a container registry of your choice, so that pipeline tasks can pull the containers from this registry instead of the original one.
+
+The mirrored containers will have the same name, digest, and metadata.
+
+The target registry must be specified using the `wave.build.repository` setting.
+
+This option is only compatible with `wave.strategy = 'container'`. It cannot be used with `wave.freeze`.
+
+:::note
+The container registry authentication must be managed by the underlying infrastructure.
+:::
+
+##### `wave.strategy`
+
+The strategy to be used when resolving multiple Wave container requirements (default: `'container,dockerfile,conda'`).
+
+##### `wave.build.cacheRepository`
+
+The container repository used to cache image layers built by the Wave service.
+The corresponding credentials must be provided in your Seqera Platform account.
+
+##### `wave.build.compression.mode`
+
+<AddedInVersion version="25.05.0-edge" />
+
+The compression algorithm that should be used when building the container. Allowed values are: `gzip`, `estargz` and `zstd` (default: `gzip`).
+
+##### `wave.build.compression.level`
+
+<AddedInVersion version="25.05.0-edge" />
+
+Level of compression used when building a container depending the chosen algorithm: gzip, estargz (0-9) and zstd (0-22).
+
+##### `wave.build.compression.force`
+
+<AddedInVersion version="25.05.0-edge" />
+
+Forcefully apply compression option to all layers, including already existing layers (default: `false`).
+
+##### `wave.build.conda.basePackages`
+
+One or more Conda packages to be always added in the resulting container (default: `conda-forge::procps-ng`).
+
+##### `wave.build.conda.commands`
+
+One or more commands to be added to the Dockerfile used to build a Conda based image.
+
+##### `wave.build.conda.mambaImage`
+
+The Mamba container image is used to build Conda based container. This is expected to be [micromamba-docker](https://github.com/mamba-org/micromamba-docker) image.
+
+##### `wave.build.repository`
+
+The container repository where images built by Wave are uploaded.
+The corresponding credentials must be provided in your Seqera Platform account.
+
+##### `wave.httpClient.connectTimeout`
+
+<AddedInVersion version="25.06.0-edge" />
+
+The connection timeout for the Wave HTTP client (default: `30s`).
+
+##### `wave.httpClient.maxRate`
+
+<AddedInVersion version="25.01.0-edge" />
+
+The maximum request rate for the Wave HTTP client (default: `1/sec`).
+
+##### `wave.retryPolicy.delay`
+
+<AddedInVersion version="22.06.0-edge" />
+
+The initial delay when a failing HTTP request is retried (default: `450ms`).
+
+##### `wave.retryPolicy.jitter`
+
+<AddedInVersion version="22.06.0-edge" />
+
+The jitter factor used to randomly vary retry delays (default: `0.25`).
+
+##### `wave.retryPolicy.maxAttempts`
+
+<AddedInVersion version="22.06.0-edge" />
+
+The max number of attempts a failing HTTP request is retried (default: `5`).
+
+##### `wave.retryPolicy.maxDelay`
+
+<AddedInVersion version="22.06.0-edge" />
+
+The max delay when a failing HTTP request is retried (default: `90s`).
+
+##### `wave.scan.allowedLevels`
+
+<AddedInVersion version="24.09.1-edge" />
+
+Comma-separated list of allowed vulnerability levels when scanning containers for security vulnerabilities in `required` mode.
+
+Allowed values are: `low`, `medium`, `high`, `critical`.
+
+This option requires `wave.scan.mode = 'required'`.
+
+##### `wave.scan.mode`
+
+<AddedInVersion version="24.09.1-edge" />
+
+Enable Wave container security scanning. Wave will scan the containers in your pipeline for security vulnerabilities.
+
+The following options can be specified:
+
+###### `'none'`
+
+No security scanning is performed.
+
+###### `'async'`
+
+The containers used by your pipeline are scanned for security vulnerabilities. The task execution is carried out regardless of the security scan result.
+
+###### `'required'`
+
+The containers used by your pipeline are scanned for security vulnerabilities. The task is only executed if the corresponding container is free of vulnerabilities.
+
+## `workflow`
+
+<AddedInVersion version="24.10.0" />
+
+The `workflow` scope provides workflow execution options.
+
+The following settings are available:
+
+##### `workflow.failOnIgnore`
+
+<AddedInVersion version="24.05.0-edge" />
+
+When `true`, the pipeline will exit with a non-zero exit code if any failed tasks are ignored using the `ignore` [error strategy][process-error-strategy] (default: `false`).
+
+##### `workflow.onComplete`
+
+Specify a closure that will be invoked at the end of a workflow run (including failed runs). See [Workflow handlers][workflow-handlers] for more information.
+
+##### `workflow.onError`
+
+Specify a closure that will be invoked if a workflow run is terminated. See [Workflow handlers][workflow-handlers] for more information.
+
+##### `workflow.output.contentType`
+
+*Currently only supported for S3.*
+
+Specify the media type, also known as [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/MIME_types), of published files (default: `false`). Can be a string (e.g. `'text/html'`), or `true` to infer the content type from the file extension.
+
+##### `workflow.output.copyAttributes`
+
+<AddedInVersion version="25.01.0-edge" />
+
+*Currently only supported for local and shared filesystems.*
+
+Copy file attributes (such as the last modified timestamp) to the published file (default: `false`).
+
+##### `workflow.output.enabled`
+
+Enable or disable publishing (default: `true`).
+
+##### `workflow.output.ignoreErrors`
+
+When `true`, the workflow will not fail if a file can't be published for some reason (default: `false`).
+
+#####`workflow.output.mode`
+
+The file publishing method (default: `'symlink'`).
+
+The following options are available:
+
+###### `'copy'`
+
+Copy each file into the output directory.
+
+###### `'copyNoFollow'`
+
+Copy each file into the output directory without following symlinks, i.e. only the link is copied.
+
+###### `'link'`
+
+Create a hard link in the output directory for each file.
+
+###### `'move'`
+
+Move each file into the output directory.
+
+Should only be used for files which are not used by downstream processes in the workflow.
+
+###### `'rellink'`
+
+Create a relative symbolic link in the output directory for each file.
+
+###### `'symlink'`
+
+Create an absolute symbolic link in the output directory for each output file.
+
+##### `workflow.output.overwrite`
+
+When `true` any existing file in the specified folder will be overwritten (default: `'standard'`).
+
+The following options are available:
+
+###### `false`
+
+Never overwrite existing files.
+
+###### `true`
+
+Always overwrite existing files.
+
+###### `'deep'`
+
+Overwrite existing files when the file content is different.
+
+###### `'lenient'`
+
+Overwrite existing files when the file size is different.
+
+###### `'standard'`
+
+Overwrite existing files when the file size or last modified timestamp is different.
+
+##### `workflow.output.storageClass`
+
+*Currently only supported for S3.*
+
+Specify the storage class for published files.
+
+`workflow.output.tags`
+
+*Currently only supported for S3.*
+
+Specify arbitrary tags for published files.
+
+For example:
+
+```groovy
+workflow.output.tags = [FOO: 'hello', BAR: 'world']
+```
+
+[amazons3-page]: /nextflow_docs/nextflow_repo/docs/amazons3.mdx
+[aws-page]: /nextflow_docs/nextflow_repo/docs/aws.mdx
+[azure-page]: /nextflow_docs/nextflow_repo/docs/azure.mdx
+[config-mail]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#mail
+[azure-managed-identities]: /nextflow_docs/nextflow_repo/docs/azure.mdx#managed-identities
+[cli-lineage]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lineage
+[config-page]: /nextflow_docs/nextflow_repo/docs/config.mdx
+[config-workflow]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#workflow
+[ontainer-apptainer]: /nextflow_docs/nextflow_repo/docs/container.mdx#apptainer
+[container-charliecloud]: /nextflow_docs/nextflow_repo/docs/container.mdx#charliecloud
+[container-docker]: /nextflow_docs/nextflow_repo/docs/container.mdx#docker
+[container-podman]: /nextflow_docs/nextflow_repo/docs/container.mdx#podman
+[container-sarus]: /nextflow_docs/nextflow_repo/docs/container.mdx#sarus
+[container-shifter]: /nextflow_docs/nextflow_repo/docs/container.mdx#shifter
+[container-shifter]: /nextflow_docs/nextflow_repo/docs/container.mdx#singularity
+[execution-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#execution-report
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[google-credentials]: /nextflow_docs/nextflow_repo/docs/google.mdx#credentials
+[google-page]: /nextflow_docs/nextflow_repo/docs/google.mdx
+[k8s-page]: /nextflow_docs/nextflow_repo/docs/kubernetes.mdx
+[lsf-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#lsf
+[pbs-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#pbstorque
+[pbspro-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#pbs-pro
+[process-error-strategy]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#errorstrategy
+[process-pod]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#pod
+[sharing-page]: /nextflow_docs/nextflow_repo/docs/sharing.mdx
+[slurm-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#slurm
+[trace-fields]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-fields
+[trace-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
+[wave-singularity]: /nextflow_docs/nextflow_repo/docs/wave.mdx#build-singularity-native-images
+[workflow-diagram]: /nextflow_docs/nextflow_repo/docs/reports.mdx#workflow-diagram
+[workflow-handlers]: /nextflow_docs/nextflow_repo/docs/notifications.mdx#workflow-handlers
diff --git a/new-docs/nextflow-docs/reference/env-vars.mdx b/new-docs/nextflow-docs/reference/env-vars.mdx
new file mode 100644
index 0000000000..319ac9b6fa
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/env-vars.mdx
@@ -0,0 +1,399 @@
+
+
+# Environment variables
+
+The following environment variables control the configuration of the Nextflow runtime and the underlying Java virtual machine.
+
+## Java settings
+
+##### `JAVA_CMD`
+
+Defines the path location of the Java binary command used to launch Nextflow.
+
+##### `JAVA_HOME`
+
+Defines the path location of the Java VM installation used to run Nextflow.
+
+## Nextflow settings
+
+##### `NXF_ANSI_LOG`
+
+Enables/disables ANSI console output (default `true` when ANSI terminal is detected).
+
+##### `NXF_ANSI_SUMMARY`
+
+Enables/disables ANSI completion summary`true\|false` (defaultprint summary if execution last more than 1 minute).
+
+##### `NXF_ASSETS`
+
+Defines the directory where downloaded pipeline repositories are stored (default`$NXF_HOME/assets`)
+
+##### `NXF_CACHE_DIR`
+
+<AddedInVersion version="24.02.0-edge" />
+
+Defines the base cache directory when using the default cache store (default`"$launchDir/.nextflow"`).
+
+##### `NXF_CHARLIECLOUD_CACHEDIR`
+
+Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+##### `NXF_CLOUDCACHE_PATH`
+
+<AddedInVersion version="23.07.0-edge" />
+
+Defines the base cache path when using the cloud cache store.
+
+##### `NXF_CLOUD_DRIVER`
+
+Defines the default cloud driver to be used if not specified in the config file or as command line option, either `aws` or `google`.
+
+##### `NXF_CONDA_CACHEDIR`
+
+Directory where Conda environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+##### `NXF_CONDA_ENABLED`
+
+<AddedInVersion version="22.08.0-edge" />
+
+Enable the use of Conda recipes defined by using the [conda][process-conda] directive. (default`false`).
+
+##### `NXF_CONTAINER_ENTRYPOINT_OVERRIDE`
+
+<DeprecatedInVersion version="22.10.0" />
+
+When `true`, override the container entrypoint with `/bin/bash` (default: `false`).
+
+##### `NXF_DATE_FORMAT`
+
+<AddedInVersion version="25.07.0-edge">
+</AddedInVersion>
+
+Defines the format for date and time representations in notifications and reports. Supports custom formats (e.g., `yyyy-MM-dd HH:mm:ss`) or `iso` for ISO 8601 format with timezone (default: `dd-MMM-yyyy HH:mm:ss`).
+
+##### `NXF_DEFAULT_DSL`
+
+<AddedInVersion version="22.03.0-edge" />
+
+Defines the DSL version that should be used in not specified otherwise in the script of config file (default`2`)
+
+##### `NXF_DISABLE_CHECK_LATEST`
+
+<AddedInVersion version="23.09.0-edge" />
+
+Nextflow automatically checks for a newer version of itself unless this option is enabled (default`false`).
+
+##### `NXF_DISABLE_JOBS_CANCELLATION`
+
+<AddedInVersion version="21.12.0-edge" />
+
+Disables the cancellation of child jobs on workflow execution termination.
+
+##### `NXF_DISABLE_PARAMS_TYPE_DETECTION`
+
+<AddedInVersion version="23.07.0-edge" />
+
+Disables the automatic type detection of command line parameters.
+
+##### `NXF_DISABLE_WAVE_SERVICE`
+
+<AddedInVersion version="23.08.0-edge" />
+
+Disables the requirement for Wave service when enabling the Fusion file system.
+
+##### `NXF_ENABLE_AWS_SES`
+
+<AddedInVersion version="23.06.0-edge" />
+
+Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default`false`)
+
+##### `NXF_ENABLE_FS_SYNC`
+
+<AddedInVersion version="23.10.0" />
+
+When enabled the job script will execute Linux `sync` command on job completion. This may be useful to synchronize the job state over shared file systems (default`false`)
+
+##### `NXF_ENABLE_SECRETS`
+
+<AddedInVersion version="21.09.0-edge" />
+
+Enable Nextflow secrets features (default`true`)
+
+##### `NXF_ENABLE_STRICT`
+
+<AddedInVersion version="22.05.0-edge" />
+
+Enable Nextflow *strict* execution mode (default`false`)
+
+##### `NXF_ENABLE_VIRTUAL_THREADS`
+
+<AddedInVersion version="23.05.0-edge" />
+
+Enable the use of virtual threads in the Nextflow runtime (default`false`)
+
+##### `NXF_EXECUTOR`
+
+Defines the default process executor, e.g. `sge`
+
+##### `NXF_FILE_ROOT`
+
+<AddedInVersion version="23.05.0-edge" />
+
+The file storage path against which relative file paths are resolved.
+
+For example, with `NXF_FILE_ROOT=/some/root/path`, the use of `file('hello')` will be resolved to the absolute path `/some/root/path/hello`. A remote root path can be specified using the usual protocol prefix, e.g. `NXF_FILE_ROOT=s3://my-bucket/data`. Files defined using an absolute path are not affected by this setting.
+
+##### `NXF_HOME`
+
+Nextflow home directory (default`$HOME/.nextflow`).
+
+##### `NXF_JAVA_HOME`
+
+Defines the path location of the Java VM installation used to run Nextflow. This variable overrides the `JAVA_HOME` variable if defined.
+
+##### `NXF_JVM_ARGS`
+
+<AddedInVersion version="21.12.1-edge" />
+
+Allows the setting Java VM options. This is similar to `NXF_OPTS` however it's only applied the JVM running Nextflow and not to any java pre-launching commands.
+
+##### `NXF_LOG_FILE`
+
+The filename of the Nextflow log (default`.nextflow.log`)
+
+##### `NXF_OFFLINE`
+
+When `true` prevents Nextflow from automatically downloading and updating remote project repositories (default`false`).
+
+<ChangedInVersion version="23.09.0-edge">
+This option also disables the automatic version check (see `NXF_DISABLE_CHECK_LATEST`).
+</ChangedInVersion>
+
+<ChangedInVersion version="23.11.0-edge">
+This option also prevents plugins from being downloaded. Plugin versions must be specified in offline mode, or else Nextflow will fail.
+</ChangedInVersion>
+
+##### `NXF_OPTS`
+
+Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of `-Dkey[=value]` properties.
+
+##### `NXF_ORG`
+
+Default `organization` prefix when looking for a hosted repository (default`nextflow-io`).
+
+##### `NXF_PARAMS_FILE`
+
+<AddedInVersion version="20.10.0" />
+
+Defines the path location of the pipeline parameters file .
+
+##### `NXF_PID_FILE`
+
+Name of the file where the process PID is saved when Nextflow is launched in background.
+
+##### `NXF_PLUGINS_ALLOWED`
+
+<AddedInVersion version="25.04.0" />
+
+Comma separated list of plugin IDs that can be used in a workflow executions e.g. `NXF_PLUGINS_ALLOWED=nf-amazon,nf-tower,nf-wave`. Use empty string to disallow all plugins.
+
+##### `NXF_PLUGINS_DEFAULT`
+
+Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default`true`).
+
+##### `NXF_PLUGINS_DIR`
+
+The path where the plugin archives are loaded and stored (default`$NXF_HOME/plugins`).
+
+##### `NXF_PLUGINS_REGISTRY_URL`
+
+<AddedInVersion version="25.08.0-edge" />
+
+Specifies the URL of the plugin registry used to download and resolve plugins. This allows using custom or private plugin registries instead of the default public registry.
+
+##### `NXF_PLUGINS_TEST_REPOSITORY`
+
+<AddedInVersion version="23.04.0" />
+
+Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry.
+
+##### `NXF_PUBLISH_FAIL_ON_ERROR`
+
+<AddedInVersion version="24.04.3" />
+
+Defines the default behavior of `publishDir.failOnError` setting. See the [publishDir][process-publishdir] directive for more information.
+
+##### `NXF_RETRY_POLICY_DELAY`
+
+
+<AddedInVersion version="25.06.0-edge" />
+
+Delay used for HTTP retryable operations (default: `350ms`).
+
+##### `NXF_RETRY_POLICY_JITTER`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Jitter value used for HTTP retryable operations (default: `0.25`).
+
+##### `NXF_RETRY_POLICY_MAX_ATTEMPTS`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Max number of attempts used for HTTP retryable operations (default: `5`).
+
+##### `NXF_RETRY_POLICY_MAX_DELAY`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Max delay used for HTTP retryable operations (default: `90s`).
+
+##### `NXF_RETRY_POLICY_DELAY`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Delay used for HTTP retryable operations (default: `350ms`).
+
+##### `NXF_RETRY_POLICY_JITTER`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Jitter value used for HTTP retryable operations (default: `0.25`).
+
+##### `NXF_RETRY_POLICY_MAX_ATTEMPTS`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Max number of attempts used for HTTP retryable operations (default: `5`).
+
+##### `NXF_RETRY_POLICY_MAX_DELAY`
+
+<AddedInVersion version="25.06.0-edge" />
+
+Max delay used for HTTP retryable operations (default: `90s`).
+
+##### `NXF_RETRY_POLICY_MULTIPLIER`
+
+<AddedInVersion version="25.08.0-edge" />
+
+Delay multiplier used for HTTP retryable operations (default: `2.0`).
+
+##### `NXF_SCM_FILE`
+
+<AddedInVersion version="20.10.0" />
+
+Defines the path location of the SCM config file .
+
+##### `NXF_SINGULARITY_CACHEDIR`
+
+Directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+##### `NXF_SINGULARITY_LIBRARYDIR`
+
+<AddedInVersion version="21.09.0-edge" />
+
+Directory where remote Singularity images are retrieved. It should be a directory accessible to all compute nodes.
+
+##### `NXF_SPACK_CACHEDIR`
+
+Directory where Spack environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+##### `NXF_SPACK_ENABLED`
+
+<AddedInVersion version="23.02.0-edge" />
+
+Enable the use of Spack recipes defined by using the [spack][process-spack] directive. (default`false`).
+
+##### `NXF_SYNTAX_PARSER`
+
+<AddedInVersion version="25.02.0-edge" />
+
+Set to `'v2'` to use the [strict syntax][strict-syntax-page] for Nextflow scripts and config files (default`'v1'`).
+
+##### `NXF_TEMP`
+
+Directory where temporary files are stored
+
+##### `NXF_TRACE`
+
+Enable trace level logging for the specified packages. Equivalent to the `-trace` command-line option.
+
+##### `NXF_VER`
+
+Defines which version of Nextflow to use.
+
+##### `NXF_WORK`
+
+Directory where working files are stored (usually your *scratch* directory)
+
+##### `NXF_WRAPPER_STAGE_FILE_THRESHOLD`
+
+<AddedInVersion version="23.05.0-edge" />
+
+Defines the minimum size of the `.command.run` staging script for it to be written to a separate `.command.stage` file (default`'1 MB'`).
+This setting is useful for executors that impose a size limit on job scripts.
+
+## Seqera Platform settings
+
+##### `TOWER_ACCESS_TOKEN`
+
+Access token for authenticating with Seqera Platform. Can also be configured using the `tower.accessToken` config option.
+
+##### `TOWER_API_ENDPOINT`
+
+Seqera Platform API endpoint (default: `https://api.cloud.seqera.io`). Can also be configured using the `tower.endpoint` config option.
+
+##### `TOWER_AUTH_DOMAIN`
+
+<VersionAdded version="25.10.0" />
+
+Auth0 domain for authenticating with Seqera Platform when connecting to a custom endpoint. When specified, this value takes precedence over the built-in mappings for known Seqera endpoints. Must be used in conjunction with `TOWER_AUTH_CLIENT_ID`.
+
+##### `TOWER_AUTH_CLIENT_ID`
+
+<AddedInVersion version="25.10.0" />
+
+Auth0 client ID for authenticating with a custom Seqera Platform endpoint. Must be used in conjunction with `TOWER_AUTH_DOMAIN`.
+
+##### `TOWER_REFRESH_TOKEN`
+
+Refresh token for maintaining authentication with Seqera Platform. Can also be configured using the `tower.refreshToken` config option.
+
+##### `TOWER_WORKSPACE_ID`
+
+Seqera Platform workspace ID. Can also be configured using the `tower.workspaceId` config option.
+
+## Other settings
+
+##### `FTP_PROXY`
+
+<AddedInVersion version="21.06.0-edge" />
+
+Defines the FTP proxy server. Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `ftp://user:password@proxy-host.com:port`.
+
+##### `HTTP_PROXY`
+
+Defines the HTTP proxy server.
+
+<AddedInVersion version="21.06.0-edge">
+Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `http://user:password@proxy-host.com:port`.
+</AddedInVersion>
+
+##### `NO_COLOR`
+
+Disables ANSI color codes in Nextflow log output. When this variable is set, Nextflow prints plain text logs following the [NO_COLOR standard](https://no-color.org/).
+
+If both `NO_COLOR` and `NXF_ANSI_LOG` are set, `NXF_ANSI_LOG` takes precedence.
+
+##### `NO_PROXY`
+
+Defines one or more host names that should not use the proxy server. Separate multiple names using a comma character.
+
+##### `TERMINAL_WIDTH`
+
+Forces the terminal width of ANSI-formatted log output. Overrides automatic terminal width detection and uses the specified width for line wrapping when set to an integer value.
+
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
+[process-spack]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#spack
+[process-publishdir]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#publishdir
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
diff --git a/new-docs/nextflow-docs/reference/feature-flags.mdx b/new-docs/nextflow-docs/reference/feature-flags.mdx
new file mode 100644
index 0000000000..ac0da3113a
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/feature-flags.mdx
@@ -0,0 +1,93 @@
+
+
+# Feature flags
+
+Feature flags enable experimental or other opt-in features. They must be specified in the pipeline script.
+
+:::warning
+Feature flags with the `nextflow.preview` prefix can cause pipelines run with newer versions of Nextflow to fail due to breaking changes. Always consult the [migration notes][migrations-page] before updating to a new Nextflow version.
+:::
+
+##### `nextflow.enable.configProcessNamesValidation`
+
+<DeprecatedInVersion version="25.10.0">
+Use the [strict syntax][strict-syntax-page] instead. It validates process selectors without producing false warnings.
+</DeprecatedInVersion>
+
+When `true`, prints a warning for every `withName:` process selector that doesn't match a process in the pipeline (default: `true`).
+
+##### `nextflow.enable.dsl`
+
+<DeprecatedInVersion version="25.04.0">
+
+Defines the DSL version to use (`1` or `2`).
+
+##### `nextflow.enable.moduleBinaries`
+
+When `true`, enables the use of modules with binary scripts. See [Module binaries][module-binaries] for more information.
+
+##### `nextflow.enable.strict`
+
+When `true`, executes the pipeline in "strict" mode, which introduces the following rules:
+
+- When reading a params file, Nextflow will fail if a dynamic param value references an undefined variable
+
+- When merging params from a config file with params from the command line, Nextflow will fail if a param is specified from both sources but with different types
+
+- When using the `join` operator, the `failOnDuplicate` option is `true` regardless of any user setting
+
+- When using the `join` operator, the `failOnMismatch` option is `true` (unless `remainder` is also `true`) regardless of any user setting
+
+- When using the `publishDir` process directive, the `failOnError` option is `true` regardless of any user setting
+
+- In a process definition, Nextflow will fail if an input or output tuple has only one element
+
+- In a process definition, Nextflow will fail if an output emit name is not a valid identifier (i.e. it should match the pattern `/[A-Za-z_][A-Za-z0-9_]*/`)
+
+- During a process execution, Nextflow will fail if a received input tuple does not have the same number of elements as was declared
+
+- During a process execution, Nextflow will fail if the `storeDir` directive is used with non-file outputs
+
+- Nextflow will fail if a pipeline param is referenced before it is defined
+
+- Nextflow will fail if multiple functions and/or processes with the same name are defined in a module script
+
+##### `nextflow.preview.output`
+
+<AddedInVersion version="24.04.0"/>
+
+<DeprecatedInVersion version="25.10.0">
+This feature flag is no longer supported. Workflow outputs are out of preview.
+</DeprecatedInVersion>
+
+When `true`, enables the use of {ref}`workflow outputs <workflow-output-def>`.
+
+##### `nextflow.preview.recursion`
+
+*Experimental: may change in a future release.*
+
+When `true`, enables [process and workflow recursion][workflow-recursion].
+
+##### `nextflow.preview.topic`
+
+<AddedInVersion version="24.04.0"/>
+
+<DeprecatedInVersion version="25.04.0">
+This feature flag is no longer supported. Topic channels are out of preview.
+</DeprecatedInVersion>
+
+When `true`, enables the use of [topic channels][channel-topic].
+
+##### `nextflow.preview.types`
+
+<AddedInVersion version="25.10.0"/>
+
+When `true`, enables the use of [typed processes][process-typed-page]. Must be enabled in every script that uses typed processes. Legacy processes cannot be defined in scripts with this flag enabled.
+
+[channel-topic]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#topic
+[migrations-page]: /nextflow_docs/nextflow_repo/docs/migrations/index.mdx
+[module-binaries]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-binaries
+[process-typed-page]: /nextflow_docs/nextflow_repo/docs/process-typed.mdx#process-typed-page
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-recursion]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#process-and-workflow-recursion
diff --git a/new-docs/nextflow-docs/reference/operator.mdx b/new-docs/nextflow-docs/reference/operator.mdx
new file mode 100644
index 0000000000..6f52b26025
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/operator.mdx
@@ -0,0 +1,1572 @@
+
+
+# Operators
+
+## branch
+
+*Returns: multiple channels*
+
+The `branch` operator forwards each item from a source channel to one of multiple output channels, based on a selection criteria.
+
+The selection criteria is a [closure][script-closure] that defines, for each output channel, a unique label followed by a boolean expression. When an item is received, it is routed to the first output channel whose expression evaluates to `true`. For example:
+
+```nextflow file=../snippets/branch.nf
+```
+
+```console file=../snippets/branch.out
+```
+
+:::note
+The above output may be printed in any order since the two `view` operations are executed asynchronously.
+:::
+
+A fallback condition can be specified using `true` as the last branch condition:
+
+```nextflow file=../snippets/branch-with-fallback.nf
+```
+
+```console file=../snippets/branch-with-fallback.out
+```
+
+The value emitted to each branch can be customized with an expression statement (or statements) after the branch condition:
+
+```nextflow file=../snippets/branch-with-mapper.nf
+```
+
+```console file=../snippets/branch-with-mapper.out
+```
+
+:::tip
+When the `return` keyword is omitted, the value of the last expression statement is implicitly returned.
+:::
+
+The `branchCriteria()` method can be used to create a branch criteria as a variable that can be passed as an argument to any number of `branch` operations, as shown below:
+
+```nextflow file=../snippets/branch-criteria.nf
+```
+
+```console file=../snippets/branch-criteria.out
+```
+
+## buffer
+
+*Returns: queue channel*
+
+The `buffer` operator collects items from a source channel into subsets and emits each subset separately.
+
+This operator has multiple variants:
+
+##### `buffer( closingCondition )`
+
+Emits each subset when `closingCondition` is satisfied. The closing condition can be a literal value, a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate. For example:
+
+```nextflow file=../snippets/buffer-with-closing.nf
+```
+
+```console file=../snippets/buffer-with-closing.out
+```
+
+##### `buffer( openingCondition, closingCondition )`
+
+Creates a new subset when `openingCondition` is satisfied and emits the subset when is `closingCondition` is satisfied. The opening and closing conditions can each be a literal value, a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate. For example:
+
+```nextflow file=../snippets/buffer-with-opening-closing.nf
+```
+
+```console file=../snippets/buffer-with-opening-closing.out
+```
+
+##### `buffer( size: n, remainder: true | false )`
+
+Emits a new subset for every `n` items. Remaining items are discarded. For example:
+
+```nextflow file=../snippets/buffer-with-size.nf
+```
+
+```console file=../snippets/buffer-with-size.out
+```
+
+The `remainder` option can be used to emit any remaining items as a partial subset:
+
+```nextflow file=../snippets/buffer-with-size-remainder.nf
+```
+
+```console file=../snippets/buffer-with-size-remainder.out
+```
+
+##### `buffer( size: n, skip: m, remainder: true | false )`
+
+Emits a new subset for every `n` items, skipping `m` items before collecting each subset. For example:
+
+```nextflow file=../snippets/buffer-with-size-skip.nf
+```
+
+```console file=../snippets/buffer-with-size-skip.out
+```
+
+The `remainder` option can be used to emit any remaining items as a partial subset.
+
+#
+
+See also: [collate](#collate)
+
+## collate
+
+*Returns: channel*
+
+The `collate` operator collects items from a source channel into groups of *N* items.
+
+This operator has multiple variants:
+
+##### `collate( size, remainder = true )`
+
+Collects items into groups of `size` items:
+
+```nextflow file=../snippets/collate.nf
+```
+
+```console file=../snippets/collate.out
+```
+
+By default, any remaining items are emitted as a partial group. You can specify `false` as the second parameter to discard them instead:
+
+```nextflow file=../snippets/collate-with-no-remainder.nf
+```
+
+```console file=../snippets/collate-with-no-remainder.out
+```
+
+:::note
+This version of `collate` is equivalent to `buffer( size: n, remainder: true | false )`.
+:::
+
+##### `collate( size, step, remainder = true )`
+
+Collects items into groups of `size` items using a *sliding window* that moves by `step` items at a time:
+
+```nextflow file=../snippets/collate-with-step.nf
+```
+
+```console file=../snippets/collate-with-step.out
+```
+
+You can specify `false` as the third parameter to discard any remaining items.
+
+#
+
+See also: [buffer](#buffer)
+
+## collect
+
+*Returns: dataflow value*
+
+The `collect` operator collects all items from a source channel into a list and emits it as a single item:
+
+```nextflow file=../snippets/collect.nf
+```
+
+```console file=../snippets/collect.out
+```
+
+An optional [closure][script-closure] can be used to transform each item before it is collected:
+
+```nextflow file=../snippets/collect-with-mapper.nf
+```
+
+```console file=../snippets/collect-with-mapper.out
+```
+
+Available options:
+
+##### `flat`
+
+When `true`, nested list structures are flattened and their items are collected individually (default: `true`).
+
+##### `sort`
+
+When `true`, the collected items are sorted by their natural ordering (default: `false`). Can also be a [closure][script-closure] or a [Comparator](https://docs.oracle.com/javase/8/docs/api/java/util/Comparator.html) which defines how items are compared during sorting.
+
+#
+
+See also: [toList][operator-tolist], [toSortedList][operator-tosortedlist]
+
+## collectFile
+
+*Returns: channel*
+
+The `collectFile` operator collects the items from a source channel and saves them to one or more files, emitting the collected file(s).
+
+This operator has multiple variants:
+
+##### `collectFile( name: '...', [options] )`
+
+Collects the items and saves them to a single file specified by the `name` option:
+
+```nextflow file=../snippets/collectfile.nf
+```
+
+##### `collectFile( closure, [options] )`
+
+Collects the items into groups and saves each group to a file, using a grouping criteria. The grouping criteria is a [closure][script-closure] that maps each item to a pair, where the first element is the file name for the group and the second element is the content to be appended to that file. For example:
+
+```nextflow file=../snippets/collectfile-closure.nf
+```
+
+```console file=../snippets/collectfile-closure.out
+```
+
+When the items from the source channel are files, the grouping criteria can be omitted. In this case, the items will be grouped by their source filename.
+
+The following example shows how to use a closure to collect and sort all sequences in a FASTA file from shortest to longest:
+
+```nextflow
+channel.fromPath('/data/sequences.fa')
+    .splitFasta( record: [id: true, sequence: true] )
+    .collectFile( name: 'result.fa', sort: { v -> v.size() } ) {
+        v -> v.sequence
+    }
+    .view { fa -> fa.text }
+```
+
+:::warning
+The `collectFile` operator needs to store files in a temporary directory that is automatically deleted on workflow completion. For performance reasons, this directory is located in the machine's local storage, and it should have as much free space as the data that is being collected. The `tempDir` option can be used to specify a different temporary directory.
+:::
+
+Available options:
+
+##### `cache`
+Controls the caching ability of the `collectFile` operator when using the *resume* feature. It follows the same semantic of the [cache][process-cache] directive (default: `true`).
+
+##### `keepHeader`
+Prepend the resulting file with the header fetched in the first collected file. The header size (i.e. lines) can be specified by using the `skip` option (default: `0`), to determine how many lines to remove from all collected files except for the first (where no lines will be removed).
+
+##### `name`
+Name of the file where all received values are stored.
+
+##### `newLine`
+Appends a `newline` character automatically after each entry (default: `false`).
+
+##### `seed`
+A value or a map of values used to initialize the files content.
+
+##### `skip`
+Skip the first `n` lines e.g. `skip: 1` (default: `0`).
+
+##### `sort`
+Defines sorting criteria of content in resulting file(s). Can be one of the following values:
+
+- `false`: Disable content sorting. Entries are appended as they are produced.
+- `true`: Order the content by the entry's natural ordering, i.e. numerical for number, lexicographic for string, etc. See the [Java documentation](http://docs.oracle.com/javase/tutorial/collections/interfaces/order.html) for more information.
+- `'index'`: Order the content by the incremental index number assigned to each entry while they are collected.
+- `'hash'`: (default) Order the content by the hash number associated to each entry
+- `'deep'`: Similar to the previous, but the hash number is created on actual entry content, e.g. when the entry is a file, the hash is created on the actual file content.
+- A custom sorting criteria can be specified with a [closure][script-closure] or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
+
+The file content is sorted in such a way that it does not depend on the order in which entries were added to it, which guarantees that it is consistent (i.e. does not change) across different executions with the same data.
+
+##### `storeDir`
+Folder where the resulting file(s) are stored.
+
+##### `tempDir`
+Folder where temporary files, used by the collecting process, are stored.
+
+## combine
+
+*Returns: channel*
+
+The `combine` operator produces the combinations (i.e. cross product, "Cartesian" product) of two source channels, or a channel and a list (as the right operand), emitting each combination separately.
+
+For example:
+
+```nextflow file=../snippets/combine.nf
+```
+
+```console file=../snippets/combine.out
+```
+
+The `by` option can be used to combine items that share a matching key. The value should be the zero-based index of the tuple, or a list of indices. For example:
+
+```nextflow file=../snippets/combine-by.nf
+```
+
+```console file=../snippets/combine-by.out
+```
+
+:::note
+The `combine` operator is similar to `cross` and `join`, making them easy to confuse. Their differences can be summarized as follows:
+
+- `combine` and `cross` both produce an *outer product* or *cross product*, whereas `join` produces an *inner product*.
+
+- `combine` filters pairs with a matching key only if the `by` option is used, whereas `cross` always filters pairs with a matching key.
+
+- `combine` with the `by` option merges and flattens each pair, whereas `cross` does not. Compare the examples for `combine` and `cross` to see this difference.
+:::
+
+#
+
+See also: [cross](#cross), [join](#join)
+
+## concat
+
+*Returns: channel*
+
+The `concat` operator emits the items from two or more source channels into a single output channel. Each source channel is emitted in the order in which it was specified.
+
+In other words, given *N* channels, the items from the *i+1*-th channel are emitted only after all of the items from the *i*-th channel have been emitted.
+
+For example:
+
+```nextflow file=../snippets/concat.nf
+```
+
+```console file=../snippets/concat.out
+```
+
+#
+
+See also: [mix](#mix)
+
+## count
+
+*Returns: dataflow value*
+
+The `count` operator computes the total number of items in a source channel and emits it:
+
+```nextflow file=../snippets/count.nf
+```
+
+```console file=../snippets/count.out
+```
+
+An optional filter can be provided to select which items to count. The selection criteria can be a literal value, a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate. For example:
+
+```nextflow file=../snippets/count-with-filter-number.nf
+```
+
+```console file=../snippets/count-with-filter-number.out
+```
+
+```nextflow file=../snippets/count-with-filter-regex.nf
+```
+
+```console file=../snippets/count-with-filter-regex.out
+```
+
+```nextflow file=../snippets/count-with-filter-closure.nf
+```
+
+```console file=../snippets/count-with-filter-closure.out
+```
+
+## countFasta
+
+*Returns: dataflow value*
+
+Counts the total number of records in a channel of FASTA files, equivalent to `splitFasta | count`. See [splitFasta](#splitfasta) for the list of available options.
+
+## countFastq
+
+*Returns: dataflow value*
+
+Counts the total number of records in a channel of FASTQ files, equivalent to `splitFastq | count`. See [splitFastq](#splitfastq) for the list of available options.
+
+## countJson
+
+*Returns: dataflow value*
+
+Counts the total number of records in a channel of JSON files, equivalent to `splitJson | count`. See [splitJson](#splitjson) for the list of available options.
+
+## countLines
+
+*Returns: dataflow value*
+
+Counts the total number of lines in a channel of text files, equivalent to `splitText | count`. See [splitLines](#splittext) for the list of available options.
+
+## cross
+
+*Returns: channel*
+
+The `cross` operator emits every pairwise combination of two channels for which the pair has a matching key.
+
+By default, the key is defined as the first entry in a list or map, or the value itself for any other data type. For example:
+
+```nextflow file=../snippets/cross.nf
+```
+
+```console file=../snippets/cross.out
+```
+
+An optional [closure][script-closure] can be used to define the matching key for each item:
+
+```nextflow file=../snippets/cross-with-mapper.nf
+```
+
+```console file=../snippets/cross-with-mapper.out
+```
+
+There are two important caveats when using the `cross` operator:
+
+1. The operator is not *commutative*, i.e. `a.cross(b)` is not the same as `b.cross(a)`
+2. Each source channel should not emit any items with duplicate keys, i.e. each item should have a unique key.
+
+#
+
+See also: [combine](#combine)
+
+## distinct
+
+*Returns: channel*
+
+The `distinct` operator forwards a source channel with *consecutively* repeated items removed, such that each emitted item is different from the preceding one:
+
+```nextflow file=../snippets/distinct.nf
+```
+
+```console file=../snippets/distinct.out
+```
+
+An optional [closure][script-closure] can be used to transform each value before it is evaluated for distinct-ness:
+
+```nextflow file=../snippets/distinct-with-mapper.nf
+```
+
+```console file=../snippets/distinct-with-mapper.out
+```
+
+#
+
+See also: [unique](#unique)
+
+## dump
+
+*Returns: channel*
+
+The `dump` operator prints each item in a source channel when the pipeline is executed with the `-dump-channels` command-line option, otherwise it does nothing. It is a useful way to inspect and debug channels quickly without having to modify the pipeline script.
+
+The `tag` option can be used to select which channels to dump:
+
+```nextflow file=../snippets/dump.nf
+```
+
+Then, you can run your pipeline with `-dump-channels plus1` or `-dump-channels exp2` to dump the content of either channel. Multiple tag names can be specified as a comma-separated list.
+
+Available options:
+
+##### `pretty`
+
+<AddedInVersion version="22.10.0" />
+
+When `true`, format the output as pretty-printed JSON (default: `false`).
+
+##### `tag`
+
+Associate the channel with a tag that can be specified with the `-dump-channels` option to select which channels to dump.
+
+## filter
+
+*Returns: channel*
+
+The `filter` operator emits the items from a source channel that satisfy a condition, discarding all other items. The filter condition can be a literal value, a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate.
+
+The following example filters a channel with a regular expression that only matches strings beginning with `a`:
+
+```nextflow file=../snippets/filter-regex.nf
+```
+
+```console file=../snippets/filter-regex.out
+```
+
+The following example filters a channel with the `Number` type qualifier so that only numbers are emitted:
+
+```nextflow file=../snippets/filter-type.nf
+```
+
+```console file=../snippets/filter-type.out
+```
+
+The following example filters a channel using a boolean predicate, which is a [closure][script-closure] that returns a boolean value. In this case, the predicate is used to select only odd numbers:
+
+```nextflow file=../snippets/filter-closure.nf
+```
+
+```console file=../snippets/filter-closure.out
+```
+
+## first
+
+*Returns: dataflow value*
+
+The `first` operator emits the first item in a source channel, or the first item that matches a condition. The condition can be a [regular expression][script-regexp], a type qualifier (i.e. Java class), or a boolean predicate. For example:
+
+```nextflow file=../snippets/first.nf
+```
+
+## flatMap
+
+*Returns: channel*
+
+The `flatMap` operator applies a *mapping function* to each item from a source channel.
+
+When the mapping function returns a list, each element in the list is emitted separately:
+
+```nextflow file=../snippets/flatmap-list.nf
+```
+
+```console file=../snippets/flatmap-list.out
+```
+
+When the mapping function returns a map, each key-value pair in the map is emitted separately:
+
+```nextflow file=../snippets/flatmap-map.nf
+```
+
+```console file=../snippets/flatmap-map.out
+```
+
+## flatten
+
+*Returns: channel*
+
+The `flatten` operator flattens each item from a source channel that is a list or other collection, such that each element in each collection is emitted separately:
+
+```nextflow file=../snippets/flatten.nf
+```
+
+```console file=../snippets/flatten.out
+```
+
+As shown in the above example, deeply nested collections are also flattened.
+
+#
+
+See also: [flatMap](#flatmap)
+
+## groupTuple
+
+*Returns: queue channel*
+
+The `groupTuple` operator collects lists (i.e. *tuples*) from a source channel into groups based on a grouping key. A new tuple is emitted for each distinct key.
+
+To be more precise, the operator transforms a sequence of tuples like *(K, V, W, ..)* into a sequence of tuples like *(K, list(V), list(W), ..)*.
+
+For example:
+
+```nextflow file=../snippets/grouptuple.nf
+```
+
+```console file=../snippets/grouptuple.out
+```
+
+By default, the first element of each tuple is used as the grouping key. The `by` option can be used to specify a different index, or list of indices. For example, to group by the second element of each tuple:
+
+```nextflow file=../snippets/grouptuple-by.nf
+```
+
+```console file=../snippets/grouptuple-by.out
+```
+
+By default, if you don't specify a size, the `groupTuple` operator will not emit any groups until *all* inputs have been received. If possible, you should always try to specify the number of expected elements in each group using the `size` option, so that each group can be emitted as soon as it's ready. In cases where the size of each group varies based on the grouping key, you can use the built-in `groupKey()` function, which allows you to define a different expected size for each group:
+
+```nextflow file=../snippets/grouptuple-groupkey.nf
+```
+
+```console file=../snippets/grouptuple-groupkey.out
+```
+
+Available options:
+
+##### `by`
+
+The zero-based index of the element to use as the grouping key. Can also be a list of indices, e.g. `by: [0,2]` (default: `[0]`).
+
+##### `remainder`
+
+When `true`, incomplete tuples (i.e. groups with less than `size` items) are emitted as partial groups, otherwise they are discarded (default: `false`). This option can only be used with `size`.
+
+##### `size`
+
+The required number of items for each group. When a group reaches the required size, it is emitted.
+
+##### `sort`
+
+Defines the sorting criteria for the grouped items. Can be one of the following values:
+
+- `false`: No sorting is applied (default).
+- `true`: Order the grouped items by the item's natural ordering, i.e. numerical for number, lexicographic for string, etc. See the [Java documentation](http://docs.oracle.com/javase/tutorial/collections/interfaces/order.html) for more information.
+- `'hash'`: Order the grouped items by the hash number associated to each entry.
+- `'deep'`: Similar to the previous, but the hash number is created on actual entry content, e.g. when the item is a file, the hash is created on the actual file content.
+- A custom sorting criteria used to order the nested list elements of each tuple. It can be a [closure][script-closure] or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
+
+## ifEmpty
+
+*Returns: channel*
+
+The `ifEmpty` operator emits a source channel, or a default value if the source channel is *empty* (doesn't emit any value):
+
+```nextflow file=../snippets/ifempty-1.nf
+```
+
+```console file=../snippets/ifempty-1.out
+```
+
+```nextflow file=../snippets/ifempty-2.nf
+```
+
+```console file=../snippets/ifempty-2.out
+```
+
+The default value can also be a [closure][script-closure], in which case the closure is evaluated and the result is emitted when the source channel is empty.
+
+#
+
+See also: [empty][operator-empty] channel factory
+
+## join
+
+*Returns: channel*
+
+The `join` operator emits the inner product of two source channels using a matching key.
+
+To be more precise, the operator transforms a sequence of tuples like *(K, V1, V2, ..)* and *(K, W1, W1, ..)* into a sequence of tuples like *(K, V1, V2, .., W1, W2, ..)*.
+
+For example:
+
+```nextflow file=../snippets/join.nf
+```
+
+```console file=../snippets/join.out
+```
+
+By default, the first element of each item is used as the key. The `by` option can be used to specify a different index, or list of indices.
+
+By default, unmatched items are discarded. The `remainder` option can be used to emit them at the end:
+
+```nextflow file=../snippets/join-with-remainder.nf
+```
+
+```console file=../snippets/join-with-remainder.out
+```
+
+:::note
+The `join` operator is similar to an SQL *inner join*, or an SQL *outer join* when `remainder` is `true`. The only difference is that `join` does not support duplicate keys, whereas an SQL join produces the cross-product of duplicate keys. The `combine` operator with the `by` option is equivalent to an SQL join.
+:::
+
+Available options:
+
+##### `by`
+
+The zero-based index of each item to use as the matching key. Can also be a list of indices, e.g. `by: [0, 2]` (default: `[0]`).
+
+##### `failOnDuplicate`
+
+When `true`, an error is reported when the operator receives multiple items from the same channel with the same key (default: `false`). Value is set to `true` if [strict mode][config-feature-flags] is enabled.
+
+##### `failOnMismatch`
+
+When `true`, an error is reported when the operator receives an item from one channel for which there no matching item from the other channel (default: `false`). Value is set to `true` if [strict mode][config-feature-flags] is enabled. This option cannot be used with `remainder`.
+
+##### `remainder`
+
+When `true`, unmatched items are emitted at the end, otherwise they are discarded (default: `false`). 
+
+#
+
+See also: [combine](#combine), [cross](#cross)
+
+## last
+
+*Returns: dataflow value*
+
+The `last` operator emits the last item from a source channel:
+
+```nextflow file=../snippets/last.nf
+```
+
+```console file=../snippets/last.out
+```
+
+## map
+
+*Returns: channel*
+
+The `map` operator applies a *mapping function* to each item from a source channel:
+
+```nextflow file=../snippets/map.nf
+```
+
+```console file=../snippets/map.out
+```
+
+:::note
+`null` values are not emitted by `map`.
+:::
+
+## max
+
+*Returns: dataflow value*
+
+The `max` operator emits the item with the greatest value from a source channel:
+
+```nextflow file=../snippets/max.nf
+```
+
+```console file=../snippets/max.out
+```
+
+An optional [closure][script-closure] can be used to control how the items are compared. The closure can be a *mapping function*, which transforms each item before it is compared, or a *comparator function*, which defines how to compare two items more generally.
+
+The following examples show how to find the longest string in a channel:
+
+```nextflow file=../snippets/max-with-mapper.nf
+```
+
+```console file=../snippets/max-with-mapper.out
+```
+
+```nextflow file=../snippets/max-with-comparator.nf
+```
+
+```console file=../snippets/max-with-comparator.out
+```
+
+## merge
+
+*Returns: channel*
+
+The `merge` operator joins the items from two or more channels into a new channel:
+
+```nextflow file=../snippets/merge.nf
+```
+
+```console file=../snippets/merge.out
+```
+
+An optional [closure][script-closure] can be used to control how two items are merged:
+
+```nextflow file=../snippets/merge-with-mapper.nf
+```
+
+```console file=../snippets/merge-with-mapper.out
+```
+
+The `merge` operator may return a channel or value depending on the inputs:
+
+- If the first argument is a channel, the `merge` operator returns a channel merging as many values as are available for all inputs. Dataflow values are re-used for each merged value.
+
+- If the first argument is a dataflow value, the `merge` operator returns a dataflow value, merging the first value from each input, regardless of whether there are channel inputs with additional values.
+
+:::danger
+In general, the use of the `merge` operator is discouraged. Processes and channel operators are not guaranteed to emit items in the order that they were received, as they are executed concurrently. Therefore, if you try to merge output channels from different processes, the resulting channel may be different on each run, which will cause resumed runs to [not work properly][cache-nondeterministic-inputs].
+
+You should always use a matching key (e.g. sample ID) to merge multiple channels, so that they are combined in a deterministic way. For this purpose, you can use the [join](#join) operator.
+:::
+
+## min
+
+*Returns: dataflow value*
+
+The `min` operator emits the item with the lowest value from a source channel:
+
+```nextflow file=../snippets/min.nf
+```
+
+```console file=../snippets/min.out
+```
+
+An optional [closure][script-closure] can be used to control how the items are compared. The closure can be a *mapping function*, which transforms each item before it is compared, or a *comparator function*, which defines how to compare two items more generally.
+
+The following examples show how to find the shortest string in a channel:
+
+```nextflow file=../snippets/min-with-mapper.nf
+```
+
+```console file=../snippets/min-with-mapper.out
+```
+
+```nextflow file=../snippets/min-with-comparator.nf
+```
+
+```console file=../snippets/min-with-comparator.out
+```
+
+## mix
+
+*Returns: channel*
+
+The `mix` operator emits the items from two or more source channels into a single output channel:
+
+```nextflow file=../snippets/mix.nf
+```
+
+```console file=../snippets/mix.out
+```
+
+The items in the mixed output channel may appear in any order, regardless of which source channel they came from. Thus, the previous example could also output the following:
+
+```console
+z
+1
+a
+2
+b
+3
+```
+
+#
+
+See also: [concat](#concat)
+
+## multiMap
+
+*Returns: multiple channels*
+
+The `multiMap` operator applies a set of mapping functions to a source channel, producing a separate output channel for each mapping function.
+
+The multi-map criteria is a [closure][script-closure] that defines, for each output channel, a label followed by a mapping expression.
+
+For example:
+
+```nextflow file=../snippets/multimap.nf
+```
+
+```console file=../snippets/multimap.out
+```
+
+Multiple labels can share the same mapping expression using the following shorthand:
+
+```nextflow file=../snippets/multimap-shared.nf
+```
+
+```console file=../snippets/multimap-shared.out
+```
+
+The above example creates two channels as before, but now they both receive the same items.
+
+You can use the `multiMapCriteria()` method to create a multi-map criteria as a variable that can be passed as an argument to any number of `multiMap` operations, as shown below:
+
+```nextflow file=../snippets/multimap-criteria.nf
+```
+
+:::note
+If you use `multiMap` to split a tuple or map into multiple channels, it is recommended that you retain a matching key (e.g. sample ID) with *each* new channel, so that you can re-combine these channels later on if needed. In general, you should not expect to be able to merge channels correctly without a matching key, due to the concurrent nature of Nextflow pipelines.
+:::
+
+## randomSample
+
+*Returns: channel*
+
+The `randomSample` operator emits a randomly-selected subset of items from a source channel:
+
+```nextflow file=../snippets/random-sample.nf
+```
+
+The above snippet will print 10 randomly-selected numbers between 1 and 100 (without replacement).
+
+An optional second parameter can be used to set the initial *seed* for the random number generator, which ensures that the `randomSample` operator produces the same pseudo-random sequence across runs:
+
+```nextflow file=../snippets/random-sample-with-seed.nf
+```
+
+The above example will print 10 randomly-selected numbers between 1 and 100 (without replacement). Each subsequent script execution will produce the same sequence.
+
+## reduce
+
+*Returns: dataflow value*
+
+The `reduce` operator applies an *accumulator function* sequentially to each item in a source channel, and emits the final accumulated value. The accumulator function takes two parameters -- the accumulated value and the *i*-th emitted item -- and it should return the accumulated result, which is passed to the next invocation with the *i+1*-th item. This process is repeated for each item in the source channel.
+
+For example:
+
+```nextflow file=../snippets/reduce.nf
+```
+
+```console file=../snippets/reduce.out
+```
+
+By default, the first item is used as the initial accumulated value. You can optionally specify a different initial value as shown below:
+
+```nextflow file=../snippets/reduce-with-initial-value.nf
+```
+
+```console file=../snippets/reduce-with-initial-value.out
+```
+
+## set
+
+*Returns: nothing*
+
+The `set` operator assigns a source channel to a variable, whose name is specified as a closure parameter:
+
+```nextflow
+channel.of(10, 20, 30).set { my_channel }
+```
+
+Using `set` is semantically equivalent to assigning a variable:
+
+```nextflow
+my_channel = channel.of(10, 20, 30)
+```
+
+#
+
+See also: [tap](#tap)
+
+## splitCsv
+
+*Returns: channel*
+
+The `splitCsv` operator parses and splits [CSV](http://en.wikipedia.org/wiki/Comma-separated_values) files or text from a source channel into records.
+
+For example:
+
+```nextflow file=../snippets/splitcsv.nf
+```
+
+```console file=../snippets/splitcsv.out
+```
+
+The above example shows hows CSV text is parsed and split into individual rows, where each row is simply a list of columns.
+
+When the CSV begins with a header line defining the column names, and the `header` option is `true`, each row is returned as a map instead:
+
+```nextflow file=../snippets/splitcsv-with-header.nf
+```
+
+```console file=../snippets/splitcsv-with-header.out
+```
+
+The `header` option can also just be a list of columns:
+
+```nextflow file=../snippets/splitcsv-with-columns.nf
+```
+
+```console file=../snippets/splitcsv-with-columns.out
+```
+
+Available options:
+
+##### `by`
+
+When specified, group rows into *chunks* with the given size (default: none).
+
+##### `charset`
+
+Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
+
+##### `decompress`
+
+When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
+
+##### `elem`
+
+The index of the element to split when the source items are lists or tuples (default: first file object or first element).
+
+##### `header`
+
+When `true`, the first line is used as the columns names (default: `false`). Can also be a list of columns names.
+
+##### `limit`
+
+Limits the number of records to retrieve for each source item (default: no limit).
+
+##### `quote`
+
+The character used to quote values (default: `''` or `""`).
+
+##### `sep`
+
+The character used to separate values (default: `,`)
+
+##### `skip`
+
+Number of lines to ignore from the beginning when parsing the CSV text (default: `0`).
+
+##### `strip`
+
+When `true`, remove leading and trailing blanks from values (default: `false`).
+
+## splitFasta
+
+*Returns: channel*
+
+The `splitFasta` operator splits [FASTA](http://en.wikipedia.org/wiki/FASTA_format) files or text from a source channel into individual sequences.
+
+The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTA file and split it into chunks of 10 sequences each:
+
+```nextflow
+channel.fromPath('misc/sample.fa')
+    .splitFasta( by: 10 )
+    .view()
+```
+
+:::warning
+Chunks are stored in memory by default. When splitting large files, specify `file: true` to save the chunks into files in order to avoid running out of memory. See the list of options below for details.
+:::
+
+The `record` option can be used to split FASTA content into *records* instead of text chunks. Each record is a map that allows you to access the FASTA sequence data with ease. For example:
+
+```nextflow
+channel.fromPath('misc/sample.fa')
+    .splitFasta( record: [id: true, seqString: true] )
+    .filter { record -> record.id =~ /^ENST0.*/ }
+    .view { record -> record.seqString }
+```
+
+The above example loads the `misc/sample.fa` file, splits it into records containing the `id` and `seqString` fields (i.e. the sequence id and the sequence data), filters records by their ID, and finally prints the sequence string of each record.
+
+Available options:
+
+##### `by`
+
+Defines the number of sequences in each chunk (default: `1`).
+
+##### `charset`
+
+Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
+
+##### `compress`
+
+When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
+
+##### `decompress`
+
+When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
+
+##### `elem`
+
+The index of the element to split when the source items are lists or tuples (default: first file object or first element).
+
+##### `file`
+When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
+
+##### `limit`
+
+Limits the number of sequences to retrieve for each source item (default: no limit).
+
+##### `record`
+
+Parse each entry in the FASTA file into a record. The following fields are available:
+- `id`: The FASTA sequence identifier, i.e. the word following the `>` symbol up to the first blank or newline character
+- `header`: The first line in a FASTA sequence without the `>` character
+- `desc`: The text in the FASTA header following the ID value
+- `text`: The complete FASTA sequence including the header
+- `seqString`: The sequence as a single-line string, i.e. containing no newline characters
+- `sequence`: The sequence as a multi-line string, i.e. always ending with a newline character
+- `width`: Define the length of a single line when the `sequence` field is used, after which the sequence continues on a new line.
+
+##### `size`
+
+Defines the size of the expected chunks as a memory unit, e.g. `1.MB`.
+
+#
+
+See also: [countFasta](#countfasta)
+
+## splitFastq
+
+*Returns: channel*
+
+The `splitFastq` operator splits [FASTQ](http://en.wikipedia.org/wiki/FASTQ_format) files or text from a source channel into individual sequences.
+
+The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTQ file and split it into chunks of 10 sequences each:
+
+```nextflow
+Channel
+channel.fromPath('misc/sample.fastq')
+    .splitFastq( by: 10 )
+    .view()
+```
+
+:::warning
+Chunks are stored in memory by default. When splitting large files, specify `file: true` to save the chunks into files in order to avoid running out of memory. See the list of options below for details.
+:::
+
+The `record` option can be used to split FASTQ content into *records* instead of text chunks. Each record is a map that allows you to access the FASTQ sequence data with ease. For example:
+
+```nextflow
+channel.fromPath('misc/sample.fastq')
+    .splitFastq( record: true )
+    .view { record -> record.readHeader }
+```
+
+The `pe` option can be used to split paired-end FASTQ files. The source channel must emit tuples containing the file pairs. For example:
+
+```nextflow
+channel.fromFilePairs('/my/data/SRR*_{1,2}.fastq', flat: true)
+    .splitFastq(by: 100_000, pe: true, file: true)
+    .view()
+```
+
+:::note
+`channel.fromFilePairs()` requires the `flat: true` option in order to emit the file pairs as separate elements in the produced tuples.
+:::
+
+:::note
+This operator assumes that the order of the paired-end reads correspond with each other and that both files contain the same number of reads.
+:::
+
+Available options:
+
+##### `by`
+
+Defines the number of sequences in each chunk (default: `1`).
+
+##### `charset`
+
+Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
+
+##### `compress`
+
+When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
+
+##### `decompress`
+
+When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
+
+##### `elem`
+
+The index of the element to split when the source items are lists or tuples (default: first file object or first element).
+
+##### `file`
+
+When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
+
+##### `limit`
+
+Limits the number of sequences to retrieve for each source item (default: no limit).
+
+##### `pe`
+
+When `true`, splits paired-end read files. Items emitted by the source channel must be tuples with the file pairs.
+
+##### `record`
+
+Parse each entry in the FASTQ file into a record. The following fields are available:
+- `readHeader`: Sequence header (without the `@` prefix)
+- `readString`: The raw sequence content
+- `qualityHeader`: Base quality header (it may be empty)
+- `qualityString`: Quality values for the sequence
+
+#
+
+See also: [countFastq](#countfastq)
+
+## splitJson
+
+*Returns: channel*
+
+The `splitJson` operator splits [JSON](https://en.wikipedia.org/wiki/JSON) files or text from a source channel into individual records.
+
+If the source item is a JSON array, each element of the array will be emitted:
+
+```nextflow file=../snippets/splitjson-array.nf
+```
+
+```console file=../snippets/splitjson-array.out
+```
+
+If the source item is a JSON object, each key-value pair will be emitted as a map with the properties `key`  and `value`:
+
+```nextflow file=../snippets/splitjson-object.nf
+```
+
+```console file=../snippets/splitjson-object.out
+```
+
+The `path` option can be used to query a section of the JSON document to parse and split:
+
+```nextflow file=../snippets/splitjson-with-path.nf
+```
+
+```console file=../snippets/splitjson-with-path.out
+```
+
+Available options:
+
+##### `limit`
+
+Limits the number of records to retrieve for each source item (default: no limit).
+
+##### `path`
+
+Defines a query for a section of each source item to parse and split. The expression should be a path similar to [JSONPath](https://goessner.net/articles/JsonPath/). The empty string is the document root (default). An integer in brackets is a zero-based index in a JSON array. A string preceded by a dot `.` is a key in a JSON object.
+
+#
+
+See also: [countJson](#countjson)
+
+## splitText
+
+*Returns: channel*
+
+The `splitText` operator splits multi-line text content from a source channel into chunks of *N* lines:
+
+```nextflow
+Channel
+    .fromPath('/some/path/*.txt')
+    .splitText()
+    .view()
+```
+
+The above example loads a collection of text files, splits the content of each file into individual lines, and prints each line.
+
+The `by` option can be used to emit chunks of *N* lines:
+
+```nextflow
+channel.fromPath('/some/path/*.txt')
+    .splitText( by: 10 )
+    .subscribe { chunk ->
+        print chunk
+        print "--- end of the chunk ---\n"
+    }
+```
+
+An optional [closure][script-closure] can be used to transform each text chunk produced by the operator. The following example shows how to split text files into chunks of 10 lines and transform them to uppercase letters:
+
+```nextflow
+channel.fromPath('/some/path/*.txt')
+    .splitText( by: 10 ) { v -> v.toUpperCase() }
+    .view()
+```
+
+:::note
+Text chunks returned by the `splitText` operator are always terminated by a `\n` newline character.
+:::
+
+Available options:
+
+##### `by`
+
+Defines the number of lines in each `chunk` (default: `1`).
+
+##### `charset`
+
+Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
+
+##### `compress`
+
+When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
+
+##### `decompress`
+
+When `true`, decompresses the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
+
+##### `elem`
+
+The index of the element to split when the source items are lists or tuples (default: first file object or first element).
+
+##### `file`
+
+When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
+
+##### `keepHeader`
+
+Parses the first line as header and prepends it to each emitted chunk (default: `false`).
+
+##### `limit`
+
+Limits the number of lines to retrieve for each source item (default: no limit).
+
+#
+
+See also: [countLines](#countlines)
+
+## subscribe
+
+*Returns: nothing*
+
+The `subscribe` operator invokes a custom function for each item from a source channel:
+
+```nextflow file=../snippets/subscribe.nf
+```
+
+```console file=../snippets/subscribe.out
+```
+
+The `subscribe` operator supports multiple types of event handlers:
+
+```nextflow file=../snippets/subscribe-with-on-complete.nf
+```
+
+```console file=../snippets/subscribe-with-on-complete.out
+```
+
+:::note
+Unlike most operators, `subscribe` is a *terminal operator* and does not emit any values. It should only be used for *side effects*, such as printing to the console, writing to a file, or making HTTP requests.
+:::
+
+Available options:
+
+##### `onNext`
+
+Closure that is invoked when an item is emitted. Equivalent to providing a closure as the first argument.
+
+##### `onComplete`
+
+Closure that is invoked after the last item is emitted by the channel.
+
+##### `onError`
+
+Closure that is invoked when an exception is raised while handling the `onNext` event. It will not make further calls to `onNext` or `onComplete`. The `onError` method takes as its parameter the `Throwable` that caused the error.
+
+## sum
+
+*Returns: dataflow value*
+
+The `sum` operator emits the sum of all items in a source channel:
+
+```nextflow file=../snippets/sum.nf
+```
+
+```console file=../snippets/sum.out
+```
+
+An optional [closure][script-closure] can be used to transform each item before it is added to the sum:
+
+```nextflow file=../snippets/sum-with-mapper.nf
+```
+
+```console file=../snippets/sum-with-mapper.out
+```
+
+## take
+
+*Returns: channel*
+
+The `take` operator takes the first *N* items from a source channel:
+
+```nextflow file=../snippets/take.nf
+```
+
+```console file=../snippets/take.out
+```
+
+:::tip
+Specifying a size of `-1` causes the operator to take all values.
+:::
+
+#
+
+See also: [until](#until)
+
+## tap
+
+*Returns: channel*
+
+The `tap` operator assigns a source channel to a variable, and emits the source channel. It is a useful way to extract intermediate output channels from a chain of operators. For example:
+
+```nextflow file=../snippets/tap.nf
+```
+
+```console file=../snippets/tap.out
+```
+
+#
+
+See also: [set](#set)
+
+## toInteger
+
+*Returns: channel*
+
+The `toInteger` operator converts string values from a source channel to integer values:
+
+```nextflow file=../snippets/tointeger.nf
+```
+
+```console file=../snippets/tointeger.out
+```
+
+:::note
+`toInteger` is equivalent to:
+
+```nextflow
+map { v -> v as Integer }
+```
+:::
+
+:::note
+You can also use `toLong`, `toFloat`, and `toDouble` to convert to other numerical types.
+:::
+
+## toList
+
+*Returns: dataflow value*
+
+The `toList` operator collects all the items from a source channel into a list and emits the list as a single item:
+
+```nextflow file=../snippets/tolist.nf
+```
+
+```console file=../snippets/tolist.out
+```
+
+:::note
+There are two main differences between `toList` and `collect`:
+
+- When there is no input, `toList` emits an empty list whereas `collect` emits nothing.
+- By default, `collect` flattens list items by one level.
+
+In other words, `toList` is equivalent to:
+
+```nextflow
+collect(flat: false).ifEmpty([])
+```
+:::
+
+#
+
+See also: [collect](#collect)
+
+## toSortedList
+
+*Returns: dataflow value*
+
+The `toSortedList` operator collects all the items from a source channel into a sorted list and emits the list as a single item:
+
+```nextflow file=../snippets/tosortedlist.nf
+```
+
+```console file=../snippets/tosortedlist.out
+```
+
+An optional [closure][script-closure] can be used to control how items are compared when sorting. For example, to sort tuples by their second element in descending order:
+
+```nextflow file=../snippets/tosortedlist-with-comparator.nf
+```
+
+```console file=../snippets/tosortedlist-with-comparator.out
+```
+
+:::note
+`toSortedList` is equivalent to:
+
+```nextflow
+collect(flat: false, sort: true).ifEmpty([])
+```
+:::
+
+#
+
+See also: [collect](#collect)
+
+## transpose
+
+*Returns: channel*
+
+The `transpose` operator "transposes" each tuple from a source channel by flattening any nested list in each tuple, emitting each nested item separately.
+
+To be more precise, the operator transforms a sequence of tuples like *(K, list(V), list(W), ..)* into a sequence of tuples like *(K, V, W, ..)*.
+
+For example:
+
+```nextflow file=../snippets/transpose-1.nf
+```
+
+```console file=../snippets/transpose-1.out
+```
+
+If each source item has more than two elements, these will be flattened by the first element in the item, and a new item will be emitted only when it is complete:
+
+```nextflow file=../snippets/transpose-2.nf
+```
+
+```console file=../snippets/transpose-2.out
+```
+
+The `remainder` option can be used to emit any incomplete items:
+
+```nextflow file=../snippets/transpose-2-with-remainder.nf
+```
+
+```console file=../snippets/transpose-2-with-remainder.out
+```
+
+Available options:
+
+##### `by`
+
+The zero-based index of the element to be transposed. Can also be a list of indices, e.g. `by: [0,2]`. By default, every list element is transposed.
+
+##### `remainder`
+
+When `true`, incomplete tuples are emitted with `null` values for missing elements, otherwise they are discarded (default: `false`). 
+
+#
+
+See also: [groupTuple](#grouptuple)
+
+## unique
+
+*Returns: channel*
+
+The `unique` operator emits the unique items from a source channel:
+
+```nextflow file=../snippets/unique.nf
+```
+
+```console file=../snippets/unique.out
+```
+
+An optional [closure][script-closure] can be used to transform each item before it is evaluated for uniqueness:
+
+```nextflow file=../snippets/unique-with-mapper.nf
+```
+
+```console file=../snippets/unique-with-mapper.out
+```
+
+:::note
+The difference between `unique` and `distinct` is that `unique` removes *all* duplicate values, whereas `distinct` removes only *consecutive* duplicate values. As a result, `unique` must process the entire source channel before it can emit anything, whereas `distinct` can emit each value immediately.
+:::
+
+#
+
+See also: [distinct](#distinct)
+
+## until
+
+*Returns: channel*
+
+The `until` operator emits each item from a source channel until a stopping condition is satisfied:
+
+```nextflow file=../snippets/until.nf
+```
+
+```console file=../snippets/until.out
+```
+
+#
+
+See also: [take](#take)
+
+## view
+
+*Returns: channel*
+
+The `view` operator prints each item from a source channel to standard output:
+
+```nextflow file=../snippets/view.nf
+```
+
+```console file=../snippets/view.out
+```
+
+An optional [closure][script-closure] can be used to transform each item before it is printed:
+
+```nextflow file=../snippets/view-with-mapper.nf
+```
+
+```console file=../snippets/view-with-mapper.out
+```
+
+The `view` operator also emits every item that it receives, allowing it to be chained with other operators.
+
+Available options:
+
+##### `newLine`
+Print each item to a separate line (default: `true`).
+
+[cache-nondeterministic-inputs]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#non-deterministic-process-inputs
+[config-feature-flags]: /nextflow_docs/nextflow_repo/docs/reference/feature-flags.mdx
+[process-cache]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#cache
diff --git a/new-docs/nextflow-docs/reference/process.mdx b/new-docs/nextflow-docs/reference/process.mdx
new file mode 100644
index 0000000000..ad6999e826
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/process.mdx
@@ -0,0 +1,1802 @@
+
+
+# Process reference
+
+This page lists the task properties, input/output methods, and directives available in [process][process-page] definitions.
+
+## Task properties
+
+The following task properties are defined in the process body:
+
+##### `task.attempt`
+
+The current task attempt.
+
+##### `task.exitStatus`
+
+The exit code of the task script. Only applicable for processes with a `script:` or `shell:` block.
+
+Since the exit code is only available after the task has been executed, it can only be used by certain process directives such as [errorStrategy](#errorstrategy).
+
+##### `task.previousException`
+
+<AddedInVersion version="24.10.0"/>
+
+The exception reported by the previous task attempt.
+
+Since the exception is available after a failed task attempt, it can only be accessed when retrying a failed task execution, i.e., when `task.attempt` is greater than 1.
+
+##### `task.previousTrace`
+
+<AddedInVersion version="24.10.0"/>
+
+The trace record associated with the previous task attempt.
+
+Since the trace record is available after a failed task attempt, it can only be accessed when retrying a failed task execution, i.e., when `task.attempt` is greater than 1.
+
+##### `task.process`
+
+The name of the process that spawned the task.
+
+##### `task.workDir`
+
+*Available only in `exec:` blocks*
+
+The unique directory path for the task.
+
+:::note
+[Directive values](#directives) for a task can be accessed via `task.<directive>`.
+:::
+
+## Inputs and outputs (typed)
+
+<AddedInVersion version="25.10.0"/>
+
+:::note
+Typed processes require the `nextflow.preview.types` feature flag to be enabled in every script that uses them.
+:::
+
+### Stage directives
+
+The following directives can be used in the `stage:` section of a typed process:
+
+##### `env( name: String, String value )`
+
+Declares an environment variable with the specified name and value in the task environment.
+
+##### `stageAs( filePattern: String, value: Path )`
+
+Stages a file into the task directory under the given alias.
+
+###### `stageAs( filePattern: String, value: Iterable<Path> )`
+
+Stages a collection of files into the task directory under the given alias.
+
+##### `stdin( value: String )`
+
+Stages the given value as the standard input (i.e., `stdin`) to the task script.
+
+### Outputs
+
+The following functions are available in the `output:` and `topic:` sections of a typed process:
+
+##### `env( name: String ) -> String`
+
+Returns the value of an environment variable from the task environment.
+
+##### `eval( command: String ) -> String`
+
+Returns the standard output of the specified command, which is executed in the task environment after the task script completes.
+
+##### `file( pattern: String, [options] ) -> Path`
+
+Returns a file from the task environment that matches the specified pattern.
+
+Available options:
+
+###### `followLinks: Boolean`
+
+When `true`, target files are returned in place of any matching symlink (default: `true`).
+
+###### `glob: Boolean`
+
+When `true`, the file name is interpreted as a glob pattern (default: `true`).
+
+###### `hidden: Boolean`
+
+When `true`, hidden files are included in the matching output files (default: `false`).
+
+###### `includeInputs: Boolean`
+
+When `true` and the file name is a glob pattern, any input files matching the pattern are also included in the output (default: `false`).
+
+###### `maxDepth: Integer`
+
+Maximum number of directory levels to visit (default: no limit).
+
+###### `optional: Boolean`
+
+When `true`, the task will not fail if the given file is missing (default: `false`).
+
+###### `type: String`
+
+Type of paths returned, either `file`, `dir` or `any` (default: `any`, or `file` if the given file name contains a double star (`**`)).
+
+##### `files( pattern: String, [options] ) -> Set<Path>`
+
+Returns files from the task environment that match the given pattern.
+
+Supports the same options as `file()` (except for `optional`).
+
+##### `stdout() -> String`
+
+Returns the standard output of the task script.
+
+
+## Inputs and outputs (legacy)
+
+### Inputs
+
+##### `val( identifier )`
+
+Declare a variable input. The received value can be any type, and it will be made available to the process body (i.e. `script`, `shell`, `exec`) as a variable given by `identifier`.
+
+##### `file( identifier | stageName )`
+
+<DeprecatedInVersion version="19.10.0">
+Use `path` instead.
+</DeprecatedInVersion>
+
+Declare a file input. The received value can be any type, and it will be staged into the task directory. If the received value is not a file or collection of files, it is implicitly converted to a string and written to a file.
+
+The argument can be an identifier or string. If an identifier, the received value will be made available to the process body as a variable. If a string, the received value will be staged into the task directory under the given alias.
+
+##### `path( identifier | stageName )`
+
+Declare a file input. The received value should be a file or collection of files and will be staged into the task directory.
+
+The argument can be an identifier or string. If an identifier, the received value will be made available to the process body as a variable. If a string, the received value will be staged into the task directory under the given alias.
+
+Available options:
+
+##### `arity`
+
+<AddedInVersion version="23.09.0-edge" />
+
+Specify the number of expected files. Can be a number, e.g. `'1'`, or a range, e.g. `'1..*'`. If a task receives an invalid number of files for this `path` input, it will fail.
+
+##### `name`
+
+Specify how the file should be named in the task work directory. Can be a name or a pattern.
+
+##### `stageAs`
+
+Alias of `name`.
+
+##### `env( name )`
+
+Declare an environment variable input. The received value should be a string, and it will be exported to the task environment as an environment variable given by `name`.
+
+##### `stdin`
+
+Declare a `stdin` input. The received value should be a string, and it will be provided as the standard input (i.e. `stdin`) to the task script. It should be declared only once for a process.
+
+##### `tuple( arg1, arg2, ... )`
+
+Declare a tuple input. Each argument should be an input declaration such as `val`, `path`, `env`, or `stdin`.
+
+The received value should be a tuple with the same number of elements as the `tuple` declaration, and each received element should be compatible with the corresponding `tuple` argument. Each tuple element is treated the same way as if it were a standalone input.
+
+### Outputs
+
+##### `val( value )`
+
+Declare a variable output. The argument can be any value, and it can reference any output variables defined in the process body (i.e. variables declared without the `def` keyword).
+
+##### `file( pattern )`
+
+<DeprecatedInVersion version="19.10.0">
+Use `path` instead.
+</DeprecatedInVersion>
+
+Declare a file output. It receives the output files from the task environment that match the given pattern.
+
+Multiple patterns can be specified using the colon separator (`:`). The union of all files matched by each pattern will be collected.
+
+##### `path( pattern, [options] )`
+
+Declare a file output. It receives the output files from the task environment that match the given pattern.
+
+Available options:
+
+##### `arity`
+
+<AddedInVersion version="23.09.0-edge" />
+
+Specify the number of expected files. Can be a number or a range. If a task produces an invalid number of files for this `path` output, it will fail.
+
+If the arity is `1`, a single file will be emitted. Otherwise, a list will always be emitted, even if only one file is produced.
+
+:::warning
+If the arity is not specified, a single file or list will be emitted based on whether a single file or multiple files are produced at runtime, resulting potentially in an output channel with a mixture of files and file collections.
+:::
+
+##### `followLinks`
+
+When `true`, target files are returned in place of any matching symlink (default: `true`).
+
+##### `glob`
+
+When `true`, the specified name is interpreted as a glob pattern (default: `true`).
+
+##### `hidden`
+
+When `true`, hidden files are included in the matching output files (default: `false`).
+
+##### `includeInputs`
+
+When `true` and the output path is a glob pattern, any input files matching the pattern are also included in the output (default: `false`).
+
+##### `maxDepth`
+
+Maximum number of directory levels to visit (default: no limit).
+
+##### `type`
+
+Type of paths returned, either `file`, `dir` or `any` (default: `any`, or `file` if the specified file name pattern contains a double star (`**`)).
+
+##### `env( name )`
+
+Declare an environment variable output. It receives the value of the environment variable (given by `name`) from the task environment.
+
+<AddedInVersion version="23.12.0-edge">
+Prior to this version, if the environment variable contained multiple lines of output, the output would be compressed to a single line by converting newlines to spaces.
+</AddedInVersion>
+
+##### `stdout`
+
+Declare a `stdout` output. It receives the standard output of the task script.
+
+##### `eval( command )`
+
+<AddedInVersion version="24.02.0-edge" />
+
+Declare an `eval` output. It receives the standard output of the given command, which is executed in the task environment after the task script.
+
+If the command fails, the task will also fail.
+
+##### `tuple( arg1, arg2, ... )`
+
+Declare a tuple output. Each argument should be an output declaration such as `val`, `path`, `env`, `stdin`, or `eval`. Each tuple element is treated the same way as if it were a standalone output.
+
+### Options
+
+The following options are available for all process outputs:
+
+##### `emit: <name>`
+
+Defines the name of the output channel.
+
+##### `optional: true | false`
+
+When `true`, the task will not fail if the specified output is missing (default: `false`).
+
+##### `topic: <name>`
+
+<AddedInVersion version="23.11.0-edge" />
+
+*Experimental: may change in a future release.*
+
+Defines the [channel topic][channel-topic>] to which the output will be sent.
+
+## Directives
+
+### accelerator
+
+<AddedInVersion version="19.09.0-edge" />
+
+The `accelerator` directive allows you to request hardware accelerators (e.g. GPUs) for the task execution. For example:
+
+```nextflow
+process hello {
+    accelerator 4, type: 'nvidia-tesla-k80'
+
+    script:
+    """
+    your_gpu_enabled --command --line
+    """
+}
+```
+
+The above examples will request 4 GPUs of type `nvidia-tesla-k80`.
+
+:::note
+This directive is only used by certain executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+:::note
+Additional options may be required to fully enable the use of accelerators. When using containers with GPUs, you must pass the GPU drivers through to the container. For Docker, this requires the option `--gpus all` in the docker run command. For Apptainer/Singularity, this requires the option `--nv`. The specific implementation details depend on the accelerator and container type being used.
+:::
+
+:::note
+The accelerator `type` option depends on the target execution platform. Refer to the platform-specific documentation for details on the available accelerators:
+
+- [Google Cloud](https://cloud.google.com/compute/docs/gpus/)
+- [Kubernetes](https://kubernetes.io/docs/tasks/manage-gpus/scheduling-gpus/#clusters-containing-different-types-of-gpus)
+
+The accelerator `type` option is not supported for AWS Batch. You can control the accelerator type indirectly through the allowed instance types in your Compute Environment. See the [AWS Batch FAQs](https://aws.amazon.com/batch/faqs/?#GPU_Scheduling_) for more information.
+:::
+
+### afterScript
+
+The `afterScript` directive allows you to execute a custom (Bash) snippet immediately *after* the main process has run. This may be useful to clean up your staging area.
+
+:::note
+When combined with the [container](#container) directive, the `afterScript` will be executed outside the specified container. In other words, the `afterScript` is always executed in the host environment.
+:::
+
+### arch
+
+The `arch` directive allows you to define the CPU architecture to build the software in use by the process' task. For example:
+
+```nextflow
+process blast {
+    spack 'blast-plus@2.13.0'
+    arch 'linux/x86_64', target: 'cascadelake'
+
+    script:
+    """
+    blastp -query input_sequence -num_threads ${task.cpus}
+    """
+}
+```
+
+The example above declares that the CPU generic architecture is `linux/x86_64` (X86 64 bit), and more specifically that the microarchitecture is `cascadelake` (a specific generation of Intel CPUs).
+
+This directive is currently used by the following Nextflow functionalities:
+
+- by the [spack](#spack) directive, to build microarchitecture-optimised applications;
+- by the [Wave][wave-page] service, to build containers for one of the generic families of CPU architectures (see below);
+- by the `spack` strategy within [Wave][wave-page], to optimize the container builds for specific CPU microarchitectures.
+
+Allowed values for the `arch` directive are as follows, grouped by equivalent family (choices available for the sake of compatibility):
+- X86 64 bit: `linux/x86_64`, `x86_64`, `linux/amd64`, `amd64`
+- ARM 64 bit: `linux/aarch64`, `aarch64`, `linux/arm64`, `arm64`, `linux/arm64/v8`
+- ARM 64 bit, older generation: `linux/arm64/v7`
+
+Examples of values for the architecture `target` option are `cascadelake`, `icelake`, `zen2` and `zen3`. See the [Spack documentation](https://spack.readthedocs.io/en/latest/basic_usage.html#support-for-specific-microarchitectures) for the full and up-to-date list of meaningful targets.
+
+### array
+
+<AddedInVersion version="24.04.0" />
+
+:::warning *Experimental: may change in a future release.*
+:::
+
+The `array` directive allows you to submit tasks as *job arrays* for executors that support it.
+
+A job array is a collection of jobs with the same resource requirements and the same script (parameterized by an index). Job arrays incur significantly less scheduling overhead compared to individual jobs, and as a result they are preferred by HPC schedulers where possible.
+
+The directive should be specified with a given array size, along with an executor that supports job arrays. For example:
+
+```nextflow
+process hello {
+    executor 'slurm'
+    array 100
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Nextflow currently supports job arrays for the following executors:
+
+- [AWS Batch][awsbatch-executor]
+- [Google Cloud Batch][google-batch-executor]
+- [LSF][lsf-executor]
+- [PBS][pbs-executor]
+- [PBS Pro][pbspro-executor]
+- [SGE][sge-executor]
+- [SLURM][slurm-executor]
+
+A process using job arrays will collect tasks and submit each batch as a job array when it is ready. Any "leftover" tasks will be submitted as a partial job array.
+
+Once a job array is submitted, each "child" task is executed as an independent job. Any tasks that fail (and can be retried) will be retried without interfering with the tasks that succeeded. Retried tasks are submitted individually rather than through a job array, in order to allow for the use of [dynamic task resources][dynamic-task-resources].
+
+The following directives must be uniform across all tasks in a process that uses job arrays, because these directives are specified once for the entire job array:
+
+- [accelerator](#accelerator)
+- [clusterOptions](#clusteroptions)
+- [cpus](#cpus)
+- [disk](#disk)
+- [machineType](#machinetype)
+- [memory](#memory)
+- [queue](#queue)
+- [resourceLabels](#resourcelabels)
+- [resourceLimits](#resourcelimits)
+- [time](#time)
+
+For cloud-based executors like AWS Batch, or when using Fusion with any executor, the following additional directives must be uniform:
+
+- [container](#container)
+- [containerOptions](#containeroptions)
+
+When using Wave, the following additional directives must be uniform:
+
+- [conda](#conda)
+
+### beforeScript
+
+The `beforeScript` directive allows you to execute a custom (Bash) snippet *before* the main process script is run. This may be useful to initialize the underlying cluster environment or for other custom initialization.
+
+For example:
+
+```nextflow
+process hello {
+    beforeScript 'source /cluster/bin/setup'
+
+    script:
+    """
+    echo 'hello'
+    """
+}
+```
+
+When the process is containerized (using the [container](#container) directive), the `beforeScript` will be executed in the container only if the executor is *container-native* (e.g. cloud batch executors, Kubernetes). Otherwise, the `beforeScript` will be executed outside the container.
+
+### cache
+
+The `cache` directive allows you to store the process results to a local cache. When the cache is enabled *and* the pipeline is launched with the [resume][getstarted-resume] option, any task executions that are already cached will be re-used. See [Cache and resume][cache-resume-page] for more information about how the cache works.
+
+The cache is enabled by default, but you can disable it for a specific process by setting the `cache` directive to `false`. For example:
+
+```nextflow
+process hello {
+    cache false
+    // ...
+}
+```
+
+The following options are available:
+
+######  `true`
+
+Enable caching. Input file metadata (name, size, last updated timestamp) are included in the cache keys (default).
+
+###### `false`
+
+Disable caching.
+
+######  `'deep'`
+
+Enable caching. Input file content is included in the cache keys.
+
+###### `'lenient'`
+
+Enable caching. Minimal input file metadata (name and size only) are included in the cache keys.
+
+This strategy provides a workaround for incorrect caching invalidation observed on shared file systems due to inconsistent file timestamps.
+
+### clusterOptions
+
+The `clusterOptions` directive allows the usage of any native configuration option accepted by your cluster submit command. You can use it to request non-standard resources or use settings that are specific to your cluster and not supported out of the box by Nextflow.
+
+The cluster options can be a string:
+
+```nextflow
+process hello {
+    clusterOptions '-x 1 -y 2'
+    // ...
+}
+```
+
+<ChangedInVersion version="24.04.0">
+Prior to this version, grid executors that require each option to be on a separate line in the job script would attempt to split multiple options using a variety of different conventions. Multiple options can now be specified more clearly using a string list as shown below.
+</ChangedInVersion>
+
+The cluster options can also be a string list:
+
+```nextflow
+process hello {
+    clusterOptions '-x 1', '-y 2', '--flag'
+    // ...
+}
+```
+
+Grid executors that require one option per line will write each option to a separate line, while grid executors that allow multiple options per line will write all options to a single line, the same as with a string. This form is useful to control how the options are split across lines when it is required by the scheduler.
+
+:::note
+This directive is only used by grid executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+:::warning
+While you can use the `clusterOptions` directive to specify options that are supported as process directives (`queue`, `memory`, `time`, etc), you should not use both at the same time, as it will cause undefined behavior. Most HPC schedulers will either fail or simply ignore one or the other.
+:::
+
+### conda
+
+The `conda` directive allows for the definition of the process dependencies using the [Conda](https://conda.io) package manager.
+
+Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. For example:
+
+```nextflow
+process hello {
+    conda 'bwa=0.7.15'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Multiple packages can be specified separating them with a blank space e.g. `bwa=0.7.15 fastqc=0.11.5`. The name of the channel from where a specific package needs to be downloaded can be specified using the usual Conda notation i.e. prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
+
+The `conda` directive also allows the specification of a Conda environment file path or the path of an existing environment directory. See [Conda][conda-page] for further details.
+
+### container
+
+The `container` directive allows you to execute the process script in a [Docker](http://docker.io) container.
+
+It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the *local* executor or the cluster nodes when the pipeline is deployed through a *grid* executor.
+
+For example:
+
+```nextflow
+process hello_docker {
+    container 'dockerbox:tag'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Simply replace in the above script `dockerbox:tag` with the name of the Docker image you want to use.
+
+:::tip
+Containers are a very useful way to execute your scripts in a reproducible self-contained environment or to run your pipeline in the cloud.
+:::
+
+:::note
+This directive is ignored for processes that are [executed natively][process-native].
+:::
+
+### containerOptions
+
+The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path:
+
+```nextflow
+process hello_docker {
+    container 'busybox:latest'
+    containerOptions '--volume /data/db:/db'
+
+    output:
+    path 'output.txt'
+
+    script:
+    """
+    your_command --data /db > output.txt
+    """
+}
+```
+
+:::warning
+This feature is not supported by the [Kubernetes][k8s-executor] executor.
+:::
+
+### cpus
+
+The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. For example:
+
+```nextflow
+process blast {
+    cpus 8
+
+    script:
+    """
+    blastp -query input_sequence -num_threads ${task.cpus}
+    """
+}
+```
+
+This directive is required for tasks that execute multi-process or multi-threaded commands/tools and it is meant to reserve enough CPUs when a pipeline task is executed through a cluster resource manager.
+
+See also: [penv](#penv), [memory](#memory), [time](#time), [queue](#queue), [maxForks](#maxforks)
+
+### debug
+
+By default the `stdout` produced by the commands executed in all processes is ignored. By setting the `debug` directive to `true`, you can forward the process `stdout` to the current top running process `stdout` file, showing it in the shell terminal.
+
+For example:
+
+```nextflow
+process hello {
+    debug true
+
+    script:
+    """
+    echo Hello
+    """
+}
+```
+
+```
+Hello
+```
+
+Without specifying `debug true`, you won't see the `Hello` string printed out when executing the above example.
+
+### disk
+
+The `disk` directive allows you to define how much local disk storage the process is allowed to use. For example:
+
+```nextflow
+process hello {
+    disk 2.GB
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following memory unit suffix can be used when specifying the disk value:
+
+| Unit | Description |
+| ---- | ----------- |
+| B    | Bytes       |
+| KB   | Kilobytes   |
+| MB   | Megabytes   |
+| GB   | Gigabytes   |
+| TB   | Terabytes   |
+
+See [memoryUnit][stdlib-types-memoryunit] for more information.
+
+:::note
+This directive is only used by certain executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+See also: [cpus](#cpus), [memory](#memory) [time](#time), [queue](#queue). and [dynamic task resources][dynamic-task-resources].
+
+### echo
+
+<DeprecatedInVersion version="22.04.0">
+Use `debug` instead
+</DeprecatedInVersion>
+
+### errorStrategy
+
+The `errorStrategy` directive allows you to define how the process manages an error condition. By default, when an error status is returned by the executed script (i.e. when it ends with a non-zero exit status), the process stops immediately, forcing the entire pipeline to terminate.
+
+The following error strategies are available:
+
+##### `terminate` (default)
+
+When a task fails, terminate the pipeline immediately and report an error. Pending and running jobs are killed.
+
+##### `finish`
+
+When a task fails, wait for submitted and running tasks to finish and then terminate the pipeline, reporting an error.
+
+##### `ignore`
+
+When a task fails, ignore it and continue the pipeline execution. If the `workflow.failOnIgnore` config option is set to `true`, the pipeline will report an error (i.e. return a non-zero exit code) upon completion. Otherwise, the pipeline will complete successfully.
+
+See the [Workflow][stdlib-namespaces-workflow] namespace for more information.
+
+##### `retry`
+
+When a task fails, retry it.
+
+#
+
+When setting the `errorStrategy` directive to `ignore` the process doesn't stop on an error condition, it just reports a message notifying you of the error event.
+
+For example:
+
+```nextflow
+process hello {
+    errorStrategy 'ignore'
+
+    // ...
+}
+```
+
+In this case, the workflow will complete successfully and return an exit status of 0. However, if you set `workflow.failOnIgnore = true` in your Nextflow configuration, the workflow will return a non-zero exit status and report the failed tasks as an error.
+
+The `retry` error strategy allows you to re-submit for execution a process returning an error condition. For example:
+
+```nextflow
+process hello {
+    errorStrategy 'retry'
+
+    // ...
+}
+```
+
+The number of times a failing process is re-executed is defined by the [maxRetries](#maxretries) and [maxErrors](#maxerrors) directives.
+
+:::tip
+More complex strategies depending on the task exit status or other parametric values can be defined using a dynamic `errorStrategy`. See [Dynamic directives][dynamic-directives] for details.
+:::
+
+See also: [maxErrors](#maxerrors), [maxRetries](#maxretries) and [dynamic task resources][dynamic-task-resources].
+
+### executor
+
+The `executor` defines the underlying system where processes are executed. By default a process uses the executor defined globally in the `nextflow.config` file.
+
+The `executor` directive allows you to configure what executor has to be used by the process, overriding the default configuration.
+
+The following executors are available:
+
+| Name                  | Executor                                                                                    |
+| --------------------- | ------------------------------------------------------------------------------------------- |
+| `awsbatch`            | [AWS Batch](https://aws.amazon.com/batch/) service                                          |
+| `azurebatch`          | [Azure Batch](https://azure.microsoft.com/en-us/services/batch/) service                    |
+| `condor`              | [HTCondor](https://research.cs.wisc.edu/htcondor/) job scheduler                            |
+| `k8s`                 | [Kubernetes](https://kubernetes.io/) cluster                                                |
+| `local`               | The computer where `Nextflow` is launched                                                   |
+| `lsf`                 | [Platform LSF](http://en.wikipedia.org/wiki/Platform_LSF) job scheduler                     |
+| `moab`                | [Moab](http://www.adaptivecomputing.com/moab-hpc-basic-edition/) job scheduler              |
+| `nqsii`               | [NQSII](https://www.rz.uni-kiel.de/en/our-portfolio/hiperf/nec-linux-cluster) job scheduler |
+| `oge`                 | Alias for the `sge` executor                                                                |
+| `pbs`                 | [PBS/Torque](http://en.wikipedia.org/wiki/Portable_Batch_System) job scheduler              |
+| `pbspro`              | [PBS Pro](https://www.pbsworks.com/) job scheduler                                          |
+| `sge`                 | Sun Grid Engine / [Open Grid Engine](http://gridscheduler.sourceforge.net/)                 |
+| `slurm`               | [SLURM](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) workload manager              |
+| `uge`                 | Alias for the `sge` executor                                                                |
+
+The following example shows how to set the process's executor:
+
+```nextflow
+process hello {
+  executor 'sge'
+
+  // ...
+}
+```
+
+:::note
+Each executor supports additional directives and `executor` configuration options. See [Executors][executor-page] for more information.
+:::
+
+### ext
+
+The `ext` is a special directive used as *namespace* for user custom process directives. This can be useful for advanced configuration options. For example:
+
+```nextflow
+process star {
+    container "biocontainers/star:${task.ext.version}"
+
+    input:
+    path genome
+    tuple val(sampleId), path(reads)
+
+    script:
+    """
+    STAR --genomeDir $genome --readFilesIn $reads ${task.ext.args ?: ''}
+    """
+}
+```
+
+In the above example, the process container version is controlled by `ext.version`, and the script supports additional command line arguments through `ext.args`.
+
+The `ext` directive can be set in the process definition:
+
+```nextflow
+process hello {
+    ext version: '2.5.3', args: '--alpha --beta'
+
+    // ...
+}
+```
+
+Or in the Nextflow configuration:
+
+```groovy
+process.ext.version = '2.5.3'
+process.ext.args = '--alpha --beta'
+```
+
+### fair
+
+<AddedInVersion version="22.12.0-edge" />
+
+The `fair` directive, when enabled, guarantees that process outputs will be emitted in the order in which they were received. For example:
+
+```nextflow
+process hello {
+    fair true
+
+    input:
+    val x
+
+    output:
+    tuple val(task.index), val(x)
+
+    script:
+    """
+    sleep \$((RANDOM % 3))
+    """
+}
+
+workflow {
+    channel.of('A','B','C','D') | hello | view
+}
+```
+
+The above example produces:
+
+```
+[1, A]
+[2, B]
+[3, C]
+[4, D]
+```
+
+### label
+
+The `label` directive allows the annotation of processes with mnemonic identifier of your choice. For example:
+
+```nextflow
+process hello {
+    label 'big_mem'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The same label can be applied to more than a process and multiple labels can be applied to the same process using the `label` directive more than one time.
+
+:::note
+A label must consist of alphanumeric characters or `_`, must start with an alphabetic character and must end with an alphanumeric character.
+:::
+
+Labels are useful to organize workflow processes in separate groups which can be referenced in the configuration file to select and configure a subset of processes having similar computing requirements. See [Process selectors][config-process-selectors] for more information.
+
+See also: [resourceLabels](#resourcelabels)
+
+### machineType
+
+<AddedInVersion version="19.07.0" />
+
+The `machineType` can be used to specify a predefined Google Compute Platform [machine type](https://cloud.google.com/compute/docs/machine-types) when running using the [Google Batch][google-batch-executor], or when using the autopools feature of the [Azure Batch executor][azurebatch-executor].
+
+This directive is optional and if specified overrides the cpus and memory directives:
+
+```nextflow
+process hello {
+    machineType 'n1-highmem-8'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+See also: [cpus](#cpus) and [memory](#memory).
+
+### maxErrors
+
+The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled, you can set it as shown in the example below:
+
+```nextflow
+process hello {
+    errorStrategy 'retry'
+    maxErrors 5
+
+    script:
+    """
+    echo 'do this as that .. '
+    """
+}
+```
+:::note
+This setting considers the **total** errors accumulated for a given process, across all instances. If you want to control the number of times a process **instance** (aka task) can fail, use `maxRetries`.
+:::
+
+See also: [errorStrategy](#errorstrategy) and [maxRetries](#maxretries).
+
+### maxForks
+
+The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1.
+
+If you want to execute a process in a sequential manner, set this directive to one. For example:
+
+```nextflow
+process hello {
+    maxForks 1
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+### maxRetries
+
+The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the `retry` error strategy. By default only one retry is allowed, you can increase this value as shown below:
+
+```nextflow
+process hello {
+    errorStrategy 'retry'
+    maxRetries 3
+
+    script:
+    """
+    echo 'do this as that .. '
+    """
+}
+```
+
+:::note
+There is a subtle but important difference between `maxRetries` and the `maxErrors` directive. The latter defines the total number of errors that are allowed during the process execution (the same process can launch different execution instances), while the `maxRetries` defines the maximum number of times the same process execution can be retried in case of an error.
+:::
+
+See also: [errorStrategy](#errorstrategy) and [maxErrors](#maxerrors).
+
+### maxSubmitAwait
+
+The `maxSubmitAwait` directive allows you to specify how long a task can remain in submission queue without being executed.
+Elapsed this time the task execution will fail.
+
+When used along with `retry` error strategy, it can be useful to re-schedule the task to a difference queue or
+resource requirement. For example:
+
+```nextflow
+process hello {
+  errorStrategy 'retry'
+  maxSubmitAwait 10.m
+  maxRetries 3
+  queue "${task.submitAttempt==1 ? 'spot-compute' : 'on-demand-compute'}"
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+In the above example the task is submitted to the `spot-compute` on the first attempt (`task.submitAttempt==1`). If the
+task execution does not start in the 10 minutes, a failure is reported and a new submission is attempted using the
+queue named `on-demand-compute`.
+
+### memory
+
+The `memory` directive allows you to define how much memory the process is allowed to use. For example:
+
+```nextflow
+process hello {
+    memory 2.GB
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following memory unit suffix can be used when specifying the memory value:
+
+| Unit | Description |
+| ---- | ----------- |
+| B    | Bytes       |
+| KB   | Kilobytes   |
+| MB   | Megabytes   |
+| GB   | Gigabytes   |
+| TB   | Terabytes   |
+
+See [memoryUnit][stdlib-types-memoryunit] for more information.
+
+See also: [cpus](#cpus), [time](#time), [queue](#queue) and [dynamic task resources][dynamic-task-resources].
+
+### module
+
+[Environment Modules](http://modules.sourceforge.net/) is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool.
+
+If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline.
+
+In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. For example:
+
+```nextflow
+process blast {
+    module 'ncbi-blast/2.2.27'
+
+    script:
+    """
+    blastp -query <etc..>
+    """
+}
+```
+
+You can repeat the `module` directive for each module you need to load. Alternatively multiple modules can be specified in a single `module` directive by separating all the module names by using a `:` (colon) character as shown below:
+
+```nextflow
+process blast {
+    module 'ncbi-blast/2.2.27:t_coffee/10.0:clustalw/2.1'
+
+    script:
+    """
+    blastp -query <etc..>
+    """
+}
+```
+
+### penv
+
+The `penv` directive allows you to define the parallel environment to be used when submitting a parallel task to the [SGE][sge-executor] resource manager. For example:
+
+```nextflow
+process blast {
+    cpus 4
+    penv 'smp'
+    executor 'sge'
+
+    script:
+    """
+    blastp -query input_sequence -num_threads ${task.cpus}
+    """
+}
+```
+
+This configuration depends on the parallel environment provided by your grid engine installation. Refer to your cluster documentation or contact your admin to learn more about this.
+
+See also: [cpus](#cpus), [memory](#memory), [time](#time)
+
+### pod
+
+The `pod` directive allows the definition of pod specific settings, such as environment variables, secrets, and config maps, when using the [Kubernetes][k8s-executor] executor.
+
+For example:
+
+```nextflow
+process echo {
+    pod env: 'MESSAGE', value: 'hello world'
+
+    script:
+    """
+    echo $MESSAGE
+    """
+}
+```
+
+The above snippet defines an environment variable named `MESSAGE` whose value is `'hello world'`.
+
+When defined in the Nextflow configuration file, a pod setting can be defined as a map:
+
+```groovy
+process {
+    pod = [env: 'MESSAGE', value: 'hello world']
+}
+```
+
+Or as a list of maps:
+
+```groovy
+process {
+    pod = [
+        [env: 'MESSAGE', value: 'hello world'],
+        [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
+    ]
+}
+```
+
+The following options are available:
+
+##### `affinity: <config>`
+
+<AddedInVersion version="22.01.0-edge" />
+
+Specifies the pod [affinity](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#affinity-and-anti-affinity) with the given configuration.
+
+#####  `annotation: '<name>', value: '<value>'`
+
+*Can be specified multiple times*
+
+Defines a pod [annotation](https://kubernetes.io/docs/concepts/overview/working-with-objects/annotations/) with the given name and value.
+
+#####  `automountServiceAccountToken: true | false`
+
+<AddedInVersion version="22.01.0-edge" />
+
+Specifies whether to [automount service account token](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/#opt-out-of-api-credential-automounting) into the pod (default: `true`).
+
+#####  `config: '<configMap>/<key>', mountPath: '</absolute/path>'`
+
+*Can be specified multiple times*
+
+Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `ConfigMap` are exposed in that path.
+
+##### `csi: '<config>', mountPath: '</absolute/path>'`
+
+<AddedInVersion version="22.11.0-edge" />
+
+*Can be specified multiple times*
+
+Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) with the given configuration to the given path.
+
+##### `emptyDir: <config>, mountPath: '</absolute/path>'`
+
+<AddedInVersion version="22.11.0-edge" />
+
+*Can be specified multiple times*
+
+Mounts an [emptyDir](https://kubernetes.io/docs/concepts/storage/volumes/#emptydir) with the given configuration to the given path.
+
+##### `env: '<name>', config: '<configMap>/<key>'`
+
+*Can be specified multiple times*
+
+Defines an environment variable whose value is defined by the given [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) and key.
+
+##### `env: '<name>', fieldPath: '<fieldPath>'`
+
+<AddedInVersion version="21.09.1-edge" />
+
+*Can be specified multiple times*
+
+Defines an environment variable whose value is defined by the given [field path](https://kubernetes.io/docs/tasks/inject-data-application/environment-variable-expose-pod-information/#use-pod-fields-as-values-for-environment-variables) value.
+
+For example, the following pod option:
+
+```groovy
+pod = [env: 'MY_NODE_NAME', fieldPath: 'spec.nodeName']
+```
+
+Maps to the following pod spec:
+
+```yaml
+env:
+  - name: MY_NODE_NAME
+    valueFrom:
+      fieldRef:
+        fieldPath: spec.nodeName
+```
+
+##### `env: '<name>', secret: '<secret>/<key>'`
+
+*Can be specified multiple times*
+
+Defines an environment variable whose value is defined by the given [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) and key.
+
+##### `env: '<name>', value: '<value>'`
+
+*Can be specified multiple times*
+
+Defines an environment variable with the given name and value.
+
+##### `hostPath: '/host/absolute/path', mountPath: '</pod/absolute/path>'`
+
+<AddedInVersion version="23.10.0" />
+
+*Can be specified multiple times*
+
+Allows creating [hostPath](https://kubernetes.io/docs/concepts/storage/volumes/#hostpath) volume and access it with the specified `mountPath` in the pod.
+
+##### `imagePullPolicy: 'IfNotPresent' | 'Always' | 'Never'`
+
+Specifies the [image pull policy](https://kubernetes.io/docs/concepts/containers/images/#image-pull-policy) used by the pod to pull the container image.
+
+##### `imagePullSecret: '<name>'`
+
+Specifies the [image pull secret](https://kubernetes.io/docs/concepts/containers/images/#specifying-imagepullsecrets-on-a-pod) used to access a private container image registry.
+
+##### `label: '<name>', value: '<value>'`
+
+*Can be specified multiple times*
+
+Defines a pod [label](https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/) with the given name and value.
+
+##### `nodeSelector: <config>`
+
+Specifies the [node selector](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#nodeselector) with the given configuration.
+
+The configuration can be a map or a string:
+
+```groovy
+// map
+pod = [nodeSelector: [disktype: 'ssd', cpu: 'intel']]
+
+// string
+pod = [nodeSelector: 'disktype=ssd,cpu=intel']
+```
+
+##### `priorityClassName: '<name>'`
+
+<AddedInVersion version="22.01.0-edge" />
+
+Specifies the [priority class name](https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/) for pods.
+
+##### `privileged: true | false`
+
+<AddedInVersion version="22.05.0-edge" />
+
+Specifies whether the pod should run as a *privileged* container (default: `false`).
+
+##### `runAsUser: '<uid>'`
+
+Specifies the user ID with which to run the container. Shortcut for the `securityContext` option.
+
+##### `schedulerName: '<name>'`
+
+Specifies which [scheduler](https://kubernetes.io/docs/tasks/extend-kubernetes/configure-multiple-schedulers/#specify-schedulers-for-pods) is used to schedule the container.
+
+##### `secret: '<secret>/<key>', mountPath: '</absolute/path>'`
+
+*Can be specified multiple times*
+
+Mounts a [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `Secret` are exposed in that path.
+
+##### `securityContext: <config>`
+
+Specifies the pod [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) with the given configuration.
+
+##### `toleration: <config>`
+
+<AddedInVersion version="22.04.0" />
+
+*Can be specified multiple times*
+
+Specifies the pod [toleration](https://kubernetes.io/docs/concepts/scheduling-eviction/taint-and-toleration/) with the given configuration.
+
+The configuration should be a map corresponding to a single toleration rule. For example, the following pod options:
+
+```groovy
+pod = [
+  [toleration: [key: 'key1', operator: 'Equal', value: 'value1', effect: 'NoSchedule']],
+  [toleration: [key: 'key1', operator: 'Exists', effect: 'NoSchedule']],
+]
+```
+
+Maps to the following pod spec:
+
+```yaml
+tolerations:
+  - key: "key1"
+    operator: "Equal"
+    value: "value1"
+    effect: "NoSchedule"
+  - key: "key1"
+    operator: "Exists"
+    effect: "NoSchedule"
+```
+
+##### `ttlSecondsAfterFinished`
+
+<AddedInVersion version="24.02.0-edge" />
+
+Specifies the [TTL mechanism](https://kubernetes.io/docs/concepts/workloads/controllers/job/#ttl-mechanism-for-finished-jobs) for finished jobs in seconds. Applies to both successful and failed jobs.
+
+##### `volumeClaim: '<name>', mountPath: '</absolute/path>' [, subPath: '<path>', readOnly: true | false]`
+
+*Can be specified multiple times*
+
+Mounts a [Persistent volume claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/) with the given name to the given path.
+
+The `subPath` option can be used to mount a sub-directory of the volume instead of its root.
+
+The `readOnly` option can be used to mount the volume as read-only (default: `false`)
+
+### publishDir
+
+The `publishDir` directive allows you to publish the process output files to a specified folder. For example:
+
+```nextflow
+process hello {
+    publishDir '/data/chunks'
+
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf 'Hola' | split -b 1 - chunk_
+    """
+}
+```
+
+The above example splits the string `Hola` into file chunks of a single byte. When complete the `chunk_*` output files are published into the `/data/chunks` folder.
+
+:::note
+Only files that match the declaration in the `output` block are published, not all the outputs of the process.
+:::
+
+:::tip
+The `publishDir` directive can be specified more than once in order to publish output files to different target directories based on different rules.
+:::
+
+By default files are published to the target folder creating a *symbolic link* for each process output that links the file produced into the process working directory. This behavior can be modified using the `mode` option, for example:
+
+```nextflow
+process hello {
+    publishDir '/data/chunks', mode: 'copy', overwrite: false
+
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf 'Hola' | split -b 1 - chunk_
+    """
+}
+```
+
+:::warning
+Files are copied into the specified directory in an *asynchronous* manner, so they may not be immediately available in the publish directory at the end of the process execution. For this reason, downstream processes should not try to access output files through the publish directory, but through the outputs of the originating process.
+:::
+
+Available options:
+
+##### `contentType`
+
+<AddedInVersion version="22.10.0" />
+
+*Experimental: currently only supported for S3.*
+
+Allow specifying the media content type of the published file a.k.a. [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_Types). If set to `true`, the content type is inferred from the file extension (default: `false`).
+
+##### `enabled`
+
+Enable or disable the publish rule depending on the boolean value specified (default: `true`).
+
+##### `failOnError`
+
+<AddedInVersion version="24.03.0-edge">
+The default value was changed from `false` to `true`
+</AddedInVersion>
+
+When `true` abort the execution if some file can't be published to the specified target directory or bucket for any cause (default: `true`)
+
+##### `mode`
+
+The file publishing method. Can be one of the following values:
+
+- `'copy'`: Copies the output files into the publish directory.
+- `'copyNoFollow'`: Copies the output files into the publish directory without following symlinks ie. copies the links themselves.
+- `'link'`: Creates a hard link in the publish directory for each output file.
+- `'move'`: Moves the output files into the publish directory. **Note**: this is only supposed to be used for a *terminal* process i.e. a process whose output is not consumed by any other downstream process.
+- `'rellink'`: Creates a relative symbolic link in the publish directory for each output file.
+- `'symlink'`: Creates an absolute symbolic link in the publish directory for each output file (default).
+
+##### `overwrite`
+
+When `true` any existing file in the specified folder will be overridden (default: `true` during normal pipeline execution and `false` when pipeline execution is `resumed`).
+
+##### `path`
+
+Specifies the directory where files need to be published. **Note**: the syntax `publishDir '/some/dir'` is a shortcut for `publishDir path: '/some/dir'`.
+
+##### `pattern`
+
+Specifies a [glob][glob] file pattern that selects which files to publish from the overall set of output files.
+
+##### `saveAs`
+
+A closure which, given the name of the file being published, returns the actual file name or a full path where the file is required to be stored. This can be used to rename or change the destination directory of the published files dynamically by using a custom strategy. Return the value `null` from the closure to *not* publish a file. This is useful when the process has multiple output files, but you want to publish only some of them.
+
+##### `storageClass`
+
+<AddedInVersion version="22.12.0-edge" />
+
+*Experimental: currently only supported for S3.*
+
+Allow specifying the storage class to be used for the published file.
+
+##### `tags`
+
+<AddedInVersion version="21.12.0-edge" />
+
+*Experimental: currently only supported for S3.*
+
+Allow the association of arbitrary tags with the published file e.g. `tags: [MESSAGE: 'Hello world']`.
+
+### queue
+
+The `queue` directive allows you to set the `queue` where jobs are scheduled when using a grid based executor in your pipeline. For example:
+
+```nextflow
+process hello {
+    queue 'long'
+    executor 'sge'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+:::tip
+Some grid executors support multiple queue names as a comma-separated list:
+
+```nextflow
+queue 'short,long,cn-el6'
+```
+
+However, this does not generally apply to other executors such as AWS Batch, Azure Batch, Google Batch.
+:::
+
+:::note
+This directive is only used by certain executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+### resourceLabels
+
+<AddedInVersion version="22.09.1-edge" />
+
+The `resourceLabels` directive allows you to specify custom name-value pairs that Nextflow applies to the computing resource used to carry out the process execution. Resource labels can be specified using the syntax shown below:
+
+```nextflow
+process hello {
+    resourceLabels region: 'some-region', user: 'some-username'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The limits and the syntax of the corresponding cloud provider should be taken into consideration when using resource labels.
+
+Resource labels are currently supported by the following executors:
+
+- [AWS Batch][awsbatch-executor]
+- [Azure Batch][azurebatch-executor]
+- [Google Cloud Batch][google-batch-executor]
+- [Kubernetes][k8s-executor]
+
+<AddedInVersion version="23.09.0-edge">
+Resource labels are supported for Azure Batch when using automatic pool creation.
+
+Resource labels in Azure are added to pools, rather than jobs, in order to facilitate cost analysis. A new pool will be created for each new set of resource labels, therefore it is recommended to also set `azure.batch.deletePoolsOnCompletion = true` when using process-specific resource labels.
+</AddedInVersion>
+
+See also: [label](#label)
+
+### resourcelimits
+
+<AddedInVersion version="24.04.0" />
+
+The `resourceLimits` directive allows you to specify environment-specific limits for task resource requests. Resource limits can be specified in a process:
+
+```nextflow
+process hello {
+    resourceLimits cpus: 24, memory: 768.GB, time: 72.h
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Or in the Nextflow configuration:
+
+```nextflow
+process {
+    resourceLimits = [ cpus: 24, memory: 768.GB, time: 72.h ]
+}
+```
+
+Resource limits can be defined for the following directives:
+
+- [cpus](#cpus)
+- [disk](#disk)
+- [memory](#memory)
+- [time](#time)
+
+Resource limits are a useful way to specify environment-specific limits alongside tasks with [dynamic task resources][dynamic-task-resources]. Normally, if a task requests more resources than can be provisioned (e.g. a task requests 32 cores but the largest node in the cluster has 24), the task will either fail or cause the pipeline to hang forever as it will never be scheduled. If the `resourceLimits` directive is defined with these limits, the task resources will be automatically reduced to comply with these limits before the job is submitted.
+
+### scratch
+
+The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node.
+
+This is useful when your pipeline is launched by using a grid executor, because it allows you to decrease the NFS overhead by running the pipeline processes in a temporary directory in the local disk of the actual execution node. Only the files declared as output in the process definition will be copied in the pipeline working area.
+
+In its basic form simply specify `true` at the directive value, as shown below:
+
+```nextflow
+process hello {
+    scratch true
+
+    output:
+    path 'data_out'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+By doing this, it tries to execute the script in the directory defined by the variable `$TMPDIR` in the execution node. If this variable does not exist, it will create a new temporary directory by using the Linux command `mktemp`.
+
+Nextflow creates a subdirectory within the scratch directory for each task and automatically deletes it once the task completes.
+
+:::note
+Cloud-based executors use `scratch = true` by default, since the work directory resides in object storage.
+:::
+
+The following values are supported:
+
+##### `false`
+
+Do not use a scratch directory.
+
+##### `true`
+
+Create a scratch directory in the directory defined by the `$TMPDIR` environment variable, or `$(mktemp /tmp)` if `$TMPDIR` is not set.
+
+##### `'$YOUR_VAR'`
+
+Create a scratch directory in the directory defined by the given environment variable, or `$(mktemp /tmp)` if that variable is not set. The value must use single quotes, otherwise the environment variable will be evaluated in the pipeline script context.
+
+##### `'/my/tmp/path'`
+
+Create a scratch directory in the specified directory.
+
+##### `'ram-disk'`
+
+Create a scratch directory in the RAM disk `/dev/shm/`.
+
+### secret
+
+The `secret` directive allows a process to access secrets.
+
+Secrets can be added to a process as follows:
+
+```nextflow
+process hello_secret {
+    secret 'MY_ACCESS_KEY'
+    secret 'MY_SECRET_KEY'
+
+    script:
+    """
+    your_command --access \$MY_ACCESS_KEY --secret \$MY_SECRET_KEY
+    """
+}
+```
+
+See [Secrets][secrets-page] for more information.
+
+:::warning
+Secrets are made available as environment variables in the process script. To prevent evaluation in the Nextflow script context, escape variable names with a backslash (e.g., `\$MY_ACCESS_KEY`) as shown above.
+:::
+
+:::note
+Secrets can only be used with the local or grid executors (e.g., Slurm or Grid Engine). Secrets can be used with the AWS Batch executor when launched from Seqera Platform.
+:::
+
+### shell
+
+The `shell` directive allows you to define a custom shell command for process scripts. By default, script blocks are executed with `/bin/bash -ue`.
+
+```nextflow
+process hello {
+    shell '/bin/bash', '-euo', 'pipefail'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The same directive could be specified in your Nextflow configuration as follows:
+
+```groovy
+process.shell = ['/bin/bash', '-euo', 'pipefail']
+```
+
+### spack
+
+The `spack` directive allows for the definition of the process dependencies using the [Spack](https://spack.io) package manager.
+
+Nextflow automatically sets up an environment for the given package names listed by in the `spack` directive. For example:
+
+```nextflow
+process hello {
+    spack 'bwa@0.7.15'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Multiple packages can be specified separating them with a blank space, e.g. `bwa@0.7.15 fastqc@0.11.5`.
+
+The `spack` directive also allows the specification of a Spack environment file path or the path of an existing environment directory. See [Spack][spack-page] for further details.
+
+### stageInMode
+
+The `stageInMode` directive defines how input files are staged into the process work directory. The following values are allowed:
+
+##### `'copy'`
+
+Input files are staged in the process work directory by creating a copy.
+
+##### `'link'`
+
+Input files are staged in the process work directory by creating a hard link for each of them.
+
+##### `'rellink'`
+
+Input files are staged in the process work directory by creating a symbolic link with a relative path for each of them.
+
+##### `'symlink'`
+
+Input files are staged in the process work directory by creating a symbolic link with an absolute path for each of them (default).
+
+### stageOutMode
+
+The `stageOutMode` directive defines how output files are staged out from the scratch directory to the process work directory. The following values are allowed:
+
+##### `'copy'`
+
+Output files are copied from the scratch directory to the work directory.
+
+##### `'fcp'`
+
+<AddedInVersion version="23.02.0-edge" />
+
+Output files are copied from the scratch directory to the work directory by using the [fcp](https://github.com/Svetlitski/fcp) utility (note: it must be available in your cluster computing nodes).
+
+##### `'move'`
+
+Output files are moved from the scratch directory to the work directory.
+
+##### `'rclone'`
+
+<AddedInVersion version="23.01.0-edge" />
+
+Output files are copied from the scratch directory to the work directory by using the [rclone](https://rclone.org) utility (note: it must be available in your cluster computing nodes).
+
+##### `'rsync'`
+
+Output files are copied from the scratch directory to the work directory by using the `rsync` utility.
+
+See also: [scratch](#scratch).
+
+### storeDir
+
+The `storeDir` directive allows you to define a directory that is used as a *permanent* cache for your process results.
+
+In more detail, it affects the process execution in two main ways:
+
+1. The process is executed only if the files declared in the `output` block do not exist in the directory specified by the `storeDir` directive. When the files exist the process execution is skipped and these files are used as the actual process result.
+2. Whenever a process is successfully completed the files listed in the `output` block are moved into the directory specified by the `storeDir` directive.
+
+The following example shows how to use the `storeDir` directive to create a directory containing a BLAST database for each species specified by an input parameter:
+
+```nextflow
+process make_blast_db {
+    storeDir '/db/genomes'
+
+    input:
+    path species
+
+    output:
+    path "${dbName}.*"
+
+    script:
+    dbName = species.baseName
+    """
+    makeblastdb -dbtype nucl -in ${species} -out ${dbName}
+    """
+}
+```
+
+:::warning
+If a process uses `storeDir` and all of its outputs are optional, the process will always be skipped, even if the store directory is empty. This issue can be avoided by specifying at least one required file output.
+:::
+
+:::warning
+The `storeDir` directive should not be used to publish workflow outputs. Use the [publishDir](#publishdir) directive or the [workflow output definition][workflow-output-def] instead.
+:::
+
+### tag
+
+The `tag` directive allows you to associate each process execution with a custom label, so that it will be easier to identify them in the log file or in the trace execution report. For example:
+
+```nextflow
+process hello {
+    tag "$code"
+
+    input:
+    val code
+
+    script:
+    """
+    echo $code
+    """
+}
+
+workflow {
+    channel.of('alpha', 'gamma', 'omega') | hello
+}
+```
+
+The above snippet will print a log similar to the following one, where process names contain the tag value:
+
+```
+[6e/28919b] Submitted process > hello (alpha)
+[d2/1c6175] Submitted process > hello (gamma)
+[1c/3ef220] Submitted process > hello (omega)
+```
+
+See also: [Trace file][trace-report]
+
+### time
+
+The `time` directive allows you to define how long a process is allowed to run. For example:
+
+```nextflow
+process hello {
+    time 1.h
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following time unit suffixes can be used when specifying the duration value:
+
+| Unit | Description  |
+| ---- | ------------ |
+| `ms` | Milliseconds |
+| `s`  | Seconds      |
+| `m`  | Minutes      |
+| `h`  | Hours        |
+| `d`  | Days         |
+
+See [Duration][stdlib-types-duration] for more information.
+
+:::note
+This directive is only used by certain executors. Refer to the [Executors][executor-page] page to see which executors support this directive.
+:::
+
+See also: [cpus](#cpus), [memory](#memory), [queue](#queue) and [dynamic task resources][dynamic-task-resources].
+
+[awsbatch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#aws-batch
+[azurebatch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#azure-batch
+[cache-resume-page]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx
+[channel-topic]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#topic
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[conda-page]: /nextflow_docs/nextflow_repo/docs/conda.mdx
+[dynamic-directives]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-directives
+[dynamic-task-resources]: /nextflow_docs/nextflow_repo/docs/process.mdx#dynamic-task-resources
+[executor-page]: /nextflow_docs/nextflow_repo/docs/executor.mdx
+[google-batch-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#google-cloud-batch
+[k8s-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#kubernetes
+[lsf-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#lsf
+[pbs-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#pbstorque
+[pbspro-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#pbs-pro
+[process-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[process-native]: /nextflow_docs/nextflow_repo/docs/process.mdx#native-execution
+[getstarted-resume]: /nextflow_docs/nextflow_repo/docs/your-first-script.mdx#modify-and-resume
+[secrets-page]: /nextflow_docs/nextflow_repo/docs/secrets.mdx
+[sge-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#sge
+[slurm-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#slurm
+[spack-page]: /nextflow_docs/nextflow_repo/docs/spack.mdx
+[stdlib-namespaces-workflow]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-namespaces.mdx#workflow
+[stdlib-types-duration]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#duration
+[stdlib-types-memoryunit]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#memoryunit
+[trace-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
+[wave-page]: /nextflow_docs/nextflow_repo/docs/wave.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
diff --git a/new-docs/nextflow-docs/reference/stdlib-groovy.mdx b/new-docs/nextflow-docs/reference/stdlib-groovy.mdx
new file mode 100644
index 0000000000..c41a0ef48e
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/stdlib-groovy.mdx
@@ -0,0 +1,30 @@
+---
+title: Groovy and Java classes
+description: Groovy and Java classes available to Nextflow at runtime
+---
+
+# Groovy and Java classes
+
+Any Groovy or Java class that is available to Nextflow at runtime can be used in a Nextflow script. The following classes are imported by default:
+
+- `groovy.lang.*`
+- `groovy.util.*`
+- `java.io.*`
+- `java.lang.*`
+- `java.math.BigDecimal`
+- `java.math.BigInteger`
+- `java.net.*`
+- `java.util.*`
+
+All other classes must be referenced by their fully-qualified name:
+
+```nextflow
+def vals = [1, 2, 3]
+println groovy.json.JsonOutput.toJson(vals)
+```
+
+:::note
+The set of classes in Nextflow's runtime classpath can change between different Nextflow versions. As a best practice, any code that uses classes outside the Nextflow standard library should either be refactored to only use the Nextflow standard library or be refactored as a [plugin][plugins-dev-page] with explicit dependencies.
+:::
+
+[plugins-dev-page]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/reference/stdlib-namespaces.mdx b/new-docs/nextflow-docs/reference/stdlib-namespaces.mdx
new file mode 100644
index 0000000000..03c5ac395e
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/stdlib-namespaces.mdx
@@ -0,0 +1,379 @@
+---
+title: Namespaces
+description: Namespaces in the Nextflow standard library
+---
+
+
+
+# Namespaces
+
+This page lists all of the available namespaces in the Nextflow standard library.
+
+## Global namespace
+
+The global namespace contains globally available constants and functions.
+
+### Constants
+
+##### `baseDir: Path`
+
+<DeprecatedInVersion version="20.04.0" />
+
+Alias of `workflow.projectDir`.
+
+##### `launchDir: Path`
+
+Alias of `workflow.launchDir`.
+
+##### `moduleDir: Path`
+
+Directory where a module script is located (equivalent to `projectDir` if used in the main script).
+
+
+##### `params`
+
+Map of workflow parameters specified in the config file or as command line options.
+
+
+##### `projectDir: Path`
+
+Alias of `workflow.projectDir`.
+
+##### `secrets: Map<String,String>`
+
+<AddedInVersion version="24.02.0-edge" />
+
+Map of pipeline secrets. See [Secrets][secrets-page] for more information.
+
+##### `workDir: Path`
+
+Alias of `workflow.workDir`.
+
+### Functions
+
+##### `branchCriteria( criteria: Closure ) -> Closure`
+
+Create a branch criteria to use with the [branch][operator-branch] operator.
+
+##### `env( name: String ) -> String`
+
+<AddedInVersion version="24.11.0-edge" />
+
+Get the value of the environment variable with the specified name in the Nextflow launch environment.
+
+##### `error( message: String = null )`
+
+Throw a script runtime error with an optional error message.
+
+##### `exit( exitCode: int = 0, message: String = null )`
+
+<DeprecatedInVersion version="22.06.0-edge">
+Use `error()` instead
+</DeprecatedInVersion>
+
+Stop the pipeline execution and return an exit code and optional error message.
+
+##### `file( filePattern: String, [options] ) -> Path | List<Path>`
+
+Get a file from a file name or glob pattern. Returns a collection of files if the glob pattern yields zero or multiple files.
+
+The following options are available:
+
+###### `checkIfExists: boolean`
+
+When `true`, throws an exception if the specified path does not exist in the file system (default: `false`).
+
+###### `followLinks: boolean`
+
+When `true`, follows symbolic links when traversing a directory tree, otherwise treats them as files (default: `true`).
+
+###### `glob: boolean`
+
+When `true`, interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`).
+
+###### `hidden: boolean`
+
+When `true`, includes hidden files in the resulting paths (default: `false`).
+
+
+###### `maxDepth: int`
+
+Maximum number of directory levels to visit (default: *no limit*).
+
+###### `type: String`
+
+Type of paths returned, can be `'file'`, `'dir'` or `'any'` (default: `'file'`).
+
+See also: [channel.fromPath][channel-path].
+
+##### `files( filePattern: String, [options] ) -> List<Path>`
+
+Get a collection of files from a file name or glob pattern. Supports the same options as `file()`.
+
+##### `groupKey( key, size: int ) -> GroupKey`
+
+Create a grouping key to use with the [groupTuple][operator-grouptuple] operator.
+
+##### `multiMapCriteria( criteria: Closure ) -> Closure`
+
+Create a multi-map criteria to use with the [multiMap][operator-multimap] operator.
+
+##### `print( value )`
+
+Print a value to standard output.
+
+##### `printf( format: String, values... )`
+
+Print a formatted string with the given values to standard output.
+
+##### `println( value )`
+
+Print a value to standard output with a newline.
+
+##### `sendMail( [options] )`
+
+Send an email. See [Notifications][mail-page] for more information.
+
+##### `sleep( milliseconds: long )`
+
+Sleep for the given number of milliseconds.
+
+##### `tuple( collection: List ) -> ArrayTuple`
+
+Create a tuple object from the given arguments.
+
+## `channel`
+
+The `channel` namespace contains the built-in channel factories. See [Channel factories][channel-factory] for details.
+
+## `log`
+
+The `log` namepsace contains functions for logging messages to the console.
+
+##### `error( message: String )`
+
+Log an error message to the console.
+
+This function does not terminate the pipeline -- use the global `error()` function instead.
+
+##### `info( message: String )`
+
+Log an info message to the console.
+
+##### `warn( message: String )`
+
+Log a warning message to the console.
+
+## `nextflow`
+
+The `nextflow` namespace contains information about the current Nextflow runtime.
+
+##### `build: int`
+
+Nextflow runtime build number.
+
+##### `timestamp: String`
+
+Nextflow runtime compile timestamp.
+
+##### `version: VersionNumber`
+
+Nextflow runtime version number. See [VersionNumber][stdlib-types-versionnumber] for more information.
+
+## `workflow`
+
+The `workflow` namespace contains information about the current workflow run.
+
+### Properties
+
+##### `commandLine: String`
+
+Command line as entered by the user to launch the workflow execution.
+
+##### `commitId: String`
+
+Git commit ID of the executed workflow repository.
+
+When providing a Git tag, branch name, or commit hash using the `-r` CLI option, the associated `workflow.commitId` is also populated.
+
+##### `complete: OffsetDateTime`
+
+*Available only in the `workflow.onComplete` handler*
+
+Timestamp of workflow when execution is completed.
+
+##### `configFiles: List<Path>`
+
+Configuration files used for the workflow execution.
+
+##### `container: String | Map<String,String>`
+
+Docker image used to run workflow tasks, or a map of process names to process containers when multiple images are used.
+
+##### `containerEngine: String`
+
+Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.
+
+##### `duration: Duration`
+
+*Available only in the `workflow.onComplete` handler*
+
+Time elapsed to complete workflow execution.
+
+##### `errorMessage: String`
+
+*Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+
+Error message of the task that caused the workflow execution to fail.
+
+##### `errorReport: String`
+
+*Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+
+Detailed error of the task that caused the workflow execution to fail.
+
+##### `exitStatus: int`
+
+*Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+
+Exit status of the task that caused the workflow execution to fail.
+
+##### `failOnIgnore: boolean`
+
+<AddedInVersion version="24.05.0-edge" />
+Whether the `workflow.failOnIgnore` config option was enabled.
+
+See also: [errorStrategy][process-error-strategy]
+
+##### `fusion`
+
+Namespace containing information about the current Fusion runtime.
+
+The following properties are available:
+
+###### `enabled: boolean`
+
+Whether Fusion is enabled.
+
+###### `version: String`
+
+The Fusion version being used.
+
+##### `homeDir: Path`
+
+User system home directory.
+
+##### `launchDir: Path`
+
+Directory where the workflow was launched.
+
+##### `manifest`
+
+Namespace corresponding to the [`manifest`][config-manifest] config scope.
+
+##### `outputDir: Path`
+
+<AddedInVersion version="24.10.0" />
+
+Workflow output directory.
+
+##### `preview: boolean`
+
+<AddedInVersion version="24.04.0" />
+
+Whether the current workflow run is a preview run.
+
+##### `profile: String`
+
+Comma-separated list of active configuration profiles.
+
+##### `projectDir: Path`
+
+Directory where the workflow project is located.
+
+##### `repository: String`
+
+Project repository Git remote URL.
+
+##### `resume: boolean`
+
+Returns `true` whenever the current instance is resumed from a previous execution.
+
+##### `revision: String`
+
+Git branch/tag of the executed workflow repository.
+
+When providing a Git tag or branch name using the `-r` CLI option, the `workflow.revision` is also populated.
+
+##### `runName: String`
+
+Mnemonic name assigned to this execution instance.
+
+##### `scriptFile: Path`
+
+Project main script file path.
+
+##### `scriptId: String`
+
+Project main script unique hash ID.
+
+##### `scriptName: String`
+
+Project main script file name.
+
+##### `sessionId: UUID`
+
+Unique identifier (UUID) associated to current execution.
+
+##### `start: OffsetDateTime`
+
+Timestamp of workflow at execution start.
+
+##### `stubRun: boolean`
+
+Returns `true` whenever the current instance is a stub-run execution .
+
+##### `success: boolean`
+
+*Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+
+Reports if the execution completed successfully.
+
+##### `userName: String`
+
+User system account name.
+
+##### `wave`
+
+Namespace containing Wave runtime information.
+
+The following properties are available:
+
+###### `enabled: boolean`
+
+Whether Wave is enabled.
+
+##### `workDir: Path`
+
+The directory where task temporary files are stored.
+
+### Functions
+
+##### `onComplete( action: Closure )`
+
+Define an action to take when the workflow completes (whether successful or not).
+
+##### `onError( action: Closure )`
+
+Define an action to take if the workflow is terminated due to a runtime error or task failure.
+
+[channel-factory]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx
+[channel-path]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#frompath
+[config-manifest]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#manifest
+[mail-page]: /nextflow_docs/nextflow_repo/docs/notifications.mdx
+[operator-branch]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#branch
+[operator-grouptuple]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#grouptuple
+[operator-multimap]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#multimap
+[process-error-strategy]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#errorstrategy
+[secrets-page]: /nextflow_docs/nextflow_repo/docs/secrets.mdx
+[stdlib-types-versionnumber]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#versionnumber
diff --git a/new-docs/nextflow-docs/reference/stdlib-types.mdx b/new-docs/nextflow-docs/reference/stdlib-types.mdx
new file mode 100644
index 0000000000..1544f1612a
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/stdlib-types.mdx
@@ -0,0 +1,1252 @@
+---
+title: Types
+description: Types in the Nextflow standard library
+---
+
+# Types
+
+This page describes the standard types in the Nextflow standard library.
+
+## Bag\<E\>
+
+*Implements the [Iterable\<E\>][stdlib-types-iterable] trait.*
+
+A bag is an unordered collection.
+
+The following operations are supported for bags:
+
+##### `+ : (Bag<E>, Bag<E>) -> Bag<E>`
+
+Concatenates two bags.
+
+##### `in, !in : (E, Bag<E>) -> Boolean`
+
+Given a value and a bag, returns `true` if the bag contains the value (or not).
+
+:::note
+Lists in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Collection.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Collection.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## Boolean
+
+A boolean can be `true` or `false`.
+
+The following operations are supported for booleans:
+
+- `&&`: logical AND
+- `||`: logical OR
+- `!`: logical NOT
+
+:::note
+Booleans in Nextflow can be backed by any of the following Java types: `boolean`, `Boolean`.
+:::
+
+## Channel\<E\>
+
+A channel (also known as a *dataflow channel* or *queue channel*) is an asynchronous sequence of values of type `E`. It is used to facilitate dataflow logic in a workflow.
+
+See [Dataflow][dataflow-page] for an overview of dataflow types. See [Operators][operator-page] or the available methods for channels.
+
+## Duration
+
+A Duration represents a duration of time with millisecond precision.
+
+A Duration can be created by adding a unit suffix to an integer (e.g. `1.h`), or by explicitly casting to `Duration`:
+
+```nextflow
+// integer with suffix
+oneDay = 24.h
+
+// integer value (milliseconds)
+oneSecond = 1000 as Duration
+
+// simple string value
+oneHour = '1h' as Duration
+
+// complex string value
+complexDuration = '1day 6hours 3minutes 30seconds' as Duration
+```
+
+The following suffixes are available:
+
+| Unit                            | Description  |
+| ------------------------------- | ------------ |
+| `ms`, `milli`, `millis`         | Milliseconds |
+| `s`, `sec`, `second`, `seconds` | Seconds      |
+| `m`, `min`, `minute`, `minutes` | Minutes      |
+| `h`, `hour`, `hours`            | Hours        |
+| `d`, `day`, `days`              | Days         |
+
+Durations can be compared like numbers, and they support basic arithmetic operations:
+
+```nextflow
+a = 1.h
+b = 2.h
+
+assert a < b
+assert a + a == b
+assert b - a == a
+assert a * 2 == b
+assert b / 2 == a
+```
+
+The following methods are available for a Duration:
+
+##### `toDays() -> Integer`
+
+Get the duration value in days (rounded down).
+
+##### `toHours() -> Integer`
+
+Get the duration value in hours (rounded down).
+
+##### `toMillis() -> Integer`
+
+Get the duration value in milliseconds.
+
+##### `toMinutes() -> Integer`
+
+Get the duration value in minutes (rounded down).
+
+##### `toSeconds() -> Integer`
+
+Get the duration value in seconds (rounded down).
+
+:::note
+These methods are also available as `getDays()`, `getHours()`, `getMillis()`, `getMinutes()`, and `getSeconds()`.
+:::
+
+## Float
+
+A float is a floating-point number (i.e. real number) that can be positive or negative.
+
+The following operations are supported for floats:
+
+- `+, -, *, /`: addition, subtraction, multiplication, division
+- `**`: exponentation
+
+:::note
+Floats in Nextflow can be backed by any of the following Java types: `float`, `double`, `Float`, `Double`.
+:::
+
+## Integer
+
+An integer is a whole number that can be positive or negative.
+
+The following operations are supported for integers:
+
+- `+, -, *, /`: addition, subtraction, multiplication, integer division
+- `%`: remainder of integer division (i.e. modulus)
+- `**`: exponentation
+- `&`, `|`, `^`, `~`: bitwise AND, OR, XOR, NOT
+- `<<`, `>>`: left and right bit-shift
+
+:::note
+Integers in Nextflow can be backed by any of the following Java types: `int`, `long`, `Integer`, `Long`.
+:::
+
+## Iterable\<E\>
+
+*Implemented by the following types: [Bag\<E\>][stdlib-types-bag], [List\<E\>][stdlib-types-list], [Set\<E\>][stdlib-types-set]*
+
+`Iterable` is a trait implemented by collection types that support iteration.
+
+Types that implement `Iterable` can be passed as an `Iterable` parameter of a method, and they can use all of the methods described below.
+
+The following methods are available for iterables:
+
+##### `any( condition: (E) -> Boolean ) -> Boolean`
+
+Returns `true` if any element in the iterable satisfies the given condition.
+
+##### `collect( transform: (E) -> R ) -> Iterable<R>`
+
+Returns a new iterable with each element transformed by the given closure.
+
+##### `collectMany( transform: (E) -> Iterable<R> ) -> Iterable<R>`
+
+Transforms each element in the iterable into a collection with the given closure and concatenates the resulting collections into a list.
+
+##### `contains( value: E ) -> Boolean`
+
+Returns `true` if the iterable contains the given value.
+
+##### `each( action: (E) -> () )`
+
+Invokes the given closure for each element in the iterable.
+
+##### `every( condition: (E) -> Boolean ) -> Boolean`
+
+Returns `true` if every element in the iterable satisfies the given condition.
+
+##### `findAll( condition: (E) -> Boolean ) -> Iterable<E>`
+
+Returns the elements in the iterable that satisfy the given condition.
+
+##### `groupBy( transform: (E) -> K ) -> Map<K,Iterable<E>>`
+
+Collect the elements of an iterable into groups based on a matching key. The closure should return the key for a given element.
+
+##### `inject( accumulator: (E,E) -> E ) -> E`
+
+Apply the given accumulator to each element in the iterable and return the final accumulated value. The closure should accept two parameters, corresponding to the current accumulated value and the current iterable element, and return the next accumulated value.
+
+The first element from the iterable is used as the initial accumulated value.
+
+##### `inject( initialValue: R, accumulator: (R,E) -> R ) -> R`
+
+Apply the given accumulator to each element in the iterable and return the final accumulated value. The closure should accept two parameters, corresponding to the current accumulated value and the current iterable element, and return the next accumulated value.
+
+##### `isEmpty() -> Boolean`
+
+Returns `true` if the iterable is empty.
+
+##### `join( separator: String = '' ) -> String`
+
+Concatenates the string representation of each element in the iterable, with the given string as the separator between each element.
+
+##### `max() -> E`
+
+Returns the maximum element in the iterable.
+
+##### `max( comparator: (E) -> R ) -> E`
+
+Returns the maximum element in the iterable according to the given closure.
+
+The closure should follow the same semantics as the closure parameter of `toSorted()`.
+
+##### `max( comparator: (E,E) -> Integer ) -> E`
+
+Returns the maximum element in the iterable according to the given closure.
+
+The closure should follow the same semantics as the closure parameter of `toSorted()`.
+
+##### `min() -> E`
+
+Returns the minimum element in the iterable.
+
+##### `min( comparator: (E,E) -> Integer ) -> E`
+
+Returns the minimum element in the iterable according to the given closure.
+
+The closure should follow the same semantics as the closure parameter of `toSorted()`.
+
+##### `size() -> Integer`
+
+Returns the number of elements in the iterable.
+
+##### `sum() -> E`
+
+Returns the sum of the elements in the iterable. The elements should support addition (`+`).
+
+##### `sum( transform: (E) -> R ) -> R`
+
+Transforms each element in the iterable with the given closure and returns the sum. The values returned by the closure should support addition (`+`).
+
+##### `toList() -> List<E>`
+
+Converts the iterable to a list.
+
+:::danger
+Converting an unordered collection to a list can lead to non-deterministic behavior. Consider using `toSorted()` instead to ensure a deterministic ordering. See [Non-deterministic process inputs][cache-nondeterministic-inputs] for more information.
+:::
+
+##### `toSet() -> Set<E>`
+
+Converts the iterable to a set. Duplicate elements are excluded.
+
+##### `toSorted() -> List<E>`
+
+Returns a sorted list of the iterable's elements.
+
+##### `toSorted( comparator: (E) -> R ) -> List<E>`
+
+Returns the iterable as a list sorted according to the given closure.
+
+The closure should accept one parameter and transform each element into the value that will be used for comparisons.
+
+##### `toSorted( comparator: (E,E) -> Integer ) -> List<E>`
+
+Returns the iterable as a list sorted according to the given closure.
+
+The closure should accept two parameters and return a negative integer, zero, or a positive integer to denote whether the first argument is less than, equal to, or greater than the second.
+
+##### `toUnique() -> Iterable<E>`
+
+Returns a shallow copy of the iterable with duplicate elements excluded.
+
+**`toUnique( comparator: (E) -> R ) -> Iterable<E>`**
+
+##### `toUnique( comparator: (E,E) -> Integer ) -> Iterable<E>`
+
+Returns a shallow copy of the iterable with duplicate elements excluded.
+
+The closure should follow the same semantics as the closure parameter of `toSorted()`.
+
+:::note
+Iterables in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Iterable.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/Iterable.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## List\<E\>
+
+*Implements the [Iterable\<E\>][stdlib-types-iterable] trait.*
+
+A list is an ordered collection of elements of type `E`. See [Lists][script-list] for an overview.
+
+The following operations are supported for lists:
+
+##### `+ : (List<E>, List<E>) -> List<E>`
+
+Concatenates two lists.
+
+##### `* : (List<E>, Integer) -> List<E>`
+
+Given a list and an integer *n*, repeats the list *n* times.
+
+##### `[] : (List<E>, Integer) -> E`
+
+Given a list and an index, returns the element at the given index in the list, or `null` if the index is out of range.
+
+##### `in, !in : (E, List<E>) -> Boolean`
+
+Given a value and a list, returns `true` if the list contains the value (or not).
+
+The following methods are available for a list:
+
+##### `collate( size: Integer, keepRemainder: Boolean = true ) -> List<List<E>>`
+
+Collates the list into a list of sub-lists of length `size`. If `keepRemainder` is `true`, any remaining elements are included as a partial sub-list, otherwise they are excluded.
+
+For example:
+```nextflow
+assert [1, 2, 3, 4, 5, 6, 7].collate(3)        == [[1, 2, 3], [4, 5, 6], [7]]
+assert [1, 2, 3, 4, 5, 6, 7].collate(3, false) == [[1, 2, 3], [4, 5, 6]]
+```
+
+##### `collate( size: Integer, step: Integer, keepRemainder: Boolean = true ) -> List<List<E>>`
+
+Collates the list into a list of sub-lists of length `size`, stepping through the list `step` elements for each sub-list. If `keepRemainder` is `true`, any remaining elements are included as a partial sub-list, otherwise they are excluded.
+
+For example:
+
+```nextflow
+assert [1, 2, 3, 4].collate(3, 1)        == [[1, 2, 3], [2, 3, 4], [3, 4], [4]]
+assert [1, 2, 3, 4].collate(3, 1, false) == [[1, 2, 3], [2, 3, 4]]
+```
+
+##### `find( condition: (E) -> Boolean ) -> E`
+
+Returns the first element in the list that satisfies the given condition.
+
+##### `first() -> E`
+
+Returns the first element in the list. Raises an error if the list is empty.
+
+##### `getIndices() -> List<Integer>`
+
+Returns the list of integers from 0 to *n - 1*, where *n* is the number of elements in the list.
+
+##### `head() -> E`
+
+Equivalent to `first()`.
+
+##### `indexOf( value: E ) -> Integer`
+
+Returns the index of the first occurrence of the given value in the list, or -1 if the list does not contain the value.
+
+##### `init() -> List<E>`
+
+Returns a shallow copy of the list with the last element excluded.
+
+##### `last() -> E`
+
+Returns the last element in the list. Raises an error if the list is empty.
+
+##### `reverse() -> List<E>`
+
+Returns a shallow copy of the list with the elements reversed.
+
+##### `subList( fromIndex: Integer, toIndex: Integer ) -> List<E>`
+
+Returns the portion of the list between the given `fromIndex` (inclusive) and `toIndex` (exclusive).
+
+##### `tail() -> List<E>`
+
+Returns a shallow copy of the list with the first element excluded.
+
+##### `take( n: Integer ) -> List<E>`
+
+Returns the first *n* elements of the list.
+
+##### `takeWhile( condition: (E) -> Boolean ) -> List<E>`
+
+Returns the longest prefix of the list where each element satisfies the given condition.
+
+##### `withIndex() -> List<(E,Integer)>`
+
+Returns a list of 2-tuples corresponding to the value and index of each element in the list.
+
+:::note
+Lists in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/List.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/List.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## Map\<K,V\>
+
+A map associates or "maps" keys of type `K` to values of type `V`. Each key can map to at most one value -- a map cannot contain duplicate keys. See [Maps][script-map] for an overview.
+
+The following operations are supported for maps:
+
+`+ : (Map<K,V>, Map<K,V>) -> Map<K,V>`
+
+Concatenates two maps. If a key exists in both maps, the mapping from the right-hand side is used.
+
+##### `[] : (Map<K,V>, K) -> V`
+
+Given a map and a key, returns the value for the given key in the map, or `null` if the key is not in the map.
+
+##### `in, !in : (K, Map<K,V>) -> Boolean`
+
+Given a key and a map, returns `true` if the map contains the key and the corresponding value is *truthy* (e.g. not `null`, `0`, or `false`).
+
+The following methods are available for a map:
+
+##### `any( condition: (K,V) -> Boolean ) -> Boolean`
+
+Returns `true` if any key-value pair in the map satisfies the given condition. The closure should accept two parameters corresponding to the key and value of an entry.
+
+##### `containsKey( key: K ) -> Boolean`
+
+Returns `true` if the map contains a mapping for the given key.
+
+##### `containsValue( value: V ) -> Boolean`
+
+Returns `true` if the map maps one or more keys to the given value.
+
+##### `each( action: (K,V) -> () )`
+
+Invokes the given closure for each key-value pair in the map. The closure should accept two parameters corresponding to the key and value of an entry.
+
+##### `entrySet() -> Set<(K,V)>`
+
+Returns a set of the key-value pairs in the map.
+
+##### `every( condition: (K,V) -> Boolean ) -> Boolean`
+
+Returns `true` if every key-value pair in the map satisfies the given condition. The closure should accept two parameters corresponding to the key and value of an entry.
+
+##### `isEmpty() -> Boolean`
+
+Returns `true` if the map is empty.
+
+##### `keySet() -> Set<K>`
+
+Returns a set of the keys in the map.
+
+##### `size() -> Integer`
+
+Returns the number of key-value pairs in the map.
+
+##### `subMap( keys: Iterable<K> ) -> Map<K,V>`
+
+Returns a sub-map containing the given keys.
+
+##### `values() -> Bag<V>`
+
+Returns a collection of the values in the map.
+
+:::note
+Maps in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Map.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Map.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## MemoryUnit
+
+A MemoryUnit represents a quantity of bytes.
+
+A MemoryUnit can be created by adding a unit suffix to an integer (e.g. `1.GB`), or by explicitly casting to `MemoryUnit`:
+
+```nextflow
+// integer with suffix
+oneMegabyte = 1.MB
+
+// integer value (bytes)
+oneKilobyte = 1024 as MemoryUnit
+
+// string value
+oneGigabyte = '1 GB' as MemoryUnit
+```
+
+The following suffixes are available:
+
+| Unit | Description |
+| ---- | ----------- |
+| `B`  | Bytes       |
+| `KB` | Kilobytes   |
+| `MB` | Megabytes   |
+| `GB` | Gigabytes   |
+| `TB` | Terabytes   |
+| `PB` | Petabytes   |
+| `EB` | Exabytes    |
+| `ZB` | Zettabytes  |
+
+:::note
+Technically speaking, a kilobyte is equal to 1000 bytes, whereas 1024 bytes is called a "kibibyte" and abbreviated as "KiB", and so on for the other units. In practice, however, kilobyte is commonly understood to mean 1024 bytes, and Nextflow follows this convention in its implementation as well as this documentation.
+:::
+
+Memory units can be compared like numbers, and they support basic arithmetic operations:
+
+```nextflow
+a = 1.GB
+b = 2.GB
+
+assert a < b
+assert a + a == b
+assert b - a == a
+assert a * 2 == b
+assert b / 2 == a
+```
+
+The following methods are available for a `MemoryUnit` object:
+
+##### `toBytes() -> Integer`
+
+Get the memory value in bytes (B).
+
+##### `toGiga() -> Integer`
+
+Get the memory value in gigabytes (rounded down), where 1 GB = 1024 MB.
+
+##### `toKilo() -> Integer`
+
+Get the memory value in kilobytes (rounded down), where 1 KB = 1024 B.
+
+##### `toMega() -> Integer`
+
+Get the memory value in megabytes (rounded down), where 1 MB = 1024 KB.
+
+##### `toUnit( unit: String ) -> Integer`
+
+Get the memory value in terms of a given unit (rounded down). The unit can be one of: `'B'`, `'KB'`, `'MB'`, `'GB'`, `'TB'`, `'PB'`, `'EB'`, `'ZB'`.
+
+:::note
+These methods are also available as `getBytes()`, `getGiga()`, `getKilo()`, and `getMega()`.
+:::
+
+## Path
+
+A Path is a handle for hierarchichal paths such as local files and directories, HTTP/FTP URLs, and object storage paths (e.g. Amazon S3).
+
+The `file()` function can be used to get a Path for a given filename or URL:
+
+```nextflow
+def hello = file('hello.txt')
+println hello.text
+```
+
+The `files()` function can be used to get a collection of Paths from a glob pattern:
+
+```nextflow
+def inputs = files('*.txt')
+inputs.each { input ->
+  println "${input.name}: ${input.text}"
+}
+```
+
+The following sections describe the methods that are available for paths.
+
+:::note
+Paths in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/nio/file/Path.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/nio/file/Path.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+<h3>Operations</h3>
+
+The following operations are supported for paths:
+
+##### `/ : (Path, String) -> Path`
+
+Resolves a relative path string against a directory path. Equivalent to `resolve()`.
+
+##### `<< : (Path, String)`
+
+Appends text to a file without replacing existing content. Equivalent to `append()`.
+
+<h3>Getting attributes</h3>
+
+The following methods are useful for getting attributes of a path:
+
+##### `exists() -> Boolean`
+
+Returns `true` if the path exists.
+
+##### `getBaseName() -> String`
+
+Gets the path name without its extension, e.g. `/some/path/file.tar.gz` -> `file.tar`.
+
+##### `getExtension() -> String`
+
+Gets the path extension, e.g. `/some/path/file.txt` -> `txt`.
+
+##### `getName() -> String`
+
+Gets the path name, e.g. `/some/path/file.txt` -> `file.txt`.
+
+##### `getSimpleName() -> String`
+
+Gets the path name without any extension, e.g. `/some/path/file.tar.gz` -> `file`.
+
+##### `getParent() -> Path`
+
+Gets the path parent path, e.g. `/some/path/file.txt` -> `/some/path`.
+
+##### `getScheme() -> String`
+
+Gets the path URI scheme, e.g. `s3://some-bucket/hello.txt` -> `s3`.
+
+##### `isDirectory() -> Boolean`
+
+Returns `true` if the path is a directory.
+
+##### `isEmpty() -> Boolean`
+
+Returns `true` if the path is empty or does not exist.
+
+##### `isFile() -> Boolean`
+
+Returns `true` if the path is a file (i.e. not a directory).
+
+##### `isHidden() -> Boolean`
+
+Returns `true` if the path is hidden.
+
+##### `isLink() -> Boolean`
+
+Returns `true` if the path is a symbolic link.
+
+##### `lastModified() -> Integer`
+
+Returns the path last modified timestamp in Unix time (i.e. milliseconds since January 1, 1970).
+
+##### `relativize(other: Path) -> Path`
+
+Returns the relative path between this path and the given path.
+
+##### `resolve(other: String) -> Path`
+
+Resolves the given path string against this path.
+
+##### `resolveSibling(other: String) -> Path`
+
+Resolves the given path string against this path's parent path.
+
+##### `size() -> Integer`
+
+Gets the file size in bytes.
+
+##### `toUriString() -> String`
+
+Gets the file path along with the protocol scheme:
+
+```nextflow
+def ref = file('s3://some-bucket/hello.txt')
+
+assert ref.toString() == '/some-bucket/hello.txt'
+assert "$ref" == '/some-bucket/hello.txt'
+assert ref.toUriString() == 's3://some-bucket/hello.txt'
+```
+
+<h3>Reading</h3>
+
+The following methods are available for reading files:
+
+##### `eachByte( action: (byte) -> () )`
+
+Iterates over the file, applying the specified closure to each byte.
+
+##### `eachLine( action: (String) -> () )`
+
+Iterates over the file, applying the specified closure to each line.
+
+##### `getBytes() -> byte[]`
+
+Returns the file content as a byte array.
+
+##### `getText() -> String`
+
+Returns the file content as a string.
+
+##### `newInputStream() -> InputStream`
+
+Returns an [InputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/InputStream.html) object to read a binary file.
+
+##### `newReader() -> Reader`
+
+Returns a [Reader](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Reader.html) object to read a text file.
+
+##### `readLines() -> List<String>`
+
+Reads the file line by line and returns the content as a list of strings.
+
+##### `withInputStream( action: (InputStream) -> () )`
+
+Opens a file for reading and lets you access it with an [InputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/InputStream.html) object.
+
+##### `withReader( action: (Reader) -> () )`
+
+Opens a file for reading and lets you access it with a [Reader](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Reader.html) object.
+
+<h3>Writing</h3>
+
+The following methods are available for writing to files:
+
+##### `append( text: String )`
+
+Appends text to a file without replacing existing content.
+
+##### `newOutputStream() -> OutputStream`
+
+Creates an [OutputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/OutputStream.html) object that allows you to write binary data to a file.
+
+##### `newPrintWriter() -> PrintWriter`
+
+Creates a [PrintWriter](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/PrintWriter.html) object that allows you to write formatted text to a file.
+
+##### `newWriter() -> Writer`
+
+Creates a [Writer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Writer.html) object that allows you to save text data to a file.
+
+##### `setBytes( bytes: byte[] )`
+
+Writes a byte array to a file. Equivalent to setting the `bytes` property.
+
+##### `setText( text: String )`
+
+Writes text to a file. Equivalent to setting the `text` property.
+
+##### `withOutputStream( action: (OutputStream) -> () )`
+
+Applies the specified closure to an [OutputStream](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/OutputStream.html) object, closing it when finished.
+
+##### `withPrintWriter( action: (PrintWriter) -> () )`
+
+Applies the specified closure to a [PrintWriter](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/PrintWriter.html) object, closing it when finished.
+
+##### `withWriter( action: (Writer) -> () )`
+
+Applies the specified closure to a [Writer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/io/Writer.html) object, closing it when finished.
+
+##### `write( text: String )`
+
+Writes a string to a file, replacing any existing content.
+
+<h3>Filesystem operations</h3>
+
+The following methods are available for manipulating files and directories in a filesystem:
+
+##### `copyTo( target: Path )`
+
+Copies a source file or directory to a target file or directory.
+
+*When copying a file to another file:* if the target file already exists, it will be replaced.
+
+```nextflow
+file('/some/path/my_file.txt').copyTo('/another/path/new_file.txt')
+```
+
+*When copying a file to a directory:* the file will be copied into the directory, replacing any file with the same name.
+
+```nextflow
+file('/some/path/my_file.txt').copyTo('/another/path')
+```
+
+*When copying a directory to another directory:* if the target directory already exists, the source directory will be copied into the target directory, replacing any sub-directory with the same name. If the target path does not exist, it will be created automatically.
+
+```nextflow
+file('/any/dir_a').moveTo('/any/dir_b')
+```
+
+The result of the above example depends on the existence of the target directory. If the target directory exists, the source is moved into the target directory, resulting in the path `/any/dir_b/dir_a`. If the target directory does not exist, the source is just renamed to the target name, resulting in the path `/any/dir_b`.
+
+
+:::note
+The `copyTo()` function follows the semantics of the Linux command `cp -r <source> <target>`, with the following caveat: while Linux tools often treat paths ending with a slash (e.g. `/some/path/name/`) as directories, and those not (e.g. `/some/path/name`) as regular files, Nextflow (due to its use of the Java files API) views both of these paths as the same file system object. If the path exists, it is handled according to its actual type (i.e. as a regular file or as a directory). If the path does not exist, it is treated as a regular file, with any missing parent directories created automatically.
+:::
+
+##### `delete() -> Boolean`
+
+Deletes the file or directory at the given path, returning `true` if the operation succeeds, and `false` otherwise:
+
+```nextflow
+myFile = file('some/file.txt')
+result = myFile.delete()
+println result ? "OK" : "Cannot delete: $myFile"
+```
+
+If a directory is not empty, it will not be deleted and `delete()` will return `false`.
+
+##### `deleteDir() -> Boolean`
+
+Deletes a directory and all of its contents.
+
+```nextflow
+file('any/path').deleteDir()
+```
+
+##### `getPermissions() -> String`
+
+Returns a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation), e.g. `'rw-rw-r--'`.
+
+##### `list() -> List<String>`
+
+Returns the first-level elements (files and directories) of a directory as a list of strings.
+
+##### `listFiles() -> List<Path>`
+
+Returns the first-level elements (files and directories) of a directory as a list of Paths.
+
+##### `mkdir() -> Boolean`
+
+Creates a directory at the given path, returning `true` if the directory is created successfully, and `false` otherwise:
+
+```nextflow
+myDir = file('any/path')
+result = myDir.mkdir()
+println result ? "OK" : "Cannot create directory: $myDir"
+```
+
+If the parent directories do not exist, the directory will not be created and `mkdir()` will return `false`.
+
+##### `mkdirs() -> Boolean`
+
+Creates a directory at the given path, including any nonexistent parent directories:
+
+```nextflow
+file('any/path').mkdirs()
+```
+
+##### `mklink( linkName: String, [options] ) -> Path`
+
+Creates a *filesystem link* to a given path:
+
+```nextflow
+myFile = file('/some/path/file.txt')
+myFile.mklink('/user/name/link-to-file.txt')
+```
+
+Returns the Path of the link to create.
+
+Available options:
+
+###### `hard: Boolean`
+
+When `true`, creates a *hard* link, otherwise creates a *soft* (aka *symbolic*) link (default: `false`).
+
+###### `overwrite: Boolean`
+
+When `true`, overwrites any existing file with the same name, otherwise throws a [FileAlreadyExistsException](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/nio/file/FileAlreadyExistsException.html) (default: `false`).
+
+##### `moveTo( target: Path )`
+
+Moves a source file or directory to a target file or directory. Follows the same semantics as `copyTo()`.
+
+##### `renameTo( target: String ) -> Boolean`
+
+Rename a file or directory:
+
+```nextflow
+file('my_file.txt').renameTo('new_file_name.txt')
+```
+
+##### `setPermissions( permissions: String ) -> Boolean`
+
+Sets a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation):
+
+```nextflow
+myFile.setPermissions('rwxr-xr-x')
+```
+
+##### `setPermissions( owner: Integer, group: Integer, other: Integer ) -> Boolean`
+
+Sets a file's permissions using the [numeric notation](http://en.wikipedia.org/wiki/File_system_permissions#Numeric_notation), i.e. as three digits representing the **owner**, **group**, and **other** permissions:
+
+```nextflow
+myFile.setPermissions(7,5,5)
+```
+
+The following methods are available for listing and traversing directories:
+
+##### `eachDir( action: (Path) -> () )`
+
+Iterates through first-level directories only.
+
+##### `eachDirMatch( nameFilter: String, action: (Path) -> () )`
+
+Iterates through directories whose names match the given filter.
+
+##### `eachDirRecurse( action: (Path) -> () )`
+
+Iterates through directories depth-first (regular files are ignored).
+
+##### `eachFile( action: (Path) -> () )`
+
+Iterates through first-level files and directories.
+
+##### `eachFileMatch( nameFilter: String, action: (Path) -> () )`
+
+Iterates through files and directories whose names match the given filter.
+
+##### `eachFileRecurse( action: (Path) -> () )`
+
+Iterates through files and directories depth-first.
+
+<h3>Splitting files</h3>
+
+The following methods are available for splitting and counting the records in files:
+
+##### `countFasta() -> Integer`
+
+Counts the number of records in a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file. See the [splitFasta][operator-splitfasta] operator for available options.
+
+##### `countFastq() -> Integer`
+
+Counts the number of records in a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file. See the [splitFastq][operator-splitfastq] operator for available options.
+
+##### `countJson() -> Integer`
+
+Counts the number of records in a JSON file. See the [splitJson][operator-splitjson] operator for available options.
+
+##### `countLines() -> Integer`
+
+Counts the number of lines in a text file. See the [splitText][operator-splittext] operator for available options.
+
+##### `splitCsv() -> List<?>`
+
+Splits a CSV file into a list of records. See the [splitCsv][operator-splitcsv] operator for available options.
+
+##### `splitFasta() -> List<?>`
+
+Splits a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file into a list of records. See the [splitFasta][operator-splitfasta] operator for available options.
+
+##### `splitFastq() -> List<?>`
+
+Splits a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file into a list of records. See the [splitFastq][operator-splitfastq] operator for available options.
+
+##### `splitJson() -> List<?>`
+
+Splits a JSON file into a list of records. See the [splitJson][operator-splitjson] operator for available options.
+
+##### `splitText() -> List<String>`
+
+Splits a text file into a list of lines. See the [splitText][operator-splittext] operator for available options.
+
+## Set\<E\>
+
+*Implements the [Iterable\<E\>][stdlib-types-iterable] trait.*
+
+A set is an unordered collection of values of type `E` which cannot contain duplicates.
+
+A set can be created from a list using the `toSet()` method:
+
+```nextflow
+[1, 2, 2, 3].toSet()
+// -> [1, 2, 3]
+```
+
+The following operations are supported for sets:
+
+##### `+ : (Set<E>, Iterable<E>) -> Set<E>`
+
+Given a set and an iterable, returns a new set containing the elements of both collections.
+
+##### `- : (Set<E>, Iterable<E>) -> Set<E>`
+
+Given a set and an iterable, returns a shallow copy of the set minus the elements of the iterable.
+
+##### `in, !in : (E, Set<E>) -> Boolean`
+
+Given a value and a set, returns `true` if the set contains the value (or not).
+
+The following methods are available for a set:
+
+##### `intersect( right: Iterable<E> ) -> Set<E>`
+
+Returns the intersection of the set and the given iterable.
+
+:::note
+Sets in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/Set.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Set.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## String
+
+A string is an immutable sequence of characters. See [Strings][script-string] for an overview of strings.
+
+The following operations are supported for strings:
+
+##### `+ : (String, String) -> String`
+
+Concatenates two strings.
+
+##### `* : (String, Integer) -> String`
+
+Given a string and an integer *n*, repeats the string *n* times.
+
+##### `[] : (String, Integer) -> char`
+
+Given a string and an index, returns the character at the given index in the string.
+
+##### `~ : (String) -> Pattern`
+
+Creates a regular expression from a string.
+
+See [Pattern](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/regex/Pattern.html) in the Java standard library for more information.
+
+##### `=~ : (String, String) -> Matcher`
+
+Given a string and a pattern, creates a matcher that is truthy if the pattern occurs anywhere in the string.
+
+See [Matcher](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/regex/Matcher.html) in the Java standard library for more information.
+
+##### `==~ : (String, String) -> Boolean`
+
+Given a string and a pattern, returns `true` if the string matches the pattern exactly.
+
+The following methods are available for a string:
+
+##### `contains( str: String ) -> Boolean`
+
+Returns `true` if the given substring occurs anywhere in the string.
+
+##### `endsWith( suffix: String ) -> Boolean`
+
+Returns `true` if the string ends with the given suffix.
+
+##### `execute() -> Process`
+
+Execute the string as a command. Returns a [Process](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/Process.html) which provides the exit status and standard input/output/error of the executed command.
+
+##### `indexOf( str: String ) -> Integer`
+
+Returns the index within the string of the first occurrence of the given substring. Returns -1 if the string does not contain the substring.
+
+##### `indexOf( str: String, fromIndex: Integer ) -> Integer`
+
+Returns the index within the string of the first occurrence of the given substring, starting the search at the given index. Returns -1 if the string does not contain the substring.
+
+##### `isBlank() -> Boolean`
+
+Returns `true` if the string is empty or contains only whitespace characters.
+
+##### `isEmpty() -> Boolean`
+
+Returns `true` if the string is empty (i.e. `length()` is 0).
+
+##### `isDouble() -> Boolean`
+
+Returns `true` if the string can be parsed as a 64-bit (double precision) floating-point number.
+
+##### `isFloat() -> Boolean`
+
+Returns `true` if the string can be parsed as a 32-bit floating-point number.
+
+##### `isInteger() -> Boolean`
+
+Returns `true` if the string can be parsed as a 32-bit integer.
+
+##### `isLong() -> Boolean`
+
+Returns `true` if the string can be parsed as a 64-bit (long) integer.
+
+##### `lastIndexOf( str: String ) -> Integer`
+
+Returns the index within the string of the last occurrence of the given substring. Returns -1 if the string does not contain the substring.
+
+##### `lastIndexOf( str: String, fromIndex: Integer ) -> Integer`
+
+Returns the index within the string of the last occurrence of the given substring, searching backwards starting at the given index. Returns -1 if the string does not contain the substring.
+
+##### `length() -> Integer`
+
+Returns the length of the string.
+
+##### `md5() -> String`
+
+Returns the MD5 checksum of the string.
+
+##### `replace( target: String, replacement: String ) -> String`
+
+Returns a new string in which each occurrence of the target string is replaced with the given replacement string.
+
+##### `replaceAll( regex: String, replacement: String ) -> String`
+
+Returns a new string in which each occurrence of the given regular expression is replaced with the given replacement string.
+
+##### `replaceFirst( regex: String, replacement: String ) -> String`
+
+Returns a new string in which the first occurrence of the given regular expression is replaced with the given replacement string.
+
+##### `sha256() -> String`
+
+Returns the SHA-256 checksum of the string.
+
+##### `startsWith( prefix: String ) -> Boolean`
+
+Returns `true` if the string ends with the given prefix.
+
+##### `strip() -> String`
+
+Returns a copy of the string with all leading and trailing whitespace removed.
+
+##### `stripIndent() -> String`
+
+Returns a copy of the string with leading spaces on each line removed.
+
+The number of spaces to remove is determined by the line with the least number of leading spaces, excluding lines with only whitespace.
+
+##### `stripLeading() -> String`
+
+Returns a copy of the string with all leading whitespace removed.
+
+##### `stripTrailing() -> String`
+
+Returns a copy of the string with all trailing whitespace removed.
+
+##### `substring( beginIndex: Integer ) -> String`
+
+Returns a substring of this string.
+
+##### `substring( beginIndex: Integer, endIndex: Integer ) -> String`
+
+Returns a substring of this string.
+
+##### `toBoolean() -> Boolean`
+
+Returns `true` if the trimmed string is "true", "y", or "1" (ignoring case).
+
+##### `toDouble() -> Float`
+
+Parses the string into a 64-bit (double precision) floating-point number.
+
+##### `toFloat() -> Float`
+
+Parses the string into a 32-bit floating-point number.
+
+##### `toInteger() -> Integer`
+
+Parses the string into a 32-bit integer.
+
+##### `toLong() -> Integer`
+
+Parses the string into a 64-bit (long) integer.
+
+##### `toLowerCase() -> String`
+
+Returns a copy of this string with all characters converted to lower case.
+
+##### `toUpperCase() -> String`
+
+Returns a copy of this string with all characters converted to upper case.
+
+##### `tokenize( delimiters: String ) -> List<String>`
+
+Splits the string into a list of substrings using the given delimiters. Each character in the delimiter string is treated as a separate delimiter.
+
+:::note
+Strings in Nextflow are backed by the [Java](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html) and [Groovy](https://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/String.html) standard libraries, which may expose additional methods. Only methods which are recommended for use in Nextflow are documented here.
+:::
+
+## Tuple
+
+A tuple is a fixed sequence of values, where each value can have its own type. Tuples can be created using the `tuple` function.
+
+The following operations are supported for tuples:
+
+##### `[] : (Tuple, Integer) -> ?`
+
+Given a tuple and an index, returns the tuple element at the index.
+
+## Value\<V\>
+
+A dataflow value (also known as a *value channel*) is an asynchronous value of type `V`. It is used to facilitate dataflow logic in a workflow.
+
+See [Dataflow][dataflow-page] for an overview of dataflow types.
+
+The following methods are available for a dataflow value:
+
+##### `flatMap( transform: (V) -> Iterable<R> ) -> Channel<R>`
+
+Transforms the dataflow value into a collection with the given closure and emits the resulting values in a dataflow channel.
+
+##### `map( transform: (V) -> R ) -> Value<R>`
+
+Transforms the dataflow value into another dataflow value with the given closure.
+
+##### `subscribe( action: (V) -> () )`
+
+Invokes the given closure on the dataflow value.
+
+##### `view() -> Value<V>`
+
+Prints the dataflow value to standard output.
+
+##### `view( transform: (V) -> String ) -> Value<V>`
+
+Transforms the dataflow value using the given closure and print the result to standard output.
+
+## VersionNumber
+
+A VersionNumber represents a semantic or calendar version number.
+
+The following methods are available for a VersionNumber:
+
+##### `getMajor() -> String`
+
+Get the major version number, i.e. the first version component.
+
+##### `getMinor() -> String`
+
+Get the minor version number, i.e. the second version component.
+
+##### `getPatch() -> String`
+
+Get the patch version number, i.e. the third version component.
+
+##### `matches( condition: String ) -> Boolean`
+
+Check whether the version satisfies a version requirement.
+
+
+The version requirement string can be prefixed with the usual comparison operators:
+  - `=` or `==`: equal to
+  - `<` (`<=`): less than (or equal to)
+  - `>` (`>=`): greater than (or equal to)
+  - `!=` or `<>`: not equal
+
+  For example:
+
+  ```nextflow
+  if( !nextflow.version.matches('>=23.10') ) {
+      error "This workflow requires Nextflow version 23.10 or greater -- You are running version $nextflow.version"
+  }
+  ```
+
+
+Multiple constraints can be specified as a comma-separated list, e.g. `>=23.10, <=24.10`.
+
+
+Alternatively, the version can be postfixed with `+`, which is similar to `==` but also allows the last version part to be greater. For example, `23.10.1+` is satisfied by `23.10.1` and `23.10.2`, but not `23.11.x` or `23.09.x`. Additionally, `23.10.+` is equivalent to `23.10.0+`. This operator is a useful way to enforce a specific version while allowing for newer patch releases.
+
+
+[cache-nondeterministic-inputs]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#non-deterministic-process-inputs
+[dataflow-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[channel-factory]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx
+[operator-page]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx
+[operator-splitfasta]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splitfasta
+[operator-splitfastq]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splitfastq
+[operator-splitjson]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splitjson
+[operator-splittext]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splittext
+[operator-splitcsv]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#splitcsv
+[script-list]: /nextflow_docs/nextflow_repo/docs/script.mdx#lists
+[script-map]: /nextflow_docs/nextflow_repo/docs/script.mdx#maps
+[script-strings]: /nextflow_docs/nextflow_repo/docs/script.mdx#strings
+[stdlib-types-bag]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#bage
+[stdlib-types-iterable]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#iterablee
+[stdlib-types-list]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#liste
+[stdlib-types-set]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#sete
diff --git a/new-docs/nextflow-docs/reference/stdlib.mdx b/new-docs/nextflow-docs/reference/stdlib.mdx
new file mode 100644
index 0000000000..a53a1379e8
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/stdlib.mdx
@@ -0,0 +1,7 @@
+import DocCardList from "@theme/DocCardList";
+
+# Standard library
+
+This section describe the Nextflow standard library, which consists of built-in namespaces and types.
+
+<DocCardList />
diff --git a/new-docs/nextflow-docs/reference/syntax.mdx b/new-docs/nextflow-docs/reference/syntax.mdx
new file mode 100644
index 0000000000..f11c1537ff
--- /dev/null
+++ b/new-docs/nextflow-docs/reference/syntax.mdx
@@ -0,0 +1,1022 @@
+# Syntax
+
+This page provides a comprehensive description of the Nextflow language.
+
+## Comments
+
+A line comment starts with `//` and includes the rest of the line.
+
+```nextflow
+println 'Hello world!' // line comment
+```
+
+A block comment starts with `/*` and includes all subsequent characters up to the first `*/`.
+
+```nextflow
+/*
+ * block comment
+ */
+println 'Hello again!'
+```
+
+## Script declarations
+
+A Nextflow script may contain the following top-level declarations:
+
+- Shebang
+- Feature flags
+- Include declarations
+- Params block
+- Parameter declarations (legacy)
+- Workflow definitions
+- Process definitions
+- Function definitions
+- Enum types
+- Output block
+
+Script declarations are in turn composed of statements and expressions.
+
+If there are no script declarations, a script may contain one or more [statements](#statements), in which case the entire script is treated as an entry workflow. For example:
+
+```nextflow
+println 'Hello world!'
+```
+
+Is equivalent to:
+
+```nextflow
+workflow {
+    println 'Hello world!'
+}
+```
+
+:::warning
+Statements and script declarations can not be mixed at the same level.
+:::
+
+### Shebang
+
+The first line of a script can be a [shebang](https://en.wikipedia.org/wiki/Shebang_(Unix)):
+
+```sh
+#!/usr/bin/env nextflow
+```
+
+### Feature flag
+
+A feature flag declaration is an assignment. The target should be a valid [feature flag][config-feature-flags] and the source should be a literal (i.e. number, string, boolean):
+
+```nextflow
+nextflow.preview.recursion = true
+```
+
+### Include
+
+An include declaration consists of an *include source* and one or more *include clauses*:
+
+```nextflow
+include { hallo as sayHello } from './some/module'
+```
+
+The include source should be a string literal and should refer to either a local path (e.g. `./module.nf`) or a plugin (e.g. `plugin/nf-hello`). Each include clause should specify a name, and may also specify an *alias*. In the above example, `hallo` is included under the alias `sayHello`.
+
+Include clauses can be separated by semi-colons or newlines:
+
+```nextflow
+// semi-colons
+include { hallo ; bye as goodbye } from './some/module'
+
+// newlines
+include {
+    hallo
+    bye as goodbye
+} from './some/module'
+```
+
+Include clauses can also be specified as separate includes:
+
+```nextflow
+include { hallo } from './some/module'
+include { bye as goodbye } from './some/module'
+```
+
+The following definitions can be included:
+
+- Functions
+- Processes
+- Named workflows
+
+### Params block
+
+The params block consists of one or more *parameter declarations*. A parameter declaration consists of a name, type, and an optional default value:
+
+```nextflow
+params {
+    input: Path
+    save_intermeds: Boolean = false
+}
+```
+
+Only one params block may be defined in a script.
+
+### Parameter (legacy)
+
+A legacy parameter declaration is an assignment. The target should be a pipeline parameter and the source should be an expression:
+
+```nextflow
+params.message = 'Hello world!'
+```
+
+Parameters supplied via command line options, params files, and config files take precedence over parameter definitions in a script.
+
+### Workflow
+
+A workflow can be a *named workflow* or an *entry workflow*.
+
+A *named workflow* consists of a name and a body, and may consist of a *take*, *main*, and *emit* section:
+
+```nextflow
+workflow greet {
+    take:
+    greetings
+
+    main:
+    messages = greetings.map { v -> "$v world!" }
+
+    emit:
+    messages
+}
+```
+
+- The take, emit, and publish sections are optional. The `main:` section label can be omitted if they are not specified.
+
+- The take section consists of one or more parameters.
+
+- The main section consists of one or more [statements](#statements).
+
+- The emit section consists of one or more *emit statements*. An emit statement can be a [variable name](#variable), an [assignment](#assignment), or an [expression statement](#expression-statement). If an emit statement is an expression statement, it must be the only emit.
+
+
+An *entry workflow* has no name and may consist of a *main*, *publish*, *onComplete*, and *onError* section:
+
+```nextflow
+workflow {
+    main:
+    greetings = channel.of('Bonjour', 'Ciao', 'Hello', 'Hola')
+    messages = greetings.map { v -> "$v world!" }
+    greetings.view { v -> "$v world!" }
+
+    publish:
+    messages = messages
+
+    onComplete:
+    log.info 'Workflow completed successfully!'
+
+    onError:
+    log.error 'Workflow failed.'
+}
+```
+
+- Only one entry workflow may be defined in a script.
+
+- The `main:` section label can be omitted if the other sections are not specified.
+
+- The publish section consists of one or more *publish statements*. A publish statement is an [assignment](#assignment), where the assignment target is the name of a workflow output.
+
+- The `onComplete` and `onError` sections consist of one or more [statements](#statements).
+
+In order for a script to be executable, it must either define an entry workflow or be a code snippet as described [above](#script-declarations).
+
+Entry workflow definitions are ignored when a script is included as a module. This way, the same script can be included as a module or executed as a pipeline.
+
+### Process
+
+A process consists of a name and a body. The process body consists of one or more [statements](#statements). A minimal process definition must return a string:
+
+```nextflow
+process hello {
+    """
+    echo 'Hello world!'
+    """
+}
+```
+
+A process may define additional sections for *directives*, *inputs*, *outputs*, *script*, *exec*, and *stub*:
+
+```nextflow
+process greet {
+    // directives
+    errorStrategy 'retry'
+    tag { "${greeting}/${name}" }
+
+    input:
+    val greeting
+    val name
+
+    output:
+    stdout
+
+    script: // or exec:
+    """
+    echo '${greeting}, ${name}!'
+    """
+
+    stub:
+    """
+    # do nothing
+    """
+}
+```
+
+- A process must define a script or exec section (see below). All other sections are optional. Directives do not have an explicit section label, but must be defined first.
+
+- The `script:` section label can be omitted only when there are no other sections in the body.
+
+- Sections must be defined in the order shown above, with the exception of the output section, which can also be specified after the script and stub.
+
+Each section may contain one or more statements. For directives, inputs, and outputs, these statements must be [function calls](#function-call). See [Process reference][process-reference] for the set of available input qualifiers, output qualifiers, and directives.
+
+The script section can be substituted with an exec section:
+
+```nextflow
+process greet {
+    input:
+    val greeting
+    val name
+
+    exec:
+    message = "${greeting}, ${name}!"
+
+    output:
+    val message
+}
+```
+
+The script and stub sections must return a string in the same manner as a [function](#function).
+
+See [Processes][process-page] for more information on the semantics of each process section.
+
+### Process (typed)
+
+A typed process is a process that uses static types for inputs and/or outputs:
+
+```nextflow
+process greet {
+    input:
+    greeting: String
+    name: String
+
+    stage:
+    env 'NAME', name
+
+    output:
+    stdout()
+
+    topic:
+    eval('bash --version') >> 'versions'
+
+    script:
+    """
+    echo "${greeting}, \${NAME}!"
+    """
+}
+```
+
+Typed processes may specify the following sections:
+
+##### `input:`
+
+Consists of one or more process inputs. Each input has a name and type.
+
+##### `stage:`
+
+Consists of one or more stage directives. See [Inputs and outputs (typed)][inputs-and-outputs-typed] for the set of available stage directives.
+
+##### `output:`
+
+Consists of one or more *output statements*. An output statement can be a [variable name](#variable), an [assignment](#assignment), or an [expression statement](#expression-statement). An output statement must be the only output if it is an expression statement.  See [Inputs and outputs (typed)][inputs-and-outputs-typed] for the set of available output functions.
+
+##### `topic:`
+
+Consists of one or more *topic statements*. A topic statement is a right-shift expression with an output value on the left side and a string on the right side.
+
+:::note
+Typed processes use the same behavior as legacy processes for all other sections.
+:::
+
+See [Process (typed)][process-reference-typed] for more information on the semantics of typed processes.
+
+### Function
+
+A function consists of a name, parameter list, and a body:
+
+```nextflow
+def greet(greeting, name) {
+    println "${greeting}, ${name}!"
+}
+```
+
+The function body consists of one or more [statements](#statements). The last statement is implicitly treated as a return statement if it is an [expression statement](#expression-statement) that returns a value.
+
+The [return statement](#return) can be used to explicitly return from a function:
+
+```nextflow
+// return with no value
+def greet(greeting, name) {
+    if( !greeting || !name )
+        return
+    println "${greeting}, ${name}!"
+}
+
+// return a value
+def fib(x) {
+    if( x <= 1 )
+        return x
+    fib(x - 1) + fib(x - 2)
+}
+```
+
+### Enum type
+
+An enum type declaration consists of a name and a body. The body consists of a comma-separated list of identifiers:
+
+```nextflow
+enum Day {
+    MONDAY,
+    TUESDAY,
+    WEDNESDAY,
+    THURSDAY,
+    FRIDAY,
+    SATURDAY,
+    SUNDAY
+}
+```
+
+Enum values in the above example can be accessed as `Day.MONDAY`, `Day.TUESDAY`, and so on.
+
+:::note
+Enum types cannot be included across modules at this time.
+:::
+
+### Output block
+
+The output block consists of one or more *output declarations*. Each output declaration consists of a name and one or more *output directives* for defining the output:
+
+```nextflow
+output {
+    samples {
+        path 'fastq'
+        index {
+            path 'index.csv'
+        }
+    }
+}
+```
+
+Only one output block may be defined in a script. See [Workflow outputs][workflow-output-def] for the set of available output directives.
+
+## Statements
+
+Statements can be separated by either a newline or a semi-colon:
+
+```nextflow
+// newline
+println 'Hello!'
+println 'Hello again!'
+
+// semi-colon
+println 'Hello!' ; println 'Hello again!'
+```
+
+### Variable declaration
+
+Variables can be declared with the `def` keyword:
+
+```nextflow
+def x = 42
+```
+
+Multiple variables can be declared in a single statement if the initializer is a [list literal](#list) with the same number of elements and declared variables:
+
+```nextflow
+def (x, y) = [1, 2]
+```
+
+Each variable has a *scope*, which is the region of code in which the variable can be used.
+
+Variables declared in a function, as well as the parameters of that function, exist for the duration of that function call. The same applies to closures.
+
+Workflow inputs exist for the entire workflow body. Variables declared in the main section exist for the main, emit, and publish sections. Named outputs are not considered variable declarations and therefore do not have any scope.
+
+Process input variables exist for the entire process body. Variables declared in the process script, exec, and stub sections exist only in their respective section, with one exception -- variables declared without the `def` keyword also exist in the output section.
+
+Variables declared in an if or else branch exist only within that branch:
+
+```nextflow
+if( true )
+    def x = 'hello'
+println x           // error: `x` is undefined
+
+// solution: declare `x` outside of if branch
+def x
+if( true )
+    x = 'hello'
+println x
+```
+
+A variable cannot be declared with the same name as another variable in the same scope or an enclosing scope:
+
+```nextflow
+def clash(x) {
+    def x           // error: `x` is already declared
+    if( true )
+        def x       // error: `x` is already declared
+}
+```
+
+### Assignment
+
+An assignment statement consists of a *target* expression and a *source* expression separated by an equals sign:
+
+```nextflow
+v = 42
+list[0] = 'first'
+map.key = 'value'
+```
+
+The target expression must be a [variable](#variable), [index](#binary-expressions), or [property](#binary-expressions) expression. The source expression can be any expression.
+
+Multiple variables can be assigned in a single statement as long as the source expression is a [list literal](#list) with the same number of elements and assigned variables:
+
+```nextflow
+(x, y) = [1, 2]
+```
+
+### Expression statement
+
+Any [expression](#expressions) can be a statement.
+
+In general, the only expressions that can have any effect as expression statements are function calls that have side effects (e.g. `println`) or an implicit return statement in a [function](#function) or [closure](#closure).
+
+### assert
+
+An assert statement consists of the `assert` keyword followed by a boolean expression, with an optional error message separated by a colon:
+
+```nextflow
+assert 2 + 2 == 4 : 'The math broke!'
+```
+
+If the condition is false, an error will be raised with the given error message.
+
+### if/else
+
+An if/else statement consists of an *if branch* and an optional *else branch*. Each branch consists of a boolean expression in parentheses, followed by either a single statement or a *block statement* (one or more statements in curly braces). For example:
+
+```nextflow
+def x = Math.random()
+if( x < 0.5 ) {
+    println 'You lost.'
+}
+else {
+    println 'You won!'
+}
+```
+
+If the condition is true, the if branch will be executed, otherwise the else branch will be executed.
+
+If/else statements can be chained any number of times by making the else branch another if/else statement:
+
+```nextflow
+def grade = 89
+if( grade >= 90 )
+    println 'You get an A!'
+else if( grade >= 80 )
+    println 'You get a B!'
+else if( grade >= 70 )
+    println 'You get a C!'
+else if( grade >= 60 )
+    println 'You get a D!'
+else
+    println 'You failed.'
+```
+
+A more verbose way to write the same code is:
+
+```nextflow
+def grade = 89
+if( grade >= 90 ) {
+    println 'You get an A!'
+}
+else {
+    if( grade >= 80 ) {
+        println 'You get a B!'
+    }
+    else {
+        if( grade >= 70 ) {
+            println 'You get a C!'
+        }
+        else {
+            if( grade >= 60 ) {
+                println 'You get a D!'
+            }
+            else {
+                println 'You failed.'
+            }
+        }
+    }
+}
+```
+
+### return
+
+A return statement consists of the `return` keyword with an optional expression:
+
+```nextflow
+def add(a, b) {
+    return a + b
+}
+
+def sayHello(name) {
+    if( !name )
+        return
+    println "Hello, ${name}!"
+}
+```
+
+Return statements can only be used in functions and closures. In the case of a nested closure, the return statement will return from the nearest enclosing closure.
+
+If a function or closure has multiple return statements (including implicit returns), all of the return statements should either return a value or return nothing. If a function or closure does return a value, it should do so for every conditional branch.
+
+```nextflow
+def isEven1(n) {
+    if( n % 2 == 1 )
+        return          // error: return value is required here
+    return true
+}
+
+def isEven2(n) {
+    if( n % 2 == 0 )
+        return true
+                        // error: return value is required here
+}
+```
+
+:::note
+If the last statement is not a return or expression statement (implicit return), it is equivalent to appending an empty return.
+:::
+
+### throw
+
+A throw statement consists of the `throw` keyword followed by an expression that returns an error type:
+
+```nextflow
+throw new Exception('something failed!')
+```
+
+:::note
+In general, the appropriate way to raise an error is to use the [error][stdlib-namespaces-global] function:
+
+```nextflow
+error 'something failed!'
+```
+:::
+
+### try/catch
+
+A try/catch statement consists of a *try block* followed by any number of *catch clauses*:
+
+```nextflow
+def text = null
+try {
+    text = file('hello.txt').text
+}
+catch( IOException e ) {
+    log.warn "Could not load hello.txt"
+}
+```
+
+The try block will be executed, and if an error is raised and matches the expected error type of a catch clause, the code in that catch clause will be executed. If no catch clause is matched, the error will be raised to the next enclosing try/catch statement, or to the Nextflow runtime.
+
+## Expressions
+
+An expression represents a value. A *literal* value is an expression whose value is known at compile-time, such as a number, string, or boolean. All other expressions must be evaluated at run-time.
+
+Every expression has a *type*, which may be resolved at compile-time or run-time.
+
+### Variable
+
+A variable expression is a reference to a variable or other named value:
+
+```nextflow
+def x = 42
+
+x
+// -> 42
+```
+
+### Number
+
+A number literal can be an integer or floating-point number, and can be positive or negative. Integers can specified in binary with `0b`, octal with `0`, or hexadecimal with `0x`. Floating-point numbers can use scientific notation with the `e` or `E` prefix. Underscores can be used as thousands separators to make long numbers more readable.
+
+```nextflow
+// integer
+42
+-1
+0b1001  // -> 9
+031     // -> 25
+0xabcd  // -> 43981
+
+// real
+3.14
+-0.1
+1.59e7  // -> 15_900_000
+1.59e-7 // -> 0.000000159
+```
+
+### Boolean
+
+A boolean literal can be `true` or `false`:
+
+```nextflow
+assert true != false
+assert !true == false
+assert true == !false
+```
+
+### Null
+
+The null literal is specified as `null`. It can be used to represent an "empty" value:
+
+```nextflow
+def x = null
+x = 42
+```
+
+:::note
+Using a null value in certain expressions (e.g. the object of a property expression or method call) will lead to a "null reference" error. It is best to avoid the use of `null` where possible.
+:::
+
+### String
+
+A string literal consists of arbitrary text enclosed by single or double quotes:
+
+```nextflow
+println "I said 'hello'"
+println 'I said "hello" again!'
+```
+
+A triple-quoted string can span multiple lines:
+
+```nextflow
+println '''
+    Hello,
+    How are you today?
+    '''
+
+println """
+    We don't have to escape quotes anymore!
+    Even "double" quotes!
+    """
+```
+
+A *slashy string* is enclosed by slashes instead of quotes:
+
+```nextflow
+/no escape!/
+```
+
+:::note
+A slashy string cannot be empty because it would become a line comment.
+:::
+
+### Dynamic string
+
+Double-quoted strings can be interpolated using the `${}` placeholder with an expression:
+
+```nextflow
+def names = ['Thing 1', 'Thing 2']
+println "Hello, ${names.join(' and ')}!"
+// -> Hello, Thing 1 and Thing 2!
+```
+
+If the expression is a name or simple property expression (one or more identifiers separated by dots), the curly braces can be omitted:
+
+```nextflow
+def name = [first: '<FIRST_NAME>', last: '<LAST_NAME>']
+println "Hello, $name.first $name.last!"
+// -> Hello, <FIRST_NAME> <LAST_NAME>!
+```
+
+Multi-line double-quoted strings can also be interpolated:
+
+```nextflow
+"""
+blastp \
+    -in $input \
+    -out $output \
+    -db $blast_db \
+    -html
+"""
+```
+
+Single-quoted strings are not interpolated:
+
+```nextflow
+println 'Hello, ${names.join(" and ")}!'
+// -> Hello, ${names.join(" and ")}!
+```
+
+### List
+
+A list literal consists of a comma-separated list of zero or more expressions, enclosed in square brackets:
+
+```nextflow
+[1, 2, 3]
+```
+
+### Map
+
+A map literal consists of a comma-separated list of one or more *map entries*, enclosed in square brackets. Each map entry consists of a *key expression* and *value expression* separated by a colon:
+
+```nextflow
+[alpha: 1, beta: 2, gamma: 3]
+```
+
+An empty map is specified with a single colon to distinguish it from an empty list:
+
+```nextflow
+[:]
+```
+
+Both the key and value can be any expression. Identifier keys are treated as string literals (i.e. the quotes can be omitted). A variable can be used as a key by enclosing it in parentheses:
+
+```nextflow
+def x = 'alpha'
+[(x): 1]
+// -> ['alpha': 1]
+```
+
+### Closure
+
+A closure, also known as an anonymous function, consists of a parameter list followed by zero or more statements, enclosed in curly braces:
+
+```nextflow
+{ a, b -> a + b }
+```
+
+The above closure takes two arguments and returns their sum.
+
+The closure body is identical to that of a [function](#function). Statements should be separated by newlines or semi-colons, and the last statement is implicitly treated as a [return statement](#return):
+
+```nextflow
+{ v ->
+    println 'Hello!'
+    println "We're in a closure!"
+    println 'Goodbye...'
+    v * v
+}
+```
+
+Closures can access variables outside of their scope:
+
+```nextflow
+def factor = 2
+println [1, 2, 3].collect { v -> factor * v }
+// -> [2, 4, 6]
+```
+
+Closures can declare local variables that exist only for the lifetime of each closure invocation:
+
+```nextflow
+def result = 0
+[1, 2, 3].each { v ->
+    def squared = v * v
+    result += squared
+}
+
+println result
+// -> 14
+```
+
+See [standard library][stdlib-page] and [operator][operator-page] for more examples of how closures are used in practice.
+
+### Index expression
+
+An index expression consists of a *left expression* and a *right expression*, with the right expression enclosed in square brackets:
+
+```nextflow
+myList[0]
+```
+
+### Property expression
+
+A property expression consists of an *object expression* and a *property*, separated by a *dot*, *spread dot*, or *safe dot*:
+
+```nextflow
+myFile.text       // dot
+myFiles*.text     // spread dot:  myFiles.collect { myFile -> myFile.text }
+myFile?.text      // safe dot:    myFile != null ? myFile.text : null
+```
+
+The property must be an identifier or string literal.
+
+### Function call
+
+A function call consists of a name and argument list:
+
+```nextflow
+printf('Hello %s!\n', 'World')
+```
+
+A *method call* consists of an *object expression* and a function call separated by a *dot*, *spread dot*, or *safe dot*:
+
+```nextflow
+myFile.getText()    // dot
+myFiles*.getText()  // spread dot:  myFiles.collect { myFile -> myFile.getText() }
+myFile?.getText()   // safe dot:    myFile != null ? myFile.getText() : null
+```
+
+The argument list may contain any number of *positional arguments* and *named arguments*:
+
+```nextflow
+file('hello.txt', checkIfExists: true)
+```
+
+The named arguments are collected into a map and provided as the first positional argument to the function. The above function call can be rewritten as:
+
+```nextflow
+file([checkIfExists: true], 'hello.txt')
+```
+
+The argument name must be an identifier or string literal.
+
+The parentheses can be omitted when the function call is also an [expression statement](#expression-statement) and there is at least one argument:
+
+```nextflow
+// positional args
+printf 'Hello %s!\n', 'World'
+
+// positional and named args
+file 'hello.txt', checkIfExists: true
+
+// named args
+resourceLabels group: 'my-group', user: 'me'
+```
+
+If the last argument is a closure, it can be specified outside of the parentheses:
+
+```nextflow
+// closure arg with additional args
+[1, 2, 3].inject('result:') { acc, v -> acc + ' ' + v }
+
+// single closure arg
+[1, 2, 3].each() { v -> println v }
+
+// single closure arg without parentheses
+[1, 2, 3].each { v -> println v }
+```
+
+### Constructor call
+
+A constructor call consists of the `new` keyword followed by a *type name* and an argument list enclosed in parentheses:
+
+```nextflow
+new java.util.Date()
+```
+
+If the type is implicitly available in the script, the *fully-qualified type name* can be elided to the *simple type name*:
+
+```nextflow
+new Date()
+```
+
+See [Standard library][stdlib-page] for the set of types that are available in Nextflow scripts.
+
+### Unary expressions
+
+A unary expression consists of a *unary operator* followed by an expression:
+
+```nextflow
+!(2 + 2 == 4)
+```
+
+The following unary operators are available:
+
+- `~`: bitwise NOT
+- `!`: logical NOT
+- `+`: unary plus
+- `-`: unary minus
+
+### Binary expressions
+
+A binary expression consists of a *left expression* and a *right expression* separated by a *binary operator*:
+
+```nextflow
+2 + 2
+```
+
+The following binary operators are available:
+
+- `**`: power (i.e. exponentiation)
+- `*`: multiplication
+- `/`: division
+- `%`: remainder (i.e. modulo)
+- `+`: addition
+- `-`: subtraction
+- `<<`: left shift
+- `>>`: right shift
+- `>>>`: unsigned right shift
+- `..`: inclusive range
+- `..<`: right-exclusive range
+- `as`: type cast
+- `instanceof`: type relation
+- `!instanceof`: negated type relation
+- `<`: less than
+- `>`: greater than
+- `<=`: less than or equals
+- `>=`: greater than or equals
+- `in`: membership
+- `!in`: negated membership
+- `==`: equals
+- `!=`: negated equals
+- `<=>`: spaceship (i.e. three-way comparison)
+- `=~`: regex find
+- `==~`: regex match
+- `&`: bitwise AND
+- `^`: bitwise XOR (exclusive or)
+- `|`: bitwise OR
+- `&&`: logical AND
+- `||`: logical OR
+- `?:` elvis (i.e. short ternary)
+
+### Ternary expression
+
+A ternary expression consists of a *test expression*, a *true expression*, and a *false expression*, separated by a question mark and a colon:
+
+```nextflow
+println x % 2 == 0 ? 'x is even!' : 'x is odd!'
+```
+
+If the test expression is true, the true expression is evaluated, otherwise the false expression is evaluated.
+
+### Parentheses
+
+Any expression can be enclosed in parentheses:
+
+```nextflow
+1 + 2 * 3
+// -> 1 + 6 -> 7
+
+(1 + 2) * 3
+// -> 3 * 3 -> 9
+```
+
+### Precedence
+
+Compound expressions are evaluated in the following order:
+
+- parentheses
+- property expressions
+- function calls
+- index expressions
+- `~`,  `!`
+- `**`
+- `+`, `-` (unary)
+- `*`, `/`, `%`
+- `+`, `-` (binary)
+- `<<`, `>>>`, `>>`, `..`, `..<`
+- `as`
+- `instanceof`, `!instanceof`
+- `<`, `>`, `<=`, `>=`, `in`, `!in`
+- `==`, `!=`, `<=>`
+- `=~`, `==~`
+- `&`
+- `^`
+- `|`
+- `&&`
+- `||`
+- `?:` (ternary)
+- `?:` (elvis)
+
+## Deprecations
+
+The following legacy features were excluded from this page because they are deprecated:
+
+- The `addParams` and `params` clauses of include declarations. See [Module parameters][module-params] for more information.
+- The `when:` section of a process definition. See [When][process-when] for more information.
+- The `shell:` section of a process definition. See [Shell][process-shell] for more information.
+- The implicit `it` closure parameter. See [Closures][script-closure] for more information.
+
+[config-feature-flags]: /nextflow_docs/nextflow_repo/docs/reference/feature-flags.mdx
+[module-params]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-parameters
+[operator-page]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx
+[process-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[process-reference]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx
+[inputs-and-outputs-typed]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#inputs-and-outputs-typed
+[process-reference-typed]: /nextflow_docs/nextflow_repo/docs/process-typed.mdx
+[process-shell]: /nextflow_docs/nextflow_repo/docs/process.mdx#shell
+[process-when]: /nextflow_docs/nextflow_repo/docs/process.mdx#when
+[script-closure]: /nextflow_docs/nextflow_repo/docs/script.mdx#closures
+[stdlib-namespaces-global]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-namespaces.mdx
+[stdlib-page]: /nextflow_docs/nextflow_repo/docs/reference/stdlib.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
diff --git a/docs/reports.md b/new-docs/nextflow-docs/reports.mdx
similarity index 64%
rename from docs/reports.md
rename to new-docs/nextflow-docs/reports.mdx
index c198e495b1..49c876ac0c 100644
--- a/docs/reports.md
+++ b/new-docs/nextflow-docs/reports.mdx
@@ -1,18 +1,16 @@
-(tracing-page)=
 
-# Reports
 
-(execution-log)=
+# Reports
 
 ## Execution log
 
 The `nextflow log` command shows information about executed pipelines in the current folder:
 
 ```bash
-nextflow log <run name> [options]
+nextflow log <RUN_NAME> [options]
 ```
 
-:::{note}
+:::note
 Both the [execution report](#execution-report) and the [trace file](#trace-file) must be specified when the pipeline is first called. By contrast, the `log` option is useful after a pipeline has already run and is available for every executed pipeline.
 :::
 
@@ -39,7 +37,7 @@ $ nextflow log goofy_kilby
 
 ### Customizing fields
 
-By default, only the task execution paths are printed. A custom list of fields to print can be provided via the `-f` (`-fields`) option. For example:
+By default, only the task execution paths are printed. A custom list of fields to print can be provided via the `-f` (`-fields`) option:
 
 ```console
 $ nextflow log goofy_kilby -f hash,name,exit,status
@@ -50,7 +48,7 @@ ec/3100e7  mapping (ggal_gut)                                       0  COMPLETED
 94/dfdfb6  makeTranscript (ggal_gut)                                0  COMPLETED
 ```
 
-The fields accepted by the `-f` options are the ones in the {ref}`trace report<trace-fields>`, as well as: script, stdout, stderr, env. List available fields using the `-l` (`-list-fields`) option.
+The fields accepted by the `-f` options are the ones in the [trace file report][trace-file], as well as: script, stdout, stderr, env. List available fields using the `-l` (`-list-fields`) option.
 
 The `script` field is useful for examining script commands run in each task:
 
@@ -91,8 +89,6 @@ The `filter` option makes it possible to select which entries to include in the
 nextflow log goofy_kilby -filter 'name =~ /hello.*/ && status == "FAILED"'
 ```
 
-(execution-report)=
-
 ## Execution report
 
 Nextflow can create an HTML execution report: a single document which includes many useful metrics about a workflow execution. The report is organised in the three main sections: `Summary`, `Resources` and `Tasks` (see below for details).
@@ -100,7 +96,7 @@ Nextflow can create an HTML execution report: a single document which includes m
 To enable the creation of this report add the `-with-report` command line option when launching the pipeline execution. For example:
 
 ```bash
-nextflow run <pipeline> -with-report [file name]
+nextflow run main.nf -with-report [file name]
 ```
 
 The report file name can be specified as an optional parameter following the report option.
@@ -109,8 +105,7 @@ The report file name can be specified as an optional parameter following the rep
 
 The `Summary` section reports the execution status, the launch command, overall execution time and some other workflow metadata. You can see an example below:
 
-```{image} _static/report-summary-min.png
-```
+![Report summary](_static/report-summary-min.png)
 
 ### Resource Usage
 
@@ -118,31 +113,25 @@ The `Resources` section plots the distribution of resource usage for each workfl
 
 Plots are shown for CPU, memory, job duration and disk I/O. They have two (or three) tabs with the raw values and a percentage representation showing what proportion of the requested resources were used. These plots are very helpful to check that task resources are used efficiently.
 
-```{image} _static/report-resource-cpu.png
-```
-
-Learn more about how resource usage is computed in {ref}`this tutorial <metrics-page>`.
+![Usage CPUs](_static/report-resource-cpu.png)
 
-(execution-report-tasks)=
+See the [Understanding task resource metrics][metrics-page] guide to learn more about how resource usage is computed in Nextflow.
 
 ### Tasks
 
 The `Tasks` section lists all executed tasks, reporting for each of them the status, the actual command script, and many other metrics. You can see an example below:
 
-```{image} _static/report-tasks-min.png
-```
+![Tasks](_static/report-tasks-min.png)
 
-:::{note}
+:::note
 Nextflow collects these metrics through a background process for each job in the target environment. Make sure the following tools are available in the environment where tasks are executed: `awk`, `date`, `grep`, `ps`, `sed`, `tail`, `tee`. Moreover, some of these metrics are not reported when running on Mac OS X. See the corresponding note in the [trace file](#trace-file) section.
 :::
 
-:::{warning}
+:::warning
 A common problem when using a third party container image is that it does not include one or more of the above utilities, resulting in an empty execution report.
 :::
 
-Please read {ref}`Report scope <config-report>` section to learn more about the execution report configuration details.
-
-(trace-report)=
+See [Report scope][config-report] to learn more about the execution report configuration details.
 
 ## Trace file
 
@@ -151,10 +140,10 @@ Nextflow creates an execution tracing file that contains some useful information
 In order to create the execution trace file add the `-with-trace` command line option when launching the pipeline execution. For example:
 
 ```bash
-nextflow run <pipeline> -with-trace
+nextflow run main.nf -with-trace
 ```
 
-It will create a file named `trace.txt` in the current directory. The content looks like the above example:
+It will create a file named `trace.txt` in the current directory. The content looks similar the above example:
 
 | task_id | hash      | native_id | name           | status    | exit | submit                  | duration | walltime | %cpu   | rss      | vmem     | rchar    | wchar    |
 | ------- | --------- | --------- | -------------- | --------- | ---- | ----------------------- | -------- | -------- | ------ | -------- | -------- | -------- | -------- |
@@ -178,158 +167,197 @@ It will create a file named `trace.txt` in the current directory. The content lo
 | 56      | c3/ec5f4a | 2066      | similarity (5) | COMPLETED | 0    | 2014-10-23 17:13:23.948 | 30s      | 616ms    | 0.0%   | 10.4 MB  | 34.6 MB  | 238 MB   | 8.4 MB   |
 | 98      | de/d6c0a6 | 2099      | matrix (1)     | COMPLETED | 0    | 2014-10-23 17:14:27.139 | 30s      | 1s       | 0.0%   | 4.8 MB   | 42 MB    | 240.6 MB | 79 KB    |
 
-(trace-fields)=
-
 ### Trace fields
 
 The following table shows the fields that can be included in the execution report:
 
-`task_id`
-: Task ID.
+##### `task_id`
 
-`hash`
-: Task hash code.
+Task ID.
 
-`native_id`
-: Task ID given by the underlying execution system e.g. POSIX process PID when executed locally, job ID when executed by a grid engine, etc.
+##### `hash`
 
-`process`
-: Nextflow process name.
+Task hash code.
 
-`tag`
-: User provided identifier associated this task.
+##### `native_id`
 
-`name`
-: Task name.
+Task ID given by the underlying execution system e.g. POSIX process PID when executed locally, job ID when executed by a grid engine, etc.
 
-`status`
-: Task status. Possible values are: `NEW`, `SUBMITTED`, `RUNNING`, `COMPLETED`, `FAILED`, and `ABORTED`.
+##### `process`
 
-`exit`
-: POSIX process exit status.
+Nextflow process name.
 
-`module`
-: Environment module used to run the task.
+##### `tag`
 
-`container`
-: Docker image name used to execute the task.
+User provided identifier associated this task.
 
-`cpus`
-: The cpus number request for the task execution.
+##### `name`
 
-`time`
-: The time request for the task execution
+Task name.
 
-`disk`
-: The disk space request for the task execution.
+##### `status`
 
-`memory`
-: The memory request for the task execution.
+Task status. Possible values are: `NEW`, `SUBMITTED`, `RUNNING`, `COMPLETED`, `FAILED`, and `ABORTED`.
 
-`attempt`
-: Attempt at which the task completed.
+##### `exit`
 
-`submit`
-: Timestamp when the task has been submitted.
+POSIX process exit status.
 
-`start`
-: Timestamp when the task execution has started.
+##### `module`
 
-`complete`
-: Timestamp when task execution has completed.
+Environment module used to run the task.
 
-`duration`
-: Time elapsed to complete since the submission.
+##### `container`
 
-`realtime`
-: Task execution time i.e. delta between completion and start timestamp.
+Docker image name used to execute the task.
 
-`queue`
-: The queue that the executor attempted to run the process on.
+##### `cpus`
 
-`%cpu`
-: Percentage of CPU used by the process.
+The cpus number request for the task execution.
 
-`%mem`
-: Percentage of memory used by the process.
+##### `time`
 
-`rss`
-: Real memory (resident set) size of the process. Equivalent to `ps -o rss` .
+The time request for the task execution
 
-`vmem`
-: Virtual memory size of the process. Equivalent to `ps -o vsize` .
+##### `disk`
 
-`peak_rss`
-: Peak of real memory. This data is read from field `VmHWM` in `/proc/$pid/status` file.
+The disk space request for the task execution.
 
-`peak_vmem`
-: Peak of virtual memory. This data is read from field `VmPeak` in `/proc/$pid/status` file.
+##### `memory`
 
-`rchar`
-: Number of bytes the process read, using any read-like system call from files, pipes, tty, etc. This data is read from file `/proc/$pid/io`.
+The memory request for the task execution.
 
-`wchar`
-: Number of bytes the process wrote, using any write-like system call. This data is read from file `/proc/$pid/io`.
+##### `attempt`
 
-`syscr`
-: Number of read-like system call invocations that the process performed. This data is read from file `/proc/$pid/io`.
+Attempt at which the task completed.
 
-`syscw`
-: Number of write-like system call invocations that the process performed. This data is read from file `/proc/$pid/io`.
+##### `submit`
 
-`read_bytes`
-: Number of bytes the process directly read from disk. This data is read from file `/proc/$pid/io`.
+Timestamp when the task has been submitted.
 
-`write_bytes`
-: Number of bytes the process originally dirtied in the page-cache (assuming they will go to disk later). This data is read from file `/proc/$pid/io`.
+##### `start`
 
-`vol_ctxt`
-: Number of voluntary context switches. This data is read from field `voluntary_ctxt_switches` in `/proc/$pid/status` file.
+Timestamp when the task execution has started.
 
-`inv_ctxt`
-: Number of involuntary context switches. This data is read from field `nonvoluntary_ctxt_switches` in `/proc/$pid/status` file.
+##### `complete`
 
-`env`
-: The variables defined in task execution environment.
+Timestamp when task execution has completed.
 
-`workdir`
-: The directory path where the task was executed.
+##### `duration`
 
-`script`
-: The task command script.
+Time elapsed to complete since the submission.
 
-`scratch`
-: The value of the process `scratch` directive.
+##### `realtime`
 
-`error_action`
-: The action applied on error for task failure.
+Task execution time i.e. delta between completion and start timestamp.
 
-`hostname`
-: :::{versionadded} 22.05.0-edge
-  :::
-: The host on which the task was executed. Supported only for the Kubernetes executor yet. Activate with `k8s.fetchNodeName = true` in the Nextflow config file.
+##### `error_action`
 
-`cpu_model`
-: :::{versionadded} 22.07.0-edge
-  :::
-: The name of the CPU model used to execute the task. This data is read from file `/proc/cpuinfo`.
+Task execution time i.e. delta between completion and start timestamp.
 
-:::{note}
-These metrics provide an estimation of the resources used by running tasks. They are not an alternative to low-level performance analysis tools, and they may not be completely accurate, especially for very short-lived tasks (running for less than a few seconds).
-:::
+##### `queue`
+
+The queue that the executor attempted to run the process on.
+
+##### `%cpu`
+
+Percentage of CPU used by the process.
+
+##### `%mem`
+
+Percentage of memory used by the process.
+
+##### `rss`
+
+Real memory (resident set) size of the process. Equivalent to `ps -o rss` .
+
+##### `vmem`
+
+Virtual memory size of the process. Equivalent to `ps -o vsize` .
+
+##### `peak_rss`
+
+Peak of real memory. This data is read from field `VmHWM` in `/proc/$pid/status` file.
+
+##### `peak_vmem`
+
+Peak of virtual memory. This data is read from field `VmPeak` in `/proc/$pid/status` file.
+
+##### `rchar`
+
+Number of bytes the process read, using any read-like system call from files, pipes, tty, etc. This data is read from file `/proc/$pid/io`.
+
+##### `wchar`
+
+Number of bytes the process wrote, using any write-like system call. This data is read from file `/proc/$pid/io`.
+
+##### `syscr`
+
+Number of read-like system call invocations that the process performed. This data is read from file `/proc/$pid/io`.
+
+##### `syscw`
+
+Number of write-like system call invocations that the process performed. This data is read from file `/proc/$pid/io`.
+
+##### `read_bytes`
+
+Number of bytes the process directly read from disk. This data is read from file `/proc/$pid/io`.
+
+##### `write_bytes`
+
+Number of bytes the process originally dirtied in the page-cache (assuming they will go to disk later). This data is read from file `/proc/$pid/io`.
+
+##### `vol_ctxt`
 
-Trace report layout and other configuration settings can be specified by using the `nextflow.config` configuration file.
+Number of voluntary context switches. This data is read from field `voluntary_ctxt_switches` in `/proc/$pid/status` file.
 
-Please read {ref}`Trace scope <config-trace>` section to learn more about it.
+##### `inv_ctxt`
 
-(timeline-report)=
+Number of involuntary context switches. This data is read from field `nonvoluntary_ctxt_switches` in `/proc/$pid/status` file.
+
+##### `env`
+
+The variables defined in task execution environment.
+
+##### `workdir`
+
+The directory path where the task was executed.
+
+##### `script`
+
+The task command script.
+
+##### `scratch`
+
+The value of the process `scratch` directive.
+
+##### `error_action`
+
+The action applied on error task failure.
+
+##### `hostname`
+
+<AddedInVersion version="25.05.0-edge" />
+
+The host on which the task was executed. Supported only for the Kubernetes executor yet. Activate with `k8s.fetchNodeName = true` in the Nextflow config file.
+
+##### `cpu_model`
+
+<AddedInVersion version="22.07.0-edge" />
+
+The name of the CPU model used to execute the task. This data is read from file `/proc/cpuinfo`.
+
+:::note
+These metrics provide an estimation of the resources used by running tasks. They are not an alternative to low-level performance analysis tools, and they may not be completely accurate, especially for very short-lived tasks (running for less than a few seconds).
+:::
+
+Trace report layout and other configuration settings can be specified by using the `nextflow.config` configuration file. See [Trace scope][config-trace] to learn more.
 
 ## Execution timeline
 
 Nextflow can render an HTML timeline for all processes executed in your pipeline. An example of the execution timeline is shown below:
 
-```{image} _static/timeline-min.png
-```
+![Execution timeline](_static/timeline-min.png)
 
 Each bar represents a process run in the pipeline execution. The bar length represents the task duration time (wall-time). The colored area in each bar represents the real execution time. The grey area to the *left* of the colored area represents the task scheduling wait time. The grey area to the *right* of the colored area represents the task termination time (clean-up and file un-staging). The numbers on the x-axis represent the time in absolute units e.g. minutes, hours, etc.
 
@@ -340,13 +368,11 @@ As each process can spawn many tasks, colors are used to identify those tasks be
 To enable the creation of the execution timeline add the `-with-timeline` command line option when launching the pipeline execution. For example:
 
 ```bash
-nextflow run <pipeline> -with-timeline [file name]
+nextflow run main.nf -with-timeline [file name]
 ```
 
 The report file name can be specified as an optional parameter following the timeline option.
 
-(workflow-diagram)=
-
 ## Workflow diagram
 
 A Nextflow pipeline can be represented as a direct acyclic graph (DAG). The vertices in the graph represent the pipeline's processes and operators, while the edges represent the data dependencies (i.e. channels) between them.
@@ -356,47 +382,52 @@ To render the workflow DAG, run your pipeline with the `-with-dag` option. By de
 The workflow DAG can be rendered in a different format by specifying an output file name with a different extension based on the desired format. For example:
 
 ```bash
-nextflow run <pipeline> -with-dag flowchart.png
+nextflow run main.nf -with-dag flowchart.png
 ```
 
-:::{versionadded} 22.06.0-edge
-You can use the `-preview` option with `-with-dag` to render the workflow DAG without executing any tasks.
-:::
-
-:::{versionchanged} 23.10.0
+<ChangedInVersion version="23.10.0">
 The default output format was changed from DOT to HTML.
-:::
+</ChangedInVersion>
 
 The following file formats are supported:
 
-`dot`
-: Graphviz [DOT](http://www.graphviz.org/content/dot-language) file
+##### `dot`
+
+Graphviz [DOT](http://www.graphviz.org/content/dot-language) file
+
+##### `gexf`
+
+Graph Exchange XML file (Gephi)
 
-`gexf`
-: Graph Exchange XML file (Gephi)
+##### `html`
 
-`html`
-: HTML file with Mermaid diagram
-: :::{versionchanged} 23.10.0
-  The HTML format was changed to render a Mermaid diagram instead of a Cytoscape diagram.
-  :::
+HTML file with Mermaid diagram
 
-`mmd`
-: :::{versionadded} 22.04.0
-  :::
-: Mermaid diagram
+<ChangedInVersion version="23.10.0">
+The HTML format was changed to render a Mermaid diagram instead of a Cytoscape diagram.
+</ChangedInVersion>
 
-`pdf`
-: *Requires [Graphviz](http://www.graphviz.org) to be installed*
-: Graphviz PDF file
+##### `mmd`
 
-`png`
-: *Requires [Graphviz](http://www.graphviz.org) to be installed*
-: Graphviz PNG file
+Mermaid diagram
 
-`svg`
-: *Requires [Graphviz](http://www.graphviz.org) to be installed*
-: Graphviz SVG file
+##### `pdf`
+
+*Requires [Graphviz](http://www.graphviz.org) to be installed*
+
+Graphviz PDF file
+
+##### `png`
+
+*Requires [Graphviz](http://www.graphviz.org) to be installed*
+
+Graphviz PNG file
+
+##### `svg`
+
+*Requires [Graphviz](http://www.graphviz.org) to be installed*
+
+Graphviz SVG file
 
 Here is the Mermaid diagram produced by Nextflow for the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline (using the [Mermaid Live Editor](https://mermaid-js.github.io/mermaid-live-editor/edit) with the `default` theme):
 
@@ -404,5 +435,49 @@ Here is the Mermaid diagram produced by Nextflow for the [rnaseq-nf](https://git
 nextflow run rnaseq-nf -preview -with-dag
 ```
 
-```{mermaid} _static/dag.mmd
+```mermaid
+%%{
+    init: {
+        'theme': 'base',
+        'themeVariables': {
+            'primaryColor': '#B6ECE2',
+            'primaryTextColor': '#160F26',
+            'primaryBorderColor': '#065647',
+            'lineColor': '#545555',
+            'clusterBkg': '#BABCBD22',
+            'clusterBorder': '#DDDEDE',
+            'fontFamily': 'degular'
+        }
+    }
+}%%
+flowchart TB
+    subgraph " "
+    v0["Channel.fromFilePairs"]
+    v1["transcriptome"]
+    v7["config"]
+    end
+    subgraph RNASEQ
+    v2([INDEX])
+    v3([FASTQC])
+    v4([QUANT])
+    end
+    v8([MULTIQC])
+    subgraph " "
+    v9[" "]
+    end
+    v5(( ))
+    v0 --> v3
+    v0 --> v4
+    v1 --> v2
+    v2 --> v4
+    v3 --> v5
+    v4 --> v5
+    v7 --> v8
+    v5 --> v8
+    v8 --> v9
 ```
+
+[metrics-page]: /nextflow_docs/nextflow_repo/docs/tutorials/metrics.mdx
+[config-report]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#report
+[config-trace]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#trace
+[trace-file]: /nextflow_docs/nextflow_repo/docs/reports.mdx#trace-file
diff --git a/new-docs/nextflow-docs/requirements.txt b/new-docs/nextflow-docs/requirements.txt
new file mode 100644
index 0000000000..486718f0cc
--- /dev/null
+++ b/new-docs/nextflow-docs/requirements.txt
@@ -0,0 +1,7 @@
+myst-parser==0.18.1
+sphinx==5.3.0
+sphinx-rtd-theme==1.1.1
+sphinxcontrib-mermaid==0.9.2
+sphinxext-rediraffe==0.2.7
+sphinx-tabs==3.4.5
+sphinx-copybutton==0.5.2
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/script.mdx b/new-docs/nextflow-docs/script.mdx
new file mode 100644
index 0000000000..bab179ea8c
--- /dev/null
+++ b/new-docs/nextflow-docs/script.mdx
@@ -0,0 +1,527 @@
+# Scripts
+
+Nextflow is a workflow language that runs on the Java virtual machine (JVM). Nextflow's syntax is very similar to [Groovy](https://groovy-lang.org/), a scripting language for the JVM. However, Nextflow is specialized for writing computational pipelines in a declarative manner. See [Syntax][syntax-page] for a full description of the Nextflow language.
+
+Nextflow scripts can also make full use of the Java and Groovy standard libraries. See [Standard library][stdlib-page] for more information.
+
+:::warning
+Nextflow uses UTF-8 as the default character encoding for source files. Make sure to use UTF-8 encoding when editing Nextflow scripts with your preferred text editor.
+:::
+
+:::warning
+Nextflow scripts have a maximum size of 64 KiB. To avoid this limit for large pipelines, consider moving pipeline components into separate files and including them as modules.
+:::
+
+## Hello world
+
+You can use the `println` function to print to the console:
+
+```nextflow
+println 'Hello, World!'
+```
+
+## Variables
+
+Variables are declared using the `def` keyword:
+
+```nextflow
+def num = 1
+println num
+
+def date = new java.util.Date()
+println date
+
+def x = -3.1499392
+println x
+
+def flag = false
+println flag
+
+def str = "Hi"
+println str
+```
+
+:::warning
+Variables can also be declared without `def` in some cases. However, this practice is discouraged outside of simple code snippets because it can lead to a [race condition][cache-global-var-race-condition].
+:::
+
+## Lists
+
+Lists are defined using square brackets:
+
+```nextflow
+def myList = [1776, -1, 33, 99, 0, 928734928763]
+```
+
+You can access a given item in the list with square-bracket notation (indexes start at 0):
+
+```nextflow
+println myList[0]
+```
+
+In order to get the length of the list use the `size` method:
+
+```nextflow
+println myList.size()
+```
+
+See [List\<E\>][stdlib-types-list] for the set of available list operations.
+
+## Maps
+
+Maps are used to store *associative arrays* (also known as *dictionaries*). They are unordered collections of heterogeneous, named data:
+
+```nextflow
+def scores = ["Brett": 100, "Pete": "Did not finish", "Andrew": 86.87934]
+```
+
+Note that each of the values stored in the map can be of a different type. `Brett` is an integer, `Pete` is a string, and `Andrew` is a floating-point number.
+
+We can access the values in a map in two main ways:
+
+```nextflow
+println scores["Pete"]
+println scores.Pete
+```
+
+To add data to or modify a map, the syntax is similar to adding values to list:
+
+```nextflow
+scores["Pete"] = 3
+scores["Cedric"] = 120
+```
+
+You can also use the `+` operator to add two maps together:
+
+```nextflow
+def new_scores = scores + ["Pete": 3, "Cedric": 120]
+```
+
+When adding two maps, the first map is copied and then appended with the keys from the second map. Any conflicting keys are overwritten by the second map.
+
+:::tip
+Copying a map with the `+` operator is a safer way to modify maps in Nextflow, specifically when passing maps through channels. This way, a new instance of the map will be created, and any references to the original map won't be affected.
+:::
+
+See [Map\<K,V\>][stdlib-types-map] for the set of available map operations.
+
+## Tuples
+
+Tuples are used to store a fixed sequence of heterogeneous values. They are created using the `tuple` function:
+
+```nextflow
+person = tuple('Alice', 42, false)
+```
+
+Tuple elements are accessed by index:
+
+```nextflow
+name = person[0]
+age = person[1]
+is_male = person[2]
+```
+
+Tuples can be destructured in assignments:
+
+```nextflow
+(name, age, is_male) = person
+```
+
+As well as closure parameters:
+
+```nextflow
+coords = [
+    tuple(1, 2),
+    tuple(2, 4),
+    tuple(3, 6),
+    tuple(4, 8)
+]
+
+coords.each { x, y ->
+    println "x=$x, y=$y"
+}
+```
+
+Tuples are immutable -- once a tuple is created, its elements cannot be modified.
+
+See [Tuple][stdlib-types-tuple] for the set of available tuple operations.
+
+## Operators
+
+Operators are symbols that perform specific functions on one or more values, and generally make code easier to read. This section highlights some of the most commonly used operators.
+
+:::note
+Operators in this context are different from *channel operators*, which are specialized functions for working with channels. See [Dataflow][dataflow-page] for more information.
+:::
+
+The `==` and `!=` operators can be used to test whether any two values are equal (or not equal):
+
+```nextflow
+assert 2 + 2 == 4
+assert [2, 2] != [4]
+assert 'two plus two' != 'four'
+```
+
+:::tip
+The `assert` keyword simply tests a condition and raises an error if the condition is false. Every assert that you see on this page will succeed if executed.
+:::
+
+Comparison operators can be used to compare two values:
+
+```nextflow
+assert 3 < 3.14             // numbers are compared as numbers
+assert 3 <= 3
+assert 'hello' < 'world'    // strings are compared alphabetically
+```
+
+Logical operators can be used to perform Boolean logic:
+
+```nextflow
+assert true && false == false   // logical AND
+assert true || false == true    // logical OR
+assert !true == false           // logical NOT
+```
+
+The `in` and `!in` operators can be used to test *membership*, i.e. whether a collection contains a value:
+
+```nextflow
+assert 2 in [1, 2, 3]
+assert 'a' in [a: 1, b: 2, c: 3]
+```
+
+Arithmetic operators can be used to do math:
+
+```nextflow
+assert 2 + 2 == 4
+assert 2 - 2 == 0
+assert 2 * 2 == 4
+assert 2 / 2 == 1.0
+assert 2 ** 2 == 4  // exponent
+assert 2 % 2 == 0   // modulo (division remainder)
+```
+
+Some arithmetic operators can be used with other types of values. For example, `+` can be used to concatenate lists, maps, and strings:
+
+```nextflow
+assert [1, 2, 3] + [4] == [1, 2, 3, 4]
+```
+
+## Conditional execution
+
+One of the most important features of any programming language is the ability to execute different code under different conditions. This can be done with an if-else statement:
+
+```nextflow
+def x = Math.random()
+if( x < 0.5 ) {
+    println 'You lost.'
+}
+else {
+    println 'You won!'
+}
+```
+
+In some cases, conditional statements can be expressed more concisely as a conditional expression (also known as a *ternary expression*):
+
+```nextflow
+def message = Math.random() < 0.5
+    ? 'You lost.'
+    : 'You won!'
+println message
+```
+
+A shortened version of the conditional expression can be used to return a value if it is "truthy", or fallback to a second value otherwise:
+
+```nextflow
+def counts = ['A': 1, 'B', 2]
+assert counts['C'] ?: 0 == 0    // x is "truthy" if !!x == true
+```
+
+:::tip
+The `?:` operator is also known as the [elvis operator](https://en.wikipedia.org/wiki/Elvis_operator).
+:::
+
+## Strings
+
+Strings can be defined by enclosing text in single or double quotes (`'` or `"` characters):
+
+```nextflow
+println "he said 'cheese' once"
+println 'he said "cheese!" again'
+```
+
+Strings can be concatenated with `+`:
+
+```nextflow
+def a = "world"
+print "hello " + a + "\n"
+```
+
+### String interpolation
+
+There is an important difference between single-quoted and double-quoted strings: Double-quoted strings support variable interpolations, while single-quoted strings do not.
+
+In practice, double-quoted strings can contain the value of an arbitrary variable by prefixing its name with the `$` character, or the value of any expression by using the `${expression}` syntax, similar to Bash/shell scripts:
+
+```nextflow
+def foxtype = 'quick'
+def foxcolor = ['b', 'r', 'o', 'w', 'n']
+println "The $foxtype ${foxcolor.join()} fox"
+
+def x = 'Hello'
+println '$x + $y'
+```
+
+This code prints:
+
+```
+The quick brown fox
+$x + $y
+```
+
+### Multi-line strings
+
+A block of text that span multiple lines can be defined by delimiting it with triple single or double quotes:
+
+```nextflow
+def text = """
+    hello there James
+    how are you today?
+    """
+```
+
+:::note
+Like before, multi-line strings inside double quotes support variable interpolation, while single-quoted multi-line strings do not.
+:::
+
+As in Bash/shell scripts, terminating a line in a multi-line string with a `\` character prevents a newline character from separating that line from the one that follows:
+
+```nextflow
+def myLongCmdline = """
+    blastp \
+    -in $input_query \
+    -out $output_file \
+    -db $blast_database \
+    -html
+    """
+
+def result = myLongCmdline.execute().text
+```
+
+In the preceding example, `blastp` and its `-in`, `-out`, `-db` and `-html` switches and their arguments are effectively a single line.
+
+:::warning
+Do not put any spaces after the backslash when using backslashes to continue a multi-line command. Spaces after the backslash will be interpreted as an escaped space and will make your script incorrect. It will also print this warning:
+
+```
+unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException
+```
+:::
+
+## Regular expressions
+
+Regular expressions are the Swiss Army knife of text processing. They provide the ability to match and extract patterns from strings.
+
+Use `=~` to check whether a given pattern occurs anywhere in a string:
+
+```nextflow
+assert 'hello' =~ /hello/
+assert 'hello world' =~ /hello/
+```
+
+Use `==~` to check whether a string matches a given regular expression pattern exactly.
+
+```nextflow
+assert 'hello' ==~ /hello/
+assert !('hello world' ==~ /hello/)
+```
+
+### String replacement
+
+To replace pattern occurrences in a given string, use the `replaceFirst` and `replaceAll` methods:
+
+```nextflow
+def x = "colour".replaceFirst(/ou/, "o")
+println x
+// prints: color
+
+def y = "cheesecheese".replaceAll(/cheese/, "nice")
+println y
+// prints: nicenice
+```
+
+To remove part of a string, simply replace it with a blank string:
+
+```nextflow
+def z = 'Hello World!'.replaceFirst(/(?i)\s+Wo\w+/, '')
+println z
+// prints: Hello!
+```
+
+### Capturing groups
+
+You can match a pattern that includes groups. First create a matcher object with the `=~` operator. Then, you can index the matcher object to find the matches: `matcher[0]` returns a list representing the first match of the regular expression in the string. The first list element is the string that matches the entire regular expression, and the remaining elements are the strings that match each group.
+
+Here's how it works:
+
+```nextflow
+def programVersion = '2.7.3-beta'
+def m = programVersion =~ /(\d+)\.(\d+)\.(\d+)-?(.+)/
+
+assert m[0] == ['2.7.3-beta', '2', '7', '3', 'beta']
+assert m[0][1] == '2'
+assert m[0][2] == '7'
+assert m[0][3] == '3'
+assert m[0][4] == 'beta'
+```
+
+Applying some syntactic sugar, you can do the same in just one line of code:
+
+```nextflow
+def programVersion = '2.7.3-beta'
+def (full, major, minor, patch, flavor) = (programVersion =~ /(\d+)\.(\d+)\.(\d+)-?(.+)/)[0]
+
+println full    // 2.7.3-beta
+println major   // 2
+println minor   // 7
+println patch   // 3
+println flavor  // beta
+```
+
+## Closures
+
+A closure is a function that can be used like a regular value. Typically, closures are passed as arguments to *higher-order functions* to express computations in a declarative manner.
+
+For example:
+
+```nextflow
+def square = { v -> v * v }
+```
+
+The above example defines a closure, which takes one parameter named `v` and returns the "square" of `v` (`v * v`). The closure is assigned to the variable `square`.
+
+`square` can now be called like a function:
+
+```nextflow
+println square(9)
+```
+
+The above example prints `81`.
+
+The main use case for a closure is as an argument to a higher-order function:
+
+```nextflow
+[ 1, 2, 3, 4 ].collect(square)
+```
+
+The `collect` method of a list applies a mapping function to each value in the list and produces a new list. The above example produces:
+
+```nextflow
+[ 1, 4, 9, 16 ]
+```
+
+The example can be expressed more concisely as:
+
+```nextflow
+[ 1, 2, 3, 4 ].collect { v -> v * v }
+```
+
+Another example is the `each` method of a map, which takes a closure with two arguments corresponding to the key and value of each map entry:
+
+```nextflow
+[ "Yue" : "Wu", "Mark" : "Williams", "Sudha" : "Kumari" ].each { key, value ->
+    println "$key = $value"
+}
+```
+
+Prints:
+
+```
+Yue = Wu
+Mark = Williams
+Sudha = Kumari
+```
+
+Closures can access variables outside of their scope:
+
+```nextflow
+def counts = ["China": 1, "India": 2, "USA": 3]
+
+def result = 0
+counts.keySet().each { v ->
+    result += counts[v]
+}
+
+println result
+```
+
+A closure can also declare local variables that exist only for the lifetime of each closure invocation:
+
+```nextflow
+def result = 0
+myMap.keySet().each { v ->
+    def count = myMap[v]
+    result += count
+}
+```
+
+While the `each` method is a convenient way to iterate through a collection and build up some result, a more idiomatic way to do this is to use the `inject` method:
+
+```nextflow
+def result = counts.values().inject { sum, v -> sum + v }
+```
+
+This way, the closure is fully "self-contained" because it doesn't access or mutate any variables outside of its scope.
+
+:::note
+When a closure takes a single parameter, the parameter can be omitted, in which case the implicit `it` parameter will be used:
+
+```nextflow
+[1, 2, 3].each { println it }
+```
+:::
+
+## Script definitions
+
+So far, we have been focusing on the basic building blocks of Nextflow code, like variables, lists, strings, and closures.
+
+In practice, however, Nextflow scripts are composed of *workflows*, *processes*, and *functions* (collectively known as *definitions*), and can *include*  definitions from other scripts.
+
+To transition a code snippet into a proper workflow script, simply wrap it in a `workflow` block:
+
+```nextflow
+workflow {
+    println 'Hello!'
+}
+```
+
+This block is called the *entry workflow*. It serves as the entrypoint when the script is executed. A script can only have one entry workflow. Whenever a script contains only simple statements like `println 'Hello!'`, Nextflow simply treats it as an entry workflow.
+
+You can also break up code into functions, for example:
+
+```nextflow
+def sayHello() {
+    println 'Hello!'
+}
+
+def add(a, b) {
+    a + b
+}
+
+workflow {
+    sayHello()
+    println "2 + 2 = ${add(2, 2)}!"
+}
+```
+
+See [Workflows][workflow-page], [Processes][process-page], and [Modules][module-page] for more information about how to use these features in your Nextflow scripts.
+
+[cache-global-var-race-condition]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#race-condition-on-a-global-variable
+[channel-page]: /nextflow_docs/nextflow_repo/docs/channel.mdx
+[module-page]: /nextflow_docs/nextflow_repo/docs/module.mdx
+[process-page]: /nextflow_docs/nextflow_repo/docs/process.mdx
+[stdlib-page]: /nextflow_docs/nextflow_repo/docs/reference/stdlib.mdx
+[stdlib-types-list]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#liste
+[stdlib-types-map]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#mapkv
+[stdlib-types-tuple]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#tuple
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[workflow-page]: /nextflow_docs/nextflow_repo/docs/workflow.mdx
diff --git a/docs/secrets.md b/new-docs/nextflow-docs/secrets.mdx
similarity index 83%
rename from docs/secrets.md
rename to new-docs/nextflow-docs/secrets.mdx
index 07efa649ce..2b9499e9da 100644
--- a/docs/secrets.md
+++ b/new-docs/nextflow-docs/secrets.mdx
@@ -1,9 +1,9 @@
-(secrets-page)=
+
 
 # Secrets
 
-:::{versionadded} 22.10.0
-:::
+<AddedInVersion version="22.10.0">
+</AddedInVersion>
 
 Nextflow has built-in support for pipeline secrets, allowing users to safely provide sensitive information to a pipeline run.
 
@@ -17,7 +17,7 @@ Secrets can be used with the local executor and grid executors (e.g., Slurm or G
 
 ## Command line
 
-The Nextflow {ref}`cli-secrets` sub-command can be used to manage secrets:
+The Nextflow [secrets][cli-secrets] sub-command can be used to manage secrets:
 
 ```bash
 # create a new secret
@@ -46,12 +46,11 @@ aws {
 
 The above snippet accesses the secrets `MY_ACCESS_KEY` and `MY_SECRET_KEY` and assigns them to the corresponding AWS config settings.
 
-:::{warning}
+:::warning
 Secrets should not be assigned to pipeline parameters, as they can be leaked by the pipeline.
 :::
 
-:::{versionadded} 25.10.0
-:::
+<AddedInVersion version="25.10.0" />
 
 Nextflow supports the use of secrets provided by plugins (e.g., AWS secrets) in configuration. However, due to the way that plugins are loaded, there are specific considerations when using config secrets:
 
@@ -71,14 +70,12 @@ includeConfig secrets.MY_SECRET
     : '/dev/null'
 ```
 
-The above snippet includes a secured config only if the secret is present. Otherwise, it includes `/dev/null`, which is equivalent to including an empty file. The reference to `secrets.MY_SECRET` in the condition causes the config to be reloaded with secrets enabled, including secrets from plugins such as AWS secrets.
-
-(secrets-pipeline-script)=
+The above snippet includes a secured config only if the secret is present. Otherwise, it includes `/dev/null`, which is equivalent to including an empty file.
+The reference to `secrets.MY_SECRET` in the condition causes the config to be reloaded with secrets enabled, including secrets from plugins such as AWS secrets.
 
 ## Pipeline script
 
-:::{versionadded} 24.04.0
-:::
+<AddedInVersion version="24.04.0" />
 
 Secrets can be accessed in the pipeline script using the built-in `secrets` variable. For example:
 
@@ -88,13 +85,13 @@ workflow {
 }
 ```
 
-:::{warning}
+:::warning
 The above example is only meant to demonstrate how to access a secret, not how to use it. In practice, sensitive information should not be printed to the console or output files.
 :::
 
 ## Process directive
 
-Secrets can be accesses by processes using the {ref}`process-secret` directive. For example:
+Secrets can be accesses by processes using the [secret][process-secret] directive. For example:
 
 ```nextflow
 process my_task {
@@ -110,6 +107,9 @@ process my_task {
 
 In the above example, the secrets `MY_ACCESS_KEY` and `MY_SECRET_KEY` are injected into the process script as environment variables.
 
-:::{warning}
+:::warning
 Secrets are made available as environment variables in the process script. To prevent evaluation in the Nextflow script context, escape variable names with a backslash (e.g., `\$MY_ACCESS_KEY`) as shown above.
 :::
+
+[cli-secrets]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#secrets
+[process-secret]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#secret
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/sharing.mdx b/new-docs/nextflow-docs/sharing.mdx
new file mode 100644
index 0000000000..7c749fc25f
--- /dev/null
+++ b/new-docs/nextflow-docs/sharing.mdx
@@ -0,0 +1,227 @@
+# Sharing pipelines
+
+Nextflow seamlessly integrates with popular Git providers, including [BitBucket](http://bitbucket.org/), [GitHub](http://github.com), and [GitLab](http://gitlab.com) for managing Nextflow pipelines as version-controlled Git repositories. This feature allows you to easily use other people's Nextflow pipelines and publish your own pipelines.
+
+:::note
+Nextflow is not meant to completely replace the [Git](https://git-scm.com/) tool. You may still need `git` to create new repositories or commit changes, etc.
+:::
+
+## Git configuration
+
+You can configure your credentials for various Git providers in the Git configuration file, located at `$HOME/.nextflow/scm`. See [Git][git-page] for more information.
+
+## Using a local repository
+
+Nextflow can work with repositories stored in a local or shared file system. The repository must be created as a [bare repository](https://craftquest.io/articles/what-is-a-bare-git-repository).
+
+For example, given a bare repository at `/shared/projects/hello.git`, Nextflow is able to run it using the following syntax:
+
+```bash
+nextflow run file:/shared/projects/hello.git
+```
+
+See [Git documentation](https://git-scm.com/book/en/v2/Git-on-the-Server-Getting-Git-on-a-Server) for more details about how create and manage bare repositories.
+
+## Publishing your pipeline
+
+In order to publish your Nextflow pipeline to GitHub (or any other supported platform) and allow other people to use it, you only need to create a GitHub repository containing all your project script and data files. If you don't know how to do it, follow this simple tutorial that explains how [create a GitHub repository](https://help.github.com/articles/create-a-repo).
+
+Nextflow only requires that the main script in your pipeline project is called `main.nf`. A different name can be used by specifying the `manifest.mainScript` attribute in the `nextflow.config` file that must be included in your project. For example:
+
+```groovy
+manifest.mainScript = 'my_very_long_script_name.nf'
+```
+
+To learn more about this and other project metadata information, that can be defined in the Nextflow configuration file, read the [Manifest][config-manifest] section on the Nextflow configuration page.
+
+Once you have uploaded your pipeline project to GitHub other people can execute it simply using the project name or the repository URL.
+
+For if your GitHub account name is `acme` and you have uploaded a project into a repository named `hello` the repository URL will be `http://github.com/acme/hello` and people will able to download and run it by using either the command:
+
+```bash
+nextflow run acme/hello
+```
+
+or
+
+```bash
+nextflow run http://github.com/acme/hello
+```
+
+See [Command line][cli-page] to learn how to use the Nextflow command line to run pipelines and manage pipeline projects.
+
+## Managing dependencies
+
+Computational pipelines are rarely composed by a single script. In real world applications they depend on many other components, including other scripts and tools, databases, and specialized environments which provide compute and storage.
+
+These external dependencies are the primary challenge when sharing software, because the users need to recreate the environment around a tool in order to use it. This setup process is often painful and error prone, which severely hinders the ability to reproduce computational results on a system other than the one on which it was originally developed.
+
+Nextflow tackles this problem by integrating with existing tools for reproducible software, namely Git for source code and Docker for containers. These tools allow you to keep all the dependencies of your pipeline project in one place and track changes over time with version control.
+
+By making your pipeline project is self-contained, meaning all of its dependencies are fully defined in the project itself, you gain two major advantages:
+
+- **Portability**: the pipeline can be run in virtually any environment with a Java VM and a container runtime
+- **Reproducibility**: any results produced by the pipelined can be easily reproduced, even across different environments
+
+One way to account for dependencies is to break them down into three categories: code, data, and environment. Here we will describe how to include each of these dependencies in your Nextflow pipeline:
+
+### Code
+
+Aside from pipeline scripts, you may have additional scripts and tools used by individual tasks.
+
+#### Standard dependencies
+
+Many standard tools can be accessed as Docker containers or Conda/Spack packages. In this case, you only need to specify the container image URL (e.g. from [DockerHub](https://hub.docker.com)) or package name with the `container` or `conda` directive, respectively.
+
+Make sure to enable the desired method in your Nextflow configuration:
+
+```groovy
+// containers
+docker.enabled = true
+
+// conda packages
+conda.enabled = true
+```
+
+This way, when you launch your pipeline, Nextflow will automatically download the necessary dependencies to run your tasks based on this configuration.
+
+Read the [Containers][container-page] page to learn more about how to use containers with Nextflow, and the [Conda environments][conda-page] page for Conda packages.
+
+:::tip
+For maximal reproducibility, make sure to define a specific version for each tool. Otherwise, your pipeline might use different versions across subsequent runs, which can introduce subtle differences to your results.
+:::
+
+#### The `bin` directory
+
+As for custom scripts, you can include executable scripts in the `bin` directory of your pipeline repository. When configured correctly, these scripts can be executed like a regular command from any process script (i.e. without modifying the `PATH` environment variable or using an absolute path), and changing the script will cause the task to be re-executed on a resumed run (i.e. just like changing the process script itself).
+
+To configure a custom script:
+
+1. Save the script in the `bin` directory (relative to the pipeline repository root).
+2. Specify a portable shebang (see note below for details).
+3. Make the script executable. For example: `chmod a+x bin/my_script.py`
+
+:::tip
+To maximize the portability of your bundled script, use `env` to dynamically resolve the location of the interpreter instead of hard-coding it in the shebang line.
+
+For example, shebang definitions `#!/usr/bin/python` and `#!/usr/local/bin/python` both hard-code specific paths to the Python interpreter. Instead, the following approach is more portable:
+
+```bash
+#!/usr/bin/env python
+```
+:::
+
+#### The `lib` directory
+
+The `lib` directory can be used to add utility code or external libraries without cluttering the pipeline scripts. The `lib` directory in the Nextflow project root is added to the classpath by default. Classes defined in the `lib` directory will be available in pipeline scripts. Functions defined outside of classes will not be available in pipeline scripts.
+
+For example, `lib/DNASequence.groovy` defines the `DNASequence` class:
+
+```groovy
+// lib/DNASequence.groovy
+class DNASequence {
+    String sequence
+
+    // Constructor
+    DNASequence(String sequence) {
+        this.sequence = sequence.toUpperCase() // Ensure sequence is in uppercase for consistency
+    }
+
+    // Method to calculate melting temperature using the Wallace rule
+    double getMeltingTemperature() {
+        int g_count = sequence.count('G')
+        int c_count = sequence.count('C')
+        int a_count = sequence.count('A')
+        int t_count = sequence.count('T')
+
+        // Wallace rule calculation
+        double tm = 4 * (g_count + c_count) + 2 * (a_count + t_count)
+        return tm
+    }
+
+    String toString() {
+        return "DNA[$sequence]"
+    }
+}
+```
+
+The `DNASequence` class is available in the execution context:
+
+```nextflow
+// main.nf
+workflow {
+    channel.of('ACGTTGCAATGCCGTA', 'GCGTACGGTACGTTAC')
+        .map { seq -> new DNASequence(seq) }
+        .view { dna ->
+            "Found sequence '$dna' with melting temperaure ${dna.getMeltingTemperature()}°C"
+        }
+}
+```
+
+It prints:
+
+```
+Found sequence 'DNA[ACGTTGCAATGCCGTA]' with melting temperaure 48.0°C
+Found sequence 'DNA[GCGTACGGTACGTTAC]' with melting temperaure 50.0°C
+```
+
+:::note
+Package declarations in the `lib` directory are ignored. The package of a class is determined by the directory structure within the `lib` directory.
+
+For example, if the above example were defined in `lib/utils/DNASequence.groovy`, the class would need to be referenced in pipeline scripts as `utils.DNASequence`.
+:::
+
+### Data
+
+In general, input data should be provided by external sources using parameters which can be controlled by the user. This way, a pipeline can be easily reused to process different datasets which are appropriate for the pipeline.
+
+Parameters can be declared with default values in the main script or in the configuration file:
+
+```groovy
+params.my_input = 'default input file'
+params.my_output = 'default output path'
+params.my_flag = false
+// ...
+```
+
+When launching a pipeline, parameter values can be provided on the command line or in a params file (using the `-params-file` option). Options prefixed with a double dash (`--`) are interpreted as parameters:
+
+```bash
+nextflow run <your pipeline> --my_input /path/to/input/file --my_output /other/path --my_flag true
+```
+
+When a pipeline requires some small data that rarely changes, it may be easier to include the data in the pipeline repository. You can reference this data from the pipeline script in a portable manner (i.e. without relying on an absolute path) by using the `projectDir` implicit variable, which refers to the local copy of the pipeline repository.
+
+The following example references the file `dataset/sequences.fa` in the pipeline repository:
+
+```nextflow
+sequences = file("$projectDir/dataset/sequences.fa")
+sequences.splitFasta {
+    println it
+}
+```
+
+### Environment
+
+The "environment" refers to any other aspects of the environment in which your pipeline is executed, such as environment variables and resource managers like SLURM.
+
+Any environment variable that may be required by the tools in your pipeline can be defined under the `env` scope in your Nextflow configuration. For example:
+
+```groovy
+env {
+  DELTA = 'hello'
+  GAMMA = 'world'
+}
+```
+
+Similarly, if you use an HPC scheduler like SLURM or a cloud batch service like AWS Batch to execute tasks in a distributed manner, you can use a configuration profile to define the settings for a given environment.
+
+See [Configuration][config-page] for more information about Nextflow configuration and [Executors][executor-page] for more information about executors.
+
+[git-page]: /nextflow_docs/nextflow_repo/docs/git.mdx
+[config-manifest]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#manifest
+[cli-page]: /nextflow_docs/nextflow_repo/docs/cli.mdx
+[container-page]: /nextflow_docs/nextflow_repo/docs/container.mdx
+[conda-page]: /nextflow_docs/nextflow_repo/docs/conda.mdx
+[config-page]: /nextflow_docs/nextflow_repo/docs/config.mdx
+[executor-page]: /nextflow_docs/nextflow_repo/docs/executor.mdx
diff --git a/new-docs/nextflow-docs/snippets/.gitignore b/new-docs/nextflow-docs/snippets/.gitignore
new file mode 100644
index 0000000000..7ca126b99d
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/.gitignore
@@ -0,0 +1,2 @@
+.nextflow*
+work
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/branch-criteria.nf b/new-docs/nextflow-docs/snippets/branch-criteria.nf
new file mode 100644
index 0000000000..4dae6dbe43
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/branch-criteria.nf
@@ -0,0 +1,12 @@
+def criteria = branchCriteria { v ->
+    small: v < 10
+    large: v > 10
+}
+
+channel.of(1, 2, 30).branch(criteria).set { ch1 }
+channel.of(10, 20, 3).branch(criteria).set { ch2 }
+
+ch1.small.view { v -> "$v is small" }
+ch1.large.view { v -> "$v is large" }
+ch2.small.view { v -> "$v is small" }
+ch2.large.view { v -> "$v is large" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/branch-criteria.out b/new-docs/nextflow-docs/snippets/branch-criteria.out
new file mode 100644
index 0000000000..6f8490b73d
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/branch-criteria.out
@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+20 is large
+30 is large
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/branch-with-fallback.nf b/new-docs/nextflow-docs/snippets/branch-with-fallback.nf
new file mode 100644
index 0000000000..a7779762e6
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/branch-with-fallback.nf
@@ -0,0 +1,11 @@
+channel.of(1, 2, 3, 40, 50)
+    .branch { v ->
+        small: v < 10
+        large: v < 50
+        other: true
+    }
+    .set { result }
+
+result.small.view { v -> "$v is small" }
+result.large.view { v -> "$v is large" }
+result.other.view { v -> "$v is other" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/branch-with-fallback.out b/new-docs/nextflow-docs/snippets/branch-with-fallback.out
new file mode 100644
index 0000000000..c292f25e26
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/branch-with-fallback.out
@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+40 is large
+50 is other
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/branch-with-mapper.nf b/new-docs/nextflow-docs/snippets/branch-with-mapper.nf
new file mode 100644
index 0000000000..4d52651733
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/branch-with-mapper.nf
@@ -0,0 +1,16 @@
+channel.of(1, 2, 3, 40, 50)
+    .branch { v ->
+        alpha: v < 10
+            return v + 2
+
+        beta: v < 50
+            return v - 2
+
+        other: true
+            return 0
+    }
+    .set { result }
+
+result.alpha.view { v -> "$v is alpha" }
+result.beta.view { v -> "$v is beta" }
+result.other.view { v -> "$v is other" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/branch-with-mapper.out b/new-docs/nextflow-docs/snippets/branch-with-mapper.out
new file mode 100644
index 0000000000..93fd972bf5
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/branch-with-mapper.out
@@ -0,0 +1,5 @@
+3 is alpha
+4 is alpha
+5 is alpha
+38 is beta
+0 is other
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/branch.nf b/new-docs/nextflow-docs/snippets/branch.nf
new file mode 100644
index 0000000000..95540f7bd0
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/branch.nf
@@ -0,0 +1,9 @@
+channel.of(1, 2, 3, 40, 50)
+    .branch { v ->
+        small: v < 10
+        large: v > 10
+    }
+    .set { result }
+
+result.small.view { v -> "$v is small" }
+result.large.view { v -> "$v is large" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/branch.out b/new-docs/nextflow-docs/snippets/branch.out
new file mode 100644
index 0000000000..ac05166f6b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/branch.out
@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+40 is large
+50 is large
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-closing.nf b/new-docs/nextflow-docs/snippets/buffer-with-closing.nf
new file mode 100644
index 0000000000..c1e91cd83a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-closing.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 1, 2, 3 )
+    .buffer { v -> v == 2 }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-closing.out b/new-docs/nextflow-docs/snippets/buffer-with-closing.out
new file mode 100644
index 0000000000..b64a302e78
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-closing.out
@@ -0,0 +1,2 @@
+[1, 2]
+[3, 1, 2]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-opening-closing.nf b/new-docs/nextflow-docs/snippets/buffer-with-opening-closing.nf
new file mode 100644
index 0000000000..2880c7cd73
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-opening-closing.nf
@@ -0,0 +1,4 @@
+// emits bundles starting with `2` and ending with `4`
+channel.of( 1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 1, 2 )
+    .buffer( 2, 4 )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-opening-closing.out b/new-docs/nextflow-docs/snippets/buffer-with-opening-closing.out
new file mode 100644
index 0000000000..61105ec0d7
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-opening-closing.out
@@ -0,0 +1,2 @@
+[2, 3, 4]
+[2, 3, 4]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-size-remainder.nf b/new-docs/nextflow-docs/snippets/buffer-with-size-remainder.nf
new file mode 100644
index 0000000000..4bc9c695ca
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-size-remainder.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 1, 2, 3, 1 )
+    .buffer( size: 2, remainder: true )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-size-remainder.out b/new-docs/nextflow-docs/snippets/buffer-with-size-remainder.out
new file mode 100644
index 0000000000..8f9461c767
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-size-remainder.out
@@ -0,0 +1,4 @@
+[1, 2]
+[3, 1]
+[2, 3]
+[1]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-size-skip.nf b/new-docs/nextflow-docs/snippets/buffer-with-size-skip.nf
new file mode 100644
index 0000000000..29f88fd6b5
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-size-skip.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 1, 2 )
+    .buffer( size: 3, skip: 2 )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-size-skip.out b/new-docs/nextflow-docs/snippets/buffer-with-size-skip.out
new file mode 100644
index 0000000000..8354fe8d6f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-size-skip.out
@@ -0,0 +1,2 @@
+[3, 4, 5]
+[3, 4, 5]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-size.nf b/new-docs/nextflow-docs/snippets/buffer-with-size.nf
new file mode 100644
index 0000000000..ffca06acb3
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-size.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 1, 2, 3, 1 )
+    .buffer( size: 2 )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/buffer-with-size.out b/new-docs/nextflow-docs/snippets/buffer-with-size.out
new file mode 100644
index 0000000000..a8c6fc4922
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/buffer-with-size.out
@@ -0,0 +1,3 @@
+[1, 2]
+[3, 1]
+[2, 3]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collate-with-no-remainder.nf b/new-docs/nextflow-docs/snippets/collate-with-no-remainder.nf
new file mode 100644
index 0000000000..6b3b7ff281
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collate-with-no-remainder.nf
@@ -0,0 +1,3 @@
+channel.of(1, 2, 3, 1, 2, 3, 1)
+    .collate( 3, false )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collate-with-no-remainder.out b/new-docs/nextflow-docs/snippets/collate-with-no-remainder.out
new file mode 100644
index 0000000000..10ea892304
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collate-with-no-remainder.out
@@ -0,0 +1,2 @@
+[1, 2, 3]
+[1, 2, 3]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collate-with-step.nf b/new-docs/nextflow-docs/snippets/collate-with-step.nf
new file mode 100644
index 0000000000..fa40c3a5c1
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collate-with-step.nf
@@ -0,0 +1,3 @@
+channel.of(1, 2, 3, 4)
+    .collate( 3, 1 )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collate-with-step.out b/new-docs/nextflow-docs/snippets/collate-with-step.out
new file mode 100644
index 0000000000..d92034b5c4
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collate-with-step.out
@@ -0,0 +1,4 @@
+[1, 2, 3]
+[2, 3, 4]
+[3, 4]
+[4]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collate.nf b/new-docs/nextflow-docs/snippets/collate.nf
new file mode 100644
index 0000000000..79faf59352
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collate.nf
@@ -0,0 +1,3 @@
+channel.of(1, 2, 3, 1, 2, 3, 1)
+    .collate( 3 )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collate.out b/new-docs/nextflow-docs/snippets/collate.out
new file mode 100644
index 0000000000..cc547cb82b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collate.out
@@ -0,0 +1,3 @@
+[1, 2, 3]
+[1, 2, 3]
+[1]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collect-with-mapper.nf b/new-docs/nextflow-docs/snippets/collect-with-mapper.nf
new file mode 100644
index 0000000000..e7654edeb2
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collect-with-mapper.nf
@@ -0,0 +1,3 @@
+channel.of( 'hello', 'ciao', 'bonjour' )
+    .collect { v -> v.length() }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collect-with-mapper.out b/new-docs/nextflow-docs/snippets/collect-with-mapper.out
new file mode 100644
index 0000000000..23b386f57b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collect-with-mapper.out
@@ -0,0 +1 @@
+[5, 4, 7]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collect.nf b/new-docs/nextflow-docs/snippets/collect.nf
new file mode 100644
index 0000000000..47c6d526a6
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collect.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4 )
+    .collect()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collect.out b/new-docs/nextflow-docs/snippets/collect.out
new file mode 100644
index 0000000000..98d20c4307
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collect.out
@@ -0,0 +1 @@
+[1, 2, 3, 4]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collectfile-closure.nf b/new-docs/nextflow-docs/snippets/collectfile-closure.nf
new file mode 100644
index 0000000000..3639ae1eaf
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collectfile-closure.nf
@@ -0,0 +1,8 @@
+channel.of('Hola', 'Ciao', 'Hello', 'Bonjour', 'Halo')
+    .collectFile { item ->
+        [ "${item[0]}.txt", item + '\n' ]
+    }
+    .subscribe { file ->
+        println "File '${file.name}' contains:"
+        println file.text
+    }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/collectfile-closure.out b/new-docs/nextflow-docs/snippets/collectfile-closure.out
new file mode 100644
index 0000000000..c930bc0b9a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collectfile-closure.out
@@ -0,0 +1,11 @@
+File 'B.txt' contains:
+Bonjour
+
+File 'C.txt' contains:
+Ciao
+
+File 'H.txt' contains:
+Halo
+Hola
+Hello
+
diff --git a/new-docs/nextflow-docs/snippets/collectfile.nf b/new-docs/nextflow-docs/snippets/collectfile.nf
new file mode 100644
index 0000000000..f722fbc174
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/collectfile.nf
@@ -0,0 +1,6 @@
+channel.of('alpha', 'beta', 'gamma')
+    .collectFile(name: 'sample.txt', newLine: true)
+    .subscribe { file ->
+        println "Entries are saved to file: $file"
+        println "File content is: ${file.text}"
+    }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/combine-by.nf b/new-docs/nextflow-docs/snippets/combine-by.nf
new file mode 100644
index 0000000000..c26caf765e
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/combine-by.nf
@@ -0,0 +1,4 @@
+source = channel.of( [1, 'alpha'], [2, 'beta'] )
+target = channel.of( [1, 'x'], [1, 'y'], [1, 'z'], [2, 'p'], [2, 'q'], [2, 't'] )
+
+source.combine(target, by: 0).view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/combine-by.out b/new-docs/nextflow-docs/snippets/combine-by.out
new file mode 100644
index 0000000000..5f391a56fa
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/combine-by.out
@@ -0,0 +1,6 @@
+[1, alpha, x]
+[1, alpha, y]
+[1, alpha, z]
+[2, beta, p]
+[2, beta, q]
+[2, beta, t]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/combine.nf b/new-docs/nextflow-docs/snippets/combine.nf
new file mode 100644
index 0000000000..c485110088
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/combine.nf
@@ -0,0 +1,6 @@
+numbers = channel.of(1, 2, 3)
+words = channel.of('hello', 'ciao')
+
+numbers
+    .combine(words)
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/combine.out b/new-docs/nextflow-docs/snippets/combine.out
new file mode 100644
index 0000000000..67944a86ba
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/combine.out
@@ -0,0 +1,6 @@
+[1, hello]
+[2, hello]
+[3, hello]
+[1, ciao]
+[2, ciao]
+[3, ciao]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/concat.nf b/new-docs/nextflow-docs/snippets/concat.nf
new file mode 100644
index 0000000000..07a260c55c
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/concat.nf
@@ -0,0 +1,5 @@
+a = channel.of( 'a', 'b', 'c' )
+b = channel.of( 1, 2, 3 )
+c = channel.of( 'p', 'q' )
+
+c.concat( b, a ).view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/concat.out b/new-docs/nextflow-docs/snippets/concat.out
new file mode 100644
index 0000000000..3138a55a6d
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/concat.out
@@ -0,0 +1,8 @@
+p
+q
+1
+2
+3
+a
+b
+c
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/count-with-filter-closure.nf b/new-docs/nextflow-docs/snippets/count-with-filter-closure.nf
new file mode 100644
index 0000000000..777c701f1e
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/count-with-filter-closure.nf
@@ -0,0 +1,3 @@
+channel.of('a', 'c', 'c', 'q', 'b')
+    .count { v -> v <= 'c' }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/count-with-filter-closure.out b/new-docs/nextflow-docs/snippets/count-with-filter-closure.out
new file mode 100644
index 0000000000..bf0d87ab1b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/count-with-filter-closure.out
@@ -0,0 +1 @@
+4
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/count-with-filter-number.nf b/new-docs/nextflow-docs/snippets/count-with-filter-number.nf
new file mode 100644
index 0000000000..0f66b6bdfa
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/count-with-filter-number.nf
@@ -0,0 +1,3 @@
+channel.of(4, 1, 7, 1, 1)
+    .count(1)
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/count-with-filter-number.out b/new-docs/nextflow-docs/snippets/count-with-filter-number.out
new file mode 100644
index 0000000000..e440e5c842
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/count-with-filter-number.out
@@ -0,0 +1 @@
+3
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/count-with-filter-regex.nf b/new-docs/nextflow-docs/snippets/count-with-filter-regex.nf
new file mode 100644
index 0000000000..b36060443a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/count-with-filter-regex.nf
@@ -0,0 +1,3 @@
+channel.of('a', 'c', 'c', 'q', 'b')
+    .count( ~/c/ )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/count-with-filter-regex.out b/new-docs/nextflow-docs/snippets/count-with-filter-regex.out
new file mode 100644
index 0000000000..d8263ee986
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/count-with-filter-regex.out
@@ -0,0 +1 @@
+2
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/count.nf b/new-docs/nextflow-docs/snippets/count.nf
new file mode 100644
index 0000000000..1fcc1d0d8a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/count.nf
@@ -0,0 +1,3 @@
+channel.of(9, 1, 7, 5)
+    .count()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/count.out b/new-docs/nextflow-docs/snippets/count.out
new file mode 100644
index 0000000000..bf0d87ab1b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/count.out
@@ -0,0 +1 @@
+4
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/cross-with-mapper.nf b/new-docs/nextflow-docs/snippets/cross-with-mapper.nf
new file mode 100644
index 0000000000..4ece562e04
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/cross-with-mapper.nf
@@ -0,0 +1,4 @@
+source = channel.of( [1, 'alpha'], [2, 'beta'] )
+target = channel.of( [1, 'a'], [1, 'b'], [2, 'a'], [2, 'b'] )
+
+source .cross(target) { v -> v[1][0] } .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/cross-with-mapper.out b/new-docs/nextflow-docs/snippets/cross-with-mapper.out
new file mode 100644
index 0000000000..1d1dfc8fcf
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/cross-with-mapper.out
@@ -0,0 +1,4 @@
+[[1, alpha], [1, a]]
+[[1, alpha], [2, a]]
+[[2, beta], [1, b]]
+[[2, beta], [2, b]]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/cross.nf b/new-docs/nextflow-docs/snippets/cross.nf
new file mode 100644
index 0000000000..82abb19a7d
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/cross.nf
@@ -0,0 +1,4 @@
+source = channel.of( [1, 'alpha'], [2, 'beta'] )
+target = channel.of( [1, 'x'], [1, 'y'], [1, 'z'], [2, 'p'], [2, 'q'], [2, 't'] )
+
+source.cross(target).view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/cross.out b/new-docs/nextflow-docs/snippets/cross.out
new file mode 100644
index 0000000000..c83035ade5
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/cross.out
@@ -0,0 +1,6 @@
+[[1, alpha], [1, x]]
+[[1, alpha], [1, y]]
+[[1, alpha], [1, z]]
+[[2, beta], [2, p]]
+[[2, beta], [2, q]]
+[[2, beta], [2, t]]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/distinct-with-mapper.nf b/new-docs/nextflow-docs/snippets/distinct-with-mapper.nf
new file mode 100644
index 0000000000..a95652285c
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/distinct-with-mapper.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 4, 6 )
+    .distinct { v -> v % 2 }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/distinct-with-mapper.out b/new-docs/nextflow-docs/snippets/distinct-with-mapper.out
new file mode 100644
index 0000000000..fa2fa9f9b9
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/distinct-with-mapper.out
@@ -0,0 +1,4 @@
+1
+2
+3
+2
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/distinct.nf b/new-docs/nextflow-docs/snippets/distinct.nf
new file mode 100644
index 0000000000..247533643f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/distinct.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 2, 3 )
+    .distinct()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/distinct.out b/new-docs/nextflow-docs/snippets/distinct.out
new file mode 100644
index 0000000000..c7a7acee13
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/distinct.out
@@ -0,0 +1,6 @@
+1
+2
+3
+1
+2
+3
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/dump.nf b/new-docs/nextflow-docs/snippets/dump.nf
new file mode 100644
index 0000000000..ff124ec09a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/dump.nf
@@ -0,0 +1,7 @@
+channel.of( 1, 2, 3 )
+    .map { v -> v + 1 }
+    .dump(tag: 'plus1')
+
+channel.of( 1, 2, 3 )
+    .map { v -> v ** 2 }
+    .dump(tag: 'exp2')
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/filter-closure.nf b/new-docs/nextflow-docs/snippets/filter-closure.nf
new file mode 100644
index 0000000000..8ed1199d2a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/filter-closure.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4, 5 )
+    .filter { v -> v % 2 == 1 }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/filter-closure.out b/new-docs/nextflow-docs/snippets/filter-closure.out
new file mode 100644
index 0000000000..b2a630f360
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/filter-closure.out
@@ -0,0 +1,3 @@
+1
+3
+5
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/filter-regex.nf b/new-docs/nextflow-docs/snippets/filter-regex.nf
new file mode 100644
index 0000000000..78b39ae394
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/filter-regex.nf
@@ -0,0 +1,3 @@
+channel.of( 'a', 'b', 'aa', 'bc', 3, 4.5 )
+    .filter( ~/^a.*/ )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/filter-regex.out b/new-docs/nextflow-docs/snippets/filter-regex.out
new file mode 100644
index 0000000000..20c5a71c64
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/filter-regex.out
@@ -0,0 +1,2 @@
+a
+aa
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/filter-type.nf b/new-docs/nextflow-docs/snippets/filter-type.nf
new file mode 100644
index 0000000000..d838fb4c50
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/filter-type.nf
@@ -0,0 +1,3 @@
+channel.of( 'a', 'b', 'aa', 'bc', 3, 4.5 )
+    .filter( Number )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/filter-type.out b/new-docs/nextflow-docs/snippets/filter-type.out
new file mode 100644
index 0000000000..589bf560b8
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/filter-type.out
@@ -0,0 +1,2 @@
+3
+4.5
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/first.nf b/new-docs/nextflow-docs/snippets/first.nf
new file mode 100644
index 0000000000..4c0373def2
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/first.nf
@@ -0,0 +1,19 @@
+// no condition is specified, emits the very first item: 1
+channel.of( 1, 2, 3 )
+    .first()
+    .view()
+
+// emits the first item matching the regular expression: 'aa'
+channel.of( 'a', 'aa', 'aaa' )
+    .first( ~/aa.*/ )
+    .view()
+
+// emits the first String value: 'a'
+channel.of( 1, 2, 'a', 'b', 3 )
+    .first( String )
+    .view()
+
+// emits the first item for which the predicate evaluates to true: 4
+channel.of( 1, 2, 3, 4, 5 )
+    .first { v -> v > 3 }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/first.out b/new-docs/nextflow-docs/snippets/first.out
new file mode 100644
index 0000000000..63db24ea5e
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/first.out
@@ -0,0 +1,4 @@
+1
+a
+aa
+4
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/flatmap-list.nf b/new-docs/nextflow-docs/snippets/flatmap-list.nf
new file mode 100644
index 0000000000..8d2bcf9a6f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/flatmap-list.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3 )
+    .flatMap { n -> [ n, n*2, n*3 ] }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/flatmap-list.out b/new-docs/nextflow-docs/snippets/flatmap-list.out
new file mode 100644
index 0000000000..68effb8e5e
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/flatmap-list.out
@@ -0,0 +1,9 @@
+1
+2
+3
+2
+4
+6
+3
+6
+9
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/flatmap-map.nf b/new-docs/nextflow-docs/snippets/flatmap-map.nf
new file mode 100644
index 0000000000..82b434d201
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/flatmap-map.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3 )
+    .flatMap { n -> [ number: n, square: n*n, cube: n*n*n ] }
+    .view { entry -> "${entry.key}: ${entry.value}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/flatmap-map.out b/new-docs/nextflow-docs/snippets/flatmap-map.out
new file mode 100644
index 0000000000..a269dccd60
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/flatmap-map.out
@@ -0,0 +1,9 @@
+number: 1
+square: 1
+cube: 1
+number: 2
+square: 4
+cube: 8
+number: 3
+square: 9
+cube: 27
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/flatten.nf b/new-docs/nextflow-docs/snippets/flatten.nf
new file mode 100644
index 0000000000..5a234be446
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/flatten.nf
@@ -0,0 +1,3 @@
+channel.of( [1, [2, 3]], 4, [5, [6]] )
+    .flatten()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/flatten.out b/new-docs/nextflow-docs/snippets/flatten.out
new file mode 100644
index 0000000000..cf0389a5af
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/flatten.out
@@ -0,0 +1,6 @@
+1
+2
+3
+4
+5
+6
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/grouptuple-by.nf b/new-docs/nextflow-docs/snippets/grouptuple-by.nf
new file mode 100644
index 0000000000..819e0ee0b5
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/grouptuple-by.nf
@@ -0,0 +1,3 @@
+channel.of( [1, 'A'], [1, 'B'], [2, 'C'], [3, 'B'], [1, 'C'], [2, 'A'], [3, 'D'] )
+    .groupTuple(by: 1)
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/grouptuple-by.out b/new-docs/nextflow-docs/snippets/grouptuple-by.out
new file mode 100644
index 0000000000..70fb39833d
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/grouptuple-by.out
@@ -0,0 +1,4 @@
+[[1, 2], A]
+[[1, 3], B]
+[[2, 1], C]
+[[3], D]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/grouptuple-groupkey.nf b/new-docs/nextflow-docs/snippets/grouptuple-groupkey.nf
new file mode 100644
index 0000000000..dbe121061e
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/grouptuple-groupkey.nf
@@ -0,0 +1,13 @@
+channel.of(
+        ['chr1', ['/path/to/region1_chr1.vcf', '/path/to/region2_chr1.vcf']],
+        ['chr2', ['/path/to/region1_chr2.vcf', '/path/to/region2_chr2.vcf', '/path/to/region3_chr2.vcf']],
+    )
+    .flatMap { chr, vcfs ->
+        vcfs.collect { vcf ->
+            tuple(groupKey(chr, vcfs.size()), vcf)              // preserve group size with key
+        }
+    }
+    .view { v -> "scattered: ${v}" }
+    .groupTuple()
+    .map { key, vcfs -> tuple(key.getGroupTarget(), vcfs) }     // unwrap group key
+    .view { v -> "gathered: ${v}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/grouptuple-groupkey.out b/new-docs/nextflow-docs/snippets/grouptuple-groupkey.out
new file mode 100644
index 0000000000..be3f00185b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/grouptuple-groupkey.out
@@ -0,0 +1,7 @@
+scattered: [chr1, /path/to/region1_chr1.vcf]
+scattered: [chr1, /path/to/region2_chr1.vcf]
+scattered: [chr2, /path/to/region1_chr2.vcf]
+scattered: [chr2, /path/to/region2_chr2.vcf]
+scattered: [chr2, /path/to/region3_chr2.vcf]
+gathered: [chr1, [/path/to/region1_chr1.vcf, /path/to/region2_chr1.vcf]]
+gathered: [chr2, [/path/to/region1_chr2.vcf, /path/to/region2_chr2.vcf, /path/to/region3_chr2.vcf]]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/grouptuple.nf b/new-docs/nextflow-docs/snippets/grouptuple.nf
new file mode 100644
index 0000000000..1180c850e9
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/grouptuple.nf
@@ -0,0 +1,3 @@
+channel.of( [1, 'A'], [1, 'B'], [2, 'C'], [3, 'B'], [1, 'C'], [2, 'A'], [3, 'D'] )
+    .groupTuple()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/grouptuple.out b/new-docs/nextflow-docs/snippets/grouptuple.out
new file mode 100644
index 0000000000..4d11258ce8
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/grouptuple.out
@@ -0,0 +1,3 @@
+[1, [A, B, C]]
+[2, [C, A]]
+[3, [B, D]]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/ifempty-1.nf b/new-docs/nextflow-docs/snippets/ifempty-1.nf
new file mode 100644
index 0000000000..f18604d55f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/ifempty-1.nf
@@ -0,0 +1 @@
+Channel .of(1, 2, 3) .ifEmpty('Hello') .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/ifempty-1.out b/new-docs/nextflow-docs/snippets/ifempty-1.out
new file mode 100644
index 0000000000..5f5fbe759f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/ifempty-1.out
@@ -0,0 +1,3 @@
+1
+2
+3
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/ifempty-2.nf b/new-docs/nextflow-docs/snippets/ifempty-2.nf
new file mode 100644
index 0000000000..3fdc4abacb
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/ifempty-2.nf
@@ -0,0 +1 @@
+Channel .empty() .ifEmpty('Hello') .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/ifempty-2.out b/new-docs/nextflow-docs/snippets/ifempty-2.out
new file mode 100644
index 0000000000..5ab2f8a432
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/ifempty-2.out
@@ -0,0 +1 @@
+Hello
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/join-with-remainder.nf b/new-docs/nextflow-docs/snippets/join-with-remainder.nf
new file mode 100644
index 0000000000..fa6cb24f92
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/join-with-remainder.nf
@@ -0,0 +1,4 @@
+left  = channel.of( ['X', 1], ['Y', 2], ['Z', 3], ['P', 7] )
+right = channel.of( ['Z', 6], ['Y', 5], ['X', 4] )
+
+left.join(right, remainder: true).view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/join-with-remainder.out b/new-docs/nextflow-docs/snippets/join-with-remainder.out
new file mode 100644
index 0000000000..2f37fc3195
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/join-with-remainder.out
@@ -0,0 +1,4 @@
+[Y, 2, 5]
+[Z, 3, 6]
+[X, 1, 4]
+[P, 7, null]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/join.nf b/new-docs/nextflow-docs/snippets/join.nf
new file mode 100644
index 0000000000..f94f627629
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/join.nf
@@ -0,0 +1,4 @@
+left  = channel.of( ['X', 1], ['Y', 2], ['Z', 3], ['P', 7] )
+right = channel.of( ['Z', 6], ['Y', 5], ['X', 4] )
+
+left.join(right).view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/join.out b/new-docs/nextflow-docs/snippets/join.out
new file mode 100644
index 0000000000..69ebb21e93
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/join.out
@@ -0,0 +1,3 @@
+[Z, 3, 6]
+[Y, 2, 5]
+[X, 1, 4]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/last.nf b/new-docs/nextflow-docs/snippets/last.nf
new file mode 100644
index 0000000000..4dde79ec01
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/last.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4, 5, 6 )
+    .last()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/last.out b/new-docs/nextflow-docs/snippets/last.out
new file mode 100644
index 0000000000..62f9457511
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/last.out
@@ -0,0 +1 @@
+6
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/map.nf b/new-docs/nextflow-docs/snippets/map.nf
new file mode 100644
index 0000000000..56442be008
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/map.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4, 5 )
+    .map { v -> v * v }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/map.out b/new-docs/nextflow-docs/snippets/map.out
new file mode 100644
index 0000000000..1ba204d253
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/map.out
@@ -0,0 +1,5 @@
+1
+4
+9
+16
+25
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/max-with-comparator.nf b/new-docs/nextflow-docs/snippets/max-with-comparator.nf
new file mode 100644
index 0000000000..1793ea9d01
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/max-with-comparator.nf
@@ -0,0 +1,4 @@
+// comparator function
+channel.of( "hello", "hi", "hey" )
+    .max { a, b -> a.length() <=> b.length() }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/max-with-comparator.out b/new-docs/nextflow-docs/snippets/max-with-comparator.out
new file mode 100644
index 0000000000..b6fc4c620b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/max-with-comparator.out
@@ -0,0 +1 @@
+hello
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/max-with-mapper.nf b/new-docs/nextflow-docs/snippets/max-with-mapper.nf
new file mode 100644
index 0000000000..c52c938082
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/max-with-mapper.nf
@@ -0,0 +1,4 @@
+// mapping function
+channel.of( "hello", "hi", "hey" )
+    .max { v -> v.length() }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/max-with-mapper.out b/new-docs/nextflow-docs/snippets/max-with-mapper.out
new file mode 100644
index 0000000000..b6fc4c620b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/max-with-mapper.out
@@ -0,0 +1 @@
+hello
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/max.nf b/new-docs/nextflow-docs/snippets/max.nf
new file mode 100644
index 0000000000..6b7cf21785
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/max.nf
@@ -0,0 +1,3 @@
+channel.of( 8, 6, 2, 5 )
+    .max()
+    .view { v -> "Max value is $v" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/max.out b/new-docs/nextflow-docs/snippets/max.out
new file mode 100644
index 0000000000..3c19a5458f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/max.out
@@ -0,0 +1 @@
+Max value is 8
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/merge-with-mapper.nf b/new-docs/nextflow-docs/snippets/merge-with-mapper.nf
new file mode 100644
index 0000000000..779ad42ff9
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/merge-with-mapper.nf
@@ -0,0 +1,6 @@
+odds  = channel.of(1, 3, 5, 7, 9)
+evens = channel.of(2, 4, 6)
+
+odds
+    .merge( evens ) { a, b -> tuple(b*b, a) }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/merge-with-mapper.out b/new-docs/nextflow-docs/snippets/merge-with-mapper.out
new file mode 100644
index 0000000000..00cb7ff5af
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/merge-with-mapper.out
@@ -0,0 +1,3 @@
+[16, 3]
+[36, 5]
+[4, 1]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/merge.nf b/new-docs/nextflow-docs/snippets/merge.nf
new file mode 100644
index 0000000000..fc8409935f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/merge.nf
@@ -0,0 +1,6 @@
+odds  = channel.of(1, 3, 5, 7, 9)
+evens = channel.of(2, 4, 6)
+
+odds
+    .merge( evens )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/merge.out b/new-docs/nextflow-docs/snippets/merge.out
new file mode 100644
index 0000000000..f6c49d0277
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/merge.out
@@ -0,0 +1,3 @@
+[1, 2]
+[3, 4]
+[5, 6]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/min-with-comparator.nf b/new-docs/nextflow-docs/snippets/min-with-comparator.nf
new file mode 100644
index 0000000000..ae3a7b8593
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/min-with-comparator.nf
@@ -0,0 +1,4 @@
+// comparator function
+channel.of( "hello", "hi", "hey" )
+    .min { a, b -> a.length() <=> b.length() }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/min-with-comparator.out b/new-docs/nextflow-docs/snippets/min-with-comparator.out
new file mode 100644
index 0000000000..32f95c0d12
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/min-with-comparator.out
@@ -0,0 +1 @@
+hi
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/min-with-mapper.nf b/new-docs/nextflow-docs/snippets/min-with-mapper.nf
new file mode 100644
index 0000000000..f8ebe9826d
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/min-with-mapper.nf
@@ -0,0 +1,4 @@
+// mapping function
+channel.of( "hello", "hi", "hey" )
+    .min { v -> v.length() }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/min-with-mapper.out b/new-docs/nextflow-docs/snippets/min-with-mapper.out
new file mode 100644
index 0000000000..32f95c0d12
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/min-with-mapper.out
@@ -0,0 +1 @@
+hi
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/min.nf b/new-docs/nextflow-docs/snippets/min.nf
new file mode 100644
index 0000000000..2bf8d29d2c
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/min.nf
@@ -0,0 +1,3 @@
+channel.of( 8, 6, 2, 5 )
+    .min()
+    .view { v -> "Min value is $v" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/min.out b/new-docs/nextflow-docs/snippets/min.out
new file mode 100644
index 0000000000..d2da450bea
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/min.out
@@ -0,0 +1 @@
+Min value is 2
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/mix.nf b/new-docs/nextflow-docs/snippets/mix.nf
new file mode 100644
index 0000000000..002f7575cf
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/mix.nf
@@ -0,0 +1,5 @@
+c1 = channel.of( 1, 2, 3 )
+c2 = channel.of( 'a', 'b' )
+c3 = channel.of( 'z' )
+
+c1.mix(c2, c3).view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/mix.out b/new-docs/nextflow-docs/snippets/mix.out
new file mode 100644
index 0000000000..a2d71225e4
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/mix.out
@@ -0,0 +1,6 @@
+1
+2
+3
+a
+b
+z
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/multimap-criteria.nf b/new-docs/nextflow-docs/snippets/multimap-criteria.nf
new file mode 100644
index 0000000000..0b0c350940
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/multimap-criteria.nf
@@ -0,0 +1,12 @@
+def criteria = multiMapCriteria { v ->
+    small: [v, v < 10]
+    large: [v, v > 10]
+}
+
+channel.of(1, 2, 30).multiMap(criteria).set { ch1 }
+channel.of(10, 20, 1).multiMap(criteria).set { ch2 }
+
+ch1.small.view { v, is_small -> "ch1: $v is small: $is_small" }
+ch1.large.view { v, is_large -> "ch1: $v is large: $is_large" }
+ch2.small.view { v, is_small -> "ch2: $v is small: $is_small" }
+ch2.large.view { v, is_large -> "ch2: $v is large: $is_large" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/multimap-criteria.out b/new-docs/nextflow-docs/snippets/multimap-criteria.out
new file mode 100644
index 0000000000..5657e20905
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/multimap-criteria.out
@@ -0,0 +1,12 @@
+ch1: 1 is large: false
+ch1: 1 is small: true
+ch1: 2 is large: false
+ch1: 2 is small: true
+ch1: 30 is large: true
+ch1: 30 is small: false
+ch2: 1 is large: false
+ch2: 1 is small: true
+ch2: 10 is large: false
+ch2: 10 is small: false
+ch2: 20 is large: true
+ch2: 20 is small: false
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/multimap-shared.nf b/new-docs/nextflow-docs/snippets/multimap-shared.nf
new file mode 100644
index 0000000000..3622fde3db
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/multimap-shared.nf
@@ -0,0 +1,6 @@
+channel.of( 1, 2, 3 )
+    .multiMap { v -> alpha: beta: v }
+    .set { result }
+
+result.alpha.view { v -> "alpha $v" }
+result.beta.view { v -> "beta $v" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/multimap-shared.out b/new-docs/nextflow-docs/snippets/multimap-shared.out
new file mode 100644
index 0000000000..353c4b2a2a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/multimap-shared.out
@@ -0,0 +1,6 @@
+alpha 1
+alpha 2
+alpha 3
+beta 1
+beta 2
+beta 3
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/multimap.nf b/new-docs/nextflow-docs/snippets/multimap.nf
new file mode 100644
index 0000000000..37e57e41bc
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/multimap.nf
@@ -0,0 +1,9 @@
+channel.of( 1, 2, 3, 4 )
+    .multiMap { v ->
+        inc: v + 1
+        squared: v * v
+    }
+    .set { result }
+
+result.inc.view { v -> "inc $v" }
+result.squared.view { v -> "squared $v" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/multimap.out b/new-docs/nextflow-docs/snippets/multimap.out
new file mode 100644
index 0000000000..b055e7da06
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/multimap.out
@@ -0,0 +1,8 @@
+inc 2
+inc 3
+inc 4
+inc 5
+squared 1
+squared 4
+squared 9
+squared 16
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/process-out-env.nf b/new-docs/nextflow-docs/snippets/process-out-env.nf
new file mode 100644
index 0000000000..604aa6c9e3
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/process-out-env.nf
@@ -0,0 +1,13 @@
+process seq {
+    output:
+    env 'RESULT'
+
+    script:
+    '''
+    RESULT=$(seq 5)
+    '''
+}
+
+workflow {
+    seq | view
+}
diff --git a/new-docs/nextflow-docs/snippets/process-out-env.out b/new-docs/nextflow-docs/snippets/process-out-env.out
new file mode 100644
index 0000000000..85954eabcf
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/process-out-env.out
@@ -0,0 +1,5 @@
+1
+2
+3
+4
+5
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/process-out-eval.nf b/new-docs/nextflow-docs/snippets/process-out-eval.nf
new file mode 100644
index 0000000000..c3faccc6d8
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/process-out-eval.nf
@@ -0,0 +1,13 @@
+process hello {
+    output:
+    eval('echo Hello world!')
+
+    script:
+    """
+    true
+    """
+}
+
+workflow {
+    hello | view
+}
diff --git a/new-docs/nextflow-docs/snippets/process-out-eval.out b/new-docs/nextflow-docs/snippets/process-out-eval.out
new file mode 100644
index 0000000000..6769dd60bd
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/process-out-eval.out
@@ -0,0 +1 @@
+Hello world!
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/process-out-singleton.nf b/new-docs/nextflow-docs/snippets/process-out-singleton.nf
new file mode 100644
index 0000000000..11494134b5
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/process-out-singleton.nf
@@ -0,0 +1,29 @@
+process echo {
+  input:
+  val greeting
+
+  output:
+  val greeting
+
+  exec:
+  true
+}
+
+process greet {
+  input:
+  val greeting
+  val name
+
+  output:
+  val "$greeting, $name!"
+
+  exec:
+  true
+}
+
+workflow {
+  names = channel.of( 'World', 'Mundo', 'Welt' )
+  greeting = echo('Hello')
+  result = greet(greeting, names)
+  result.view()
+}
diff --git a/new-docs/nextflow-docs/snippets/process-out-singleton.out b/new-docs/nextflow-docs/snippets/process-out-singleton.out
new file mode 100644
index 0000000000..341ff0d02f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/process-out-singleton.out
@@ -0,0 +1,3 @@
+Hello, World!
+Hello, Mundo!
+Hello, Welt!
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/process-stdout.nf b/new-docs/nextflow-docs/snippets/process-stdout.nf
new file mode 100644
index 0000000000..4c6d79a368
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/process-stdout.nf
@@ -0,0 +1,13 @@
+process hello {
+    output:
+    stdout
+
+    script:
+    """
+    echo "Hello world!"
+    """
+}
+
+workflow {
+    hello | view { message -> "I say... $message" }
+}
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/process-stdout.out b/new-docs/nextflow-docs/snippets/process-stdout.out
new file mode 100644
index 0000000000..6df702c6e8
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/process-stdout.out
@@ -0,0 +1,2 @@
+I say... Hello world!
+
diff --git a/new-docs/nextflow-docs/snippets/random-sample-with-seed.nf b/new-docs/nextflow-docs/snippets/random-sample-with-seed.nf
new file mode 100644
index 0000000000..c85be233a7
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/random-sample-with-seed.nf
@@ -0,0 +1,3 @@
+channel.of( 1..100 )
+    .randomSample( 10, 234 )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/random-sample.nf b/new-docs/nextflow-docs/snippets/random-sample.nf
new file mode 100644
index 0000000000..470525a161
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/random-sample.nf
@@ -0,0 +1,3 @@
+channel.of( 1..100 )
+    .randomSample( 10 )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/recurse-process.nf b/new-docs/nextflow-docs/snippets/recurse-process.nf
new file mode 100644
index 0000000000..bbfa676aab
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/recurse-process.nf
@@ -0,0 +1,22 @@
+nextflow.preview.recursion = true
+
+params.start = 10
+
+workflow {
+    count_down
+        .recurse(params.start)
+        .until { v -> v == 0 }
+        .view { v -> "${v}..." }
+}
+
+process count_down {
+    input:
+    val v
+
+    output:
+    val v
+
+    exec:
+    sleep(1000)
+    v = v - 1
+}
diff --git a/new-docs/nextflow-docs/snippets/recurse-process.out b/new-docs/nextflow-docs/snippets/recurse-process.out
new file mode 100644
index 0000000000..870bbc2113
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/recurse-process.out
@@ -0,0 +1,10 @@
+9...
+8...
+7...
+6...
+5...
+4...
+3...
+2...
+1...
+0...
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/recurse-workflow.in b/new-docs/nextflow-docs/snippets/recurse-workflow.in
new file mode 100644
index 0000000000..ce01362503
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/recurse-workflow.in
@@ -0,0 +1 @@
+hello
diff --git a/new-docs/nextflow-docs/snippets/recurse-workflow.nf b/new-docs/nextflow-docs/snippets/recurse-workflow.nf
new file mode 100644
index 0000000000..40a1d3230c
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/recurse-workflow.nf
@@ -0,0 +1,46 @@
+nextflow.preview.recursion = true
+
+params.input = "recurse-workflow.in"
+
+workflow {
+    clock
+        .recurse(file(params.input))
+        .until { file -> file.size() > 64 }
+        .view { file -> file.text }
+}
+
+workflow clock {
+    take:
+    logfile
+
+    emit:
+    tock(tick(logfile))
+}
+
+process tick {
+    input:
+    path 'input.txt'
+
+    output:
+    path 'result.txt'
+
+    script:
+    """
+    cat input.txt > result.txt
+    echo "Task ${task.index} : tick" >> result.txt
+    """
+}
+
+process tock {
+    input:
+    path 'input.txt'
+
+    output:
+    path 'result.txt'
+
+    script:
+    """
+    cat input.txt > result.txt
+    echo "Task ${task.index} : tock" >> result.txt
+    """
+}
diff --git a/new-docs/nextflow-docs/snippets/recurse-workflow.out b/new-docs/nextflow-docs/snippets/recurse-workflow.out
new file mode 100644
index 0000000000..ad3a4c6bc0
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/recurse-workflow.out
@@ -0,0 +1,18 @@
+hello
+Task 1 : tick
+Task 1 : tock
+
+hello
+Task 1 : tick
+Task 1 : tock
+Task 2 : tick
+Task 2 : tock
+
+hello
+Task 1 : tick
+Task 1 : tock
+Task 2 : tick
+Task 2 : tock
+Task 3 : tick
+Task 3 : tock
+
diff --git a/new-docs/nextflow-docs/snippets/reduce-with-initial-value.nf b/new-docs/nextflow-docs/snippets/reduce-with-initial-value.nf
new file mode 100644
index 0000000000..c834e46f66
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/reduce-with-initial-value.nf
@@ -0,0 +1,6 @@
+channel.of( 1, 2, 3, 4, 5 )
+    .reduce( 'result:' ) { acc, v ->
+        println acc
+        acc + ' ' + v
+    }
+    .view { result -> "final $result" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/reduce-with-initial-value.out b/new-docs/nextflow-docs/snippets/reduce-with-initial-value.out
new file mode 100644
index 0000000000..9737132fa4
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/reduce-with-initial-value.out
@@ -0,0 +1,6 @@
+result:
+result: 1
+result: 1 2
+result: 1 2 3
+result: 1 2 3 4
+final result: 1 2 3 4 5
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/reduce.nf b/new-docs/nextflow-docs/snippets/reduce.nf
new file mode 100644
index 0000000000..c792ee4fc8
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/reduce.nf
@@ -0,0 +1,6 @@
+channel.of( 1, 2, 3, 4, 5 )
+    .reduce { a, b ->
+        println "a: $a b: $b"
+        a + b
+    }
+    .view { result -> "result = $result" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/reduce.out b/new-docs/nextflow-docs/snippets/reduce.out
new file mode 100644
index 0000000000..5ed1862ac3
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/reduce.out
@@ -0,0 +1,5 @@
+a: 1 b: 2
+a: 3 b: 3
+a: 6 b: 4
+a: 10 b: 5
+result = 15
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitcsv-with-columns.nf b/new-docs/nextflow-docs/snippets/splitcsv-with-columns.nf
new file mode 100644
index 0000000000..8a4dea4a88
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitcsv-with-columns.nf
@@ -0,0 +1,3 @@
+channel.of( 'alpha,beta,gamma\n10,20,30\n70,80,90' )
+    .splitCsv( header: ['col1', 'col2', 'col3'], skip: 1 )
+    .view { row -> "${row.col1} - ${row.col2} - ${row.col3}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitcsv-with-columns.out b/new-docs/nextflow-docs/snippets/splitcsv-with-columns.out
new file mode 100644
index 0000000000..7214f60d10
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitcsv-with-columns.out
@@ -0,0 +1,2 @@
+10 - 20 - 30
+70 - 80 - 90
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitcsv-with-header.nf b/new-docs/nextflow-docs/snippets/splitcsv-with-header.nf
new file mode 100644
index 0000000000..c54e81d0f7
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitcsv-with-header.nf
@@ -0,0 +1,3 @@
+channel.of( 'alpha,beta,gamma\n10,20,30\n70,80,90' )
+    .splitCsv( header: true )
+    .view { row -> "${row.alpha} - ${row.beta} - ${row.gamma}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitcsv-with-header.out b/new-docs/nextflow-docs/snippets/splitcsv-with-header.out
new file mode 100644
index 0000000000..7214f60d10
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitcsv-with-header.out
@@ -0,0 +1,2 @@
+10 - 20 - 30
+70 - 80 - 90
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitcsv.nf b/new-docs/nextflow-docs/snippets/splitcsv.nf
new file mode 100644
index 0000000000..a8b4829846
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitcsv.nf
@@ -0,0 +1,3 @@
+channel.of( '10,20,30\n70,80,90' )
+    .splitCsv()
+    .view { row -> "${row[0]} - ${row[1]} - ${row[2]}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitcsv.out b/new-docs/nextflow-docs/snippets/splitcsv.out
new file mode 100644
index 0000000000..7214f60d10
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitcsv.out
@@ -0,0 +1,2 @@
+10 - 20 - 30
+70 - 80 - 90
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitjson-array.nf b/new-docs/nextflow-docs/snippets/splitjson-array.nf
new file mode 100644
index 0000000000..d19f7deba9
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitjson-array.nf
@@ -0,0 +1,4 @@
+// Example with a JSON array
+channel.of('[1, null, ["A", {}], true]')
+    .splitJson()
+    .view { v -> "Item: ${v}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitjson-array.out b/new-docs/nextflow-docs/snippets/splitjson-array.out
new file mode 100644
index 0000000000..a64844cb9f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitjson-array.out
@@ -0,0 +1,4 @@
+Item: 1
+Item: null
+Item: [A, [:]]
+Item: true
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitjson-error.log b/new-docs/nextflow-docs/snippets/splitjson-error.log
new file mode 100644
index 0000000000..035b4bf959
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitjson-error.log
@@ -0,0 +1,106 @@
+May-18 21:16:09.405 [main] DEBUG nextflow.cli.Launcher - $> ../../launch.sh -q run splitjson-with-path.nf
+May-18 21:16:09.489 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.05.0-edge
+May-18 21:16:09.531 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=dev; embedded=false; plugins-dir=/home/bent/projects/nextflow-io_nextflow/plugins; core-plugins: nf-amazon@2.0.0,nf-azure@1.1.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.0.6,nf-google@1.7.4,nf-tower@1.5.13,nf-wave@0.9.0
+May-18 21:16:09.531 [main] DEBUG nextflow.plugin.DevPluginManager - Add plugin root repository: /home/bent/projects/nextflow-io_nextflow/plugins
+May-18 21:16:09.535 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
+May-18 21:16:09.536 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
+May-18 21:16:09.542 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'development' mode
+May-18 21:16:09.553 [main] DEBUG nextflow.plugin.DevPluginClasspath - Groovy DEV plugin classpath: classes-dirs=[build/classes/groovy/main, build/classes/main, build/resources/main]; jars-dirs=[build/target/libs]
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-wave@0.9.0' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@2.0.0' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-google@1.7.4' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-ga4gh@1.0.6' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.5.13' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-codecommit@0.1.5' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-console@1.0.6' resolved
+May-18 21:16:09.565 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-azure@1.1.0' resolved
+May-18 21:16:09.612 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
+May-18 21:16:09.623 [main] INFO  nextflow.cli.CmdRun - Launching `splitjson-with-path.nf` [sad_hawking] DSL2 - revision: 75f20d5d34
+May-18 21:16:09.624 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
+May-18 21:16:09.624 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
+May-18 21:16:09.634 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/bent/.nextflow/secrets/store.json
+May-18 21:16:09.638 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@72805168] - activable => nextflow.secret.LocalSecretsProvider@72805168
+May-18 21:16:09.687 [main] DEBUG nextflow.Session - Session UUID: cd50afbf-cb5d-4dc2-87de-474cdc70dcc6
+May-18 21:16:09.687 [main] DEBUG nextflow.Session - Run name: sad_hawking
+May-18 21:16:09.688 [main] DEBUG nextflow.Session - Executor pool size: 12
+May-18 21:16:09.693 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
+May-18 21:16:09.697 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=36; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
+May-18 21:16:09.718 [main] DEBUG nextflow.cli.CmdRun - 
+  Version: 23.05.0-edge build 5864
+  Created: 19-05-2023 02:15 UTC (18-05-2023 21:15 CDT)
+  System: Linux 5.10.16.3-microsoft-standard-WSL2
+  Runtime: Groovy 3.0.17 on OpenJDK 64-Bit Server VM 17.0.6+10
+  Encoding: UTF-8 (UTF-8)
+  Process: 31895@LAPTOP-2GR8K3GP [127.0.1.1]
+  CPUs: 12 - Mem: 7.6 GB (4.5 GB) - Swap: 2 GB (2 GB)
+May-18 21:16:09.744 [main] DEBUG nextflow.Session - Work-dir: /home/bent/projects/nextflow-io_nextflow/docs/snippets/work [ext2/ext3]
+May-18 21:16:09.745 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/bent/projects/nextflow-io_nextflow/docs/snippets/bin
+May-18 21:16:09.752 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
+May-18 21:16:09.759 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
+May-18 21:16:09.771 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
+May-18 21:16:09.777 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 13; maxThreads: 1000
+May-18 21:16:09.841 [main] DEBUG nextflow.Session - Session start
+May-18 21:16:10.198 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
+May-18 21:16:10.259 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: 
+May-18 21:16:10.260 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
+May-18 21:16:10.260 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
+May-18 21:16:10.260 [main] DEBUG nextflow.Session - Session await
+May-18 21:16:10.260 [main] DEBUG nextflow.Session - Session await > all processes finished
+May-18 21:16:10.261 [main] DEBUG nextflow.Session - Session await > all barriers passed
+May-18 21:16:10.265 [Actor Thread 3] ERROR nextflow.extension.DataflowHelper - @unknown
+java.lang.IllegalStateException: Error while parsing JSON content - cause: java.lang.NullPointerException
+	at nextflow.splitter.JsonSplitter.process(JsonSplitter.groovy:95)
+	at nextflow.splitter.JsonSplitter.process(JsonSplitter.groovy)
+	at nextflow.splitter.AbstractSplitter.apply(AbstractSplitter.groovy:154)
+	at nextflow.extension.SplitOp$_applySplittingOperator_closure1.doCall(SplitOp.groovy:190)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
+	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
+	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
+	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
+	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
+	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
+	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
+	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
+	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
+	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
+	at nextflow.extension.DataflowHelper$_subscribeImpl_closure2.doCall(DataflowHelper.groovy:284)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
+	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
+	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
+	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
+	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
+	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
+	at groovy.lang.Closure.call(Closure.java:412)
+	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
+	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108)
+	at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
+	at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
+	at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
+	at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
+	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
+	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
+	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
+	at java.base/java.lang.Thread.run(Thread.java:833)
+Caused by: java.lang.NullPointerException: null
+	at java.base/java.util.Objects.requireNonNull(Objects.java:208)
+	at java.base/java.util.ImmutableCollections$MapN.<init>(ImmutableCollections.java:1186)
+	at java.base/java.util.Map.of(Map.java:1373)
+	at nextflow.splitter.JsonSplitter.processObject(JsonSplitter.groovy:224)
+	at nextflow.splitter.JsonSplitter.scanJsonForPath(JsonSplitter.groovy:138)
+	at nextflow.splitter.JsonSplitter.scanJsonForPath(JsonSplitter.groovy:144)
+	at nextflow.splitter.JsonSplitter.scanJsonForPath(JsonSplitter.groovy:128)
+	at nextflow.splitter.JsonSplitter.scanJsonForPath(JsonSplitter.groovy:144)
+	at nextflow.splitter.JsonSplitter.process(JsonSplitter.groovy:88)
+	... 35 common frames omitted
+May-18 21:16:10.271 [Actor Thread 3] DEBUG nextflow.Session - Session aborted -- Cause: Error while parsing JSON content - cause: java.lang.NullPointerException
+May-18 21:16:10.307 [Actor Thread 3] DEBUG nextflow.Session - The following nodes are still active:
+  [operator] splitJson
+  [operator] view
+
+May-18 21:16:10.343 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
+May-18 21:16:10.363 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
+May-18 21:16:10.392 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
diff --git a/new-docs/nextflow-docs/snippets/splitjson-object.nf b/new-docs/nextflow-docs/snippets/splitjson-object.nf
new file mode 100644
index 0000000000..f793b6adfe
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitjson-object.nf
@@ -0,0 +1,4 @@
+// Example with a JSON object
+channel.of('{"A": 1, "B": [1, 2, 3], "C": {"D": null}}')
+    .splitJson()
+    .view { v -> "Item: ${v}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitjson-object.out b/new-docs/nextflow-docs/snippets/splitjson-object.out
new file mode 100644
index 0000000000..0870901294
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitjson-object.out
@@ -0,0 +1,3 @@
+Item: [key:A, value:1]
+Item: [key:B, value:[1, 2, 3]]
+Item: [key:C, value:[D:null]]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitjson-with-path.nf b/new-docs/nextflow-docs/snippets/splitjson-with-path.nf
new file mode 100644
index 0000000000..2b2e08a870
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitjson-with-path.nf
@@ -0,0 +1,3 @@
+channel.of('{"A": 1, "B": [2, 3, {"C": {"D": null, "E": 4, "F": 5}}]}')
+    .splitJson(path: 'B[2].C')
+    .view { v -> "Item: ${v}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/splitjson-with-path.out b/new-docs/nextflow-docs/snippets/splitjson-with-path.out
new file mode 100644
index 0000000000..93b88e977b
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/splitjson-with-path.out
@@ -0,0 +1,3 @@
+Item: [key:D, value:null]
+Item: [key:E, value:4]
+Item: [key:F, value:5]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/subscribe-with-on-complete.nf b/new-docs/nextflow-docs/snippets/subscribe-with-on-complete.nf
new file mode 100644
index 0000000000..f5e2cf5bc1
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/subscribe-with-on-complete.nf
@@ -0,0 +1,2 @@
+channel.of( 1, 2, 3 )
+    .subscribe onNext: { v -> println v }, onComplete: { println 'Done' }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/subscribe-with-on-complete.out b/new-docs/nextflow-docs/snippets/subscribe-with-on-complete.out
new file mode 100644
index 0000000000..42244bce80
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/subscribe-with-on-complete.out
@@ -0,0 +1,4 @@
+1
+2
+3
+Done
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/subscribe.nf b/new-docs/nextflow-docs/snippets/subscribe.nf
new file mode 100644
index 0000000000..ed271cc199
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/subscribe.nf
@@ -0,0 +1,5 @@
+// define a channel emitting three values
+source = channel.of( 'alpha', 'beta', 'delta' )
+
+// subscribe to the channel with a function that prints each value
+source.subscribe { str -> println "Got: ${str}; len: ${str.length()}" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/subscribe.out b/new-docs/nextflow-docs/snippets/subscribe.out
new file mode 100644
index 0000000000..47e4bfcb14
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/subscribe.out
@@ -0,0 +1,3 @@
+Got: alpha; len: 5
+Got: beta; len: 4
+Got: delta; len: 5
diff --git a/new-docs/nextflow-docs/snippets/sum-with-mapper.nf b/new-docs/nextflow-docs/snippets/sum-with-mapper.nf
new file mode 100644
index 0000000000..166e5bf9c6
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/sum-with-mapper.nf
@@ -0,0 +1,3 @@
+channel.of( 4, 1, 7, 5 )
+    .sum { v -> v * v }
+    .view { result -> "Square: $result" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/sum-with-mapper.out b/new-docs/nextflow-docs/snippets/sum-with-mapper.out
new file mode 100644
index 0000000000..095ddac1e4
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/sum-with-mapper.out
@@ -0,0 +1 @@
+Square: 91
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/sum.nf b/new-docs/nextflow-docs/snippets/sum.nf
new file mode 100644
index 0000000000..696bb6a268
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/sum.nf
@@ -0,0 +1,3 @@
+channel.of( 8, 6, 2, 5 )
+    .sum()
+    .view { result -> "The sum is $result" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/sum.out b/new-docs/nextflow-docs/snippets/sum.out
new file mode 100644
index 0000000000..2c4b1b41ff
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/sum.out
@@ -0,0 +1 @@
+The sum is 21
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/take.nf b/new-docs/nextflow-docs/snippets/take.nf
new file mode 100644
index 0000000000..0989218393
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/take.nf
@@ -0,0 +1,3 @@
+channel.of( 1..10 )
+    .take( 3 )
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/take.out b/new-docs/nextflow-docs/snippets/take.out
new file mode 100644
index 0000000000..5f5fbe759f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/take.out
@@ -0,0 +1,3 @@
+1
+2
+3
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tap.nf b/new-docs/nextflow-docs/snippets/tap.nf
new file mode 100644
index 0000000000..19d4f5da5e
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tap.nf
@@ -0,0 +1,9 @@
+channel.of( 'a', 'b', 'c' )
+    .tap { log1 }
+    .map { v -> v * 2 }
+    .tap { log2 }
+    .map { v -> v.toUpperCase() }
+    .view { result -> "Result: $result" }
+
+log1.view { v -> "Log 1: $v" }
+log2.view { v -> "Log 2: $v" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tap.out b/new-docs/nextflow-docs/snippets/tap.out
new file mode 100644
index 0000000000..85b5cb1377
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tap.out
@@ -0,0 +1,9 @@
+Result: AA
+Result: BB
+Result: CC
+Log 1: a
+Log 1: b
+Log 1: c
+Log 2: aa
+Log 2: bb
+Log 2: cc
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/test.sh b/new-docs/nextflow-docs/snippets/test.sh
new file mode 100755
index 0000000000..42bd7236a9
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/test.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+
+exit_status=0
+
+NXF_CMD=${NXF_CMD:-nextflow}
+NXF_FILES=${*:-'*.nf'}
+
+for pipeline in $NXF_FILES ; do
+
+    echo "> Running test: $pipeline"
+
+    # run the pipeline
+    $NXF_CMD -q run "$pipeline" > .out
+
+    # verify output (if ground truth exists)
+    outfile="$(basename "$pipeline" .nf).out"
+
+    if [[ -f "$outfile" ]] ; then
+        sort "$outfile" > a.out
+        sort .out > b.out
+        diff a.out b.out
+        status=$? ; [ $status -eq 0 ] || exit_status=$status
+    else
+        echo "> $outfile not found, skipping"
+    fi
+
+done
+
+rm -rf .nextflow* work .out a.out b.out
+
+[ $exit_status -eq 0 ] || false
diff --git a/new-docs/nextflow-docs/snippets/tointeger.nf b/new-docs/nextflow-docs/snippets/tointeger.nf
new file mode 100644
index 0000000000..a8d5c67de0
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tointeger.nf
@@ -0,0 +1,4 @@
+channel.of( '1', '7', '12' )
+    .toInteger()
+    .sum()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tointeger.out b/new-docs/nextflow-docs/snippets/tointeger.out
new file mode 100644
index 0000000000..2edeafb09d
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tointeger.out
@@ -0,0 +1 @@
+20
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tolist.nf b/new-docs/nextflow-docs/snippets/tolist.nf
new file mode 100644
index 0000000000..f9303414b8
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tolist.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4 )
+    .toList()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tolist.out b/new-docs/nextflow-docs/snippets/tolist.out
new file mode 100644
index 0000000000..98d20c4307
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tolist.out
@@ -0,0 +1 @@
+[1, 2, 3, 4]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tosortedlist-with-comparator.nf b/new-docs/nextflow-docs/snippets/tosortedlist-with-comparator.nf
new file mode 100644
index 0000000000..6837d534c1
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tosortedlist-with-comparator.nf
@@ -0,0 +1,3 @@
+channel.of( ['homer', 5], ['bart', 2], ['lisa', 10], ['marge', 3], ['maggie', 7] )
+    .toSortedList { a, b -> b[1] <=> a[1] }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tosortedlist-with-comparator.out b/new-docs/nextflow-docs/snippets/tosortedlist-with-comparator.out
new file mode 100644
index 0000000000..ba7635ebd6
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tosortedlist-with-comparator.out
@@ -0,0 +1 @@
+[[lisa, 10], [maggie, 7], [homer, 5], [marge, 3], [bart, 2]]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tosortedlist.nf b/new-docs/nextflow-docs/snippets/tosortedlist.nf
new file mode 100644
index 0000000000..472bec20ca
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tosortedlist.nf
@@ -0,0 +1,3 @@
+channel.of( 3, 2, 1, 4 )
+    .toSortedList()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/tosortedlist.out b/new-docs/nextflow-docs/snippets/tosortedlist.out
new file mode 100644
index 0000000000..98d20c4307
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/tosortedlist.out
@@ -0,0 +1 @@
+[1, 2, 3, 4]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/transpose-1.nf b/new-docs/nextflow-docs/snippets/transpose-1.nf
new file mode 100644
index 0000000000..703812d6c9
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/transpose-1.nf
@@ -0,0 +1,7 @@
+channel.of(
+        [1, ['A', 'B', 'C']],
+        [2, ['C', 'A']],
+        [3, ['B', 'D']]
+    )
+    .transpose()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/transpose-1.out b/new-docs/nextflow-docs/snippets/transpose-1.out
new file mode 100644
index 0000000000..b7670a313e
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/transpose-1.out
@@ -0,0 +1,7 @@
+[1, A]
+[1, B]
+[1, C]
+[2, C]
+[2, A]
+[3, B]
+[3, D]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/transpose-2-with-remainder.nf b/new-docs/nextflow-docs/snippets/transpose-2-with-remainder.nf
new file mode 100644
index 0000000000..1dc2d1f970
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/transpose-2-with-remainder.nf
@@ -0,0 +1,7 @@
+channel.of(
+        [1, [1], ['A']],
+        [2, [1, 2], ['B', 'C']],
+        [3, [1, 2, 3], ['D', 'E']]
+    )
+    .transpose(remainder: true)
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/transpose-2-with-remainder.out b/new-docs/nextflow-docs/snippets/transpose-2-with-remainder.out
new file mode 100644
index 0000000000..c156136ee6
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/transpose-2-with-remainder.out
@@ -0,0 +1,6 @@
+[1, 1, A]
+[2, 1, B]
+[2, 2, C]
+[3, 1, D]
+[3, 2, E]
+[3, 3, null]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/transpose-2.nf b/new-docs/nextflow-docs/snippets/transpose-2.nf
new file mode 100644
index 0000000000..4d89345b42
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/transpose-2.nf
@@ -0,0 +1,7 @@
+channel.of(
+        [1, [1], ['A']],
+        [2, [1, 2], ['B', 'C']],
+        [3, [1, 2, 3], ['D', 'E']]
+    )
+    .transpose()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/transpose-2.out b/new-docs/nextflow-docs/snippets/transpose-2.out
new file mode 100644
index 0000000000..6c9ede99ac
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/transpose-2.out
@@ -0,0 +1,5 @@
+[1, 1, A]
+[2, 1, B]
+[2, 2, C]
+[3, 1, D]
+[3, 2, E]
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/unique-with-mapper.nf b/new-docs/nextflow-docs/snippets/unique-with-mapper.nf
new file mode 100644
index 0000000000..497855a078
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/unique-with-mapper.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 4, 6 )
+    .unique { v -> v % 2 }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/unique-with-mapper.out b/new-docs/nextflow-docs/snippets/unique-with-mapper.out
new file mode 100644
index 0000000000..7a754f414c
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/unique-with-mapper.out
@@ -0,0 +1,2 @@
+1
+2
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/unique.nf b/new-docs/nextflow-docs/snippets/unique.nf
new file mode 100644
index 0000000000..a4e44ecb9a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/unique.nf
@@ -0,0 +1,3 @@
+channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 2, 3 )
+    .unique()
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/unique.out b/new-docs/nextflow-docs/snippets/unique.out
new file mode 100644
index 0000000000..5f5fbe759f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/unique.out
@@ -0,0 +1,3 @@
+1
+2
+3
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/until.nf b/new-docs/nextflow-docs/snippets/until.nf
new file mode 100644
index 0000000000..fd20f3726a
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/until.nf
@@ -0,0 +1,3 @@
+channel.of( 3, 2, 1, 5, 1, 5 )
+    .until { v -> v == 5 }
+    .view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/until.out b/new-docs/nextflow-docs/snippets/until.out
new file mode 100644
index 0000000000..339b1ea033
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/until.out
@@ -0,0 +1,3 @@
+3
+2
+1
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/view-with-mapper.nf b/new-docs/nextflow-docs/snippets/view-with-mapper.nf
new file mode 100644
index 0000000000..70f8000171
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/view-with-mapper.nf
@@ -0,0 +1,3 @@
+channel.of(1, 2, 3)
+    .map { v -> [v, v*v] }
+    .view { num, sqr -> "The square of $num is $sqr" }
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/view-with-mapper.out b/new-docs/nextflow-docs/snippets/view-with-mapper.out
new file mode 100644
index 0000000000..4244d7cbfa
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/view-with-mapper.out
@@ -0,0 +1,3 @@
+The square of 1 is 1
+The square of 2 is 4
+The square of 3 is 9
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/view.nf b/new-docs/nextflow-docs/snippets/view.nf
new file mode 100644
index 0000000000..ec0933dc39
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/view.nf
@@ -0,0 +1 @@
+channel.of(1, 2, 3).view()
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/view.out b/new-docs/nextflow-docs/snippets/view.out
new file mode 100644
index 0000000000..5f5fbe759f
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/view.out
@@ -0,0 +1,3 @@
+1
+2
+3
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/snippets/your-first-script.nf b/new-docs/nextflow-docs/snippets/your-first-script.nf
new file mode 100644
index 0000000000..97574858b2
--- /dev/null
+++ b/new-docs/nextflow-docs/snippets/your-first-script.nf
@@ -0,0 +1,28 @@
+params.str = 'Hello world!'
+
+process split_letters {
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf '${params.str}' | split -b 6 - chunk_
+    """
+}
+
+process convert_to_upper {
+    input:
+    path x
+
+    output:
+    stdout
+
+    script:
+    """
+    cat $x | tr '[a-z]' '[A-Z]'
+    """
+}
+
+workflow {
+    split_letters | flatten | convert_to_upper | view { v -> v.trim() }
+}
diff --git a/docs/spack.md b/new-docs/nextflow-docs/spack.mdx
similarity index 79%
rename from docs/spack.md
rename to new-docs/nextflow-docs/spack.mdx
index 1f044afc04..7b53c4be4e 100644
--- a/docs/spack.md
+++ b/new-docs/nextflow-docs/spack.mdx
@@ -1,9 +1,8 @@
-(spack-page)=
+
 
 # Spack environments
 
-:::{versionadded} 23.02.0-edge
-:::
+<AddedInVersion version="23.02.0-edge" />
 
 [Spack](https://spack.io/) is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. Spack is not tied to a particular language; you can build a software stack in Python or R, link to libraries written in C, C++, or Fortran, and easily swap compilers or target specific CPU microarchitectures.
 
@@ -19,21 +18,21 @@ This feature requires the [Spack](https://spack.io) package manager to be instal
 
 Nextflow automatically creates and activates the Spack environment(s) given the dependencies specified by each process.
 
-Dependencies are specified by using the {ref}`process-spack` directive, providing either the names of the required Spack packages, the path of a Spack environment yaml file or the path of an existing Spack environment directory.
+Dependencies are specified by using the [spack][process-spack] directive, providing either the names of the required Spack packages, the path of a Spack environment yaml file or the path of an existing Spack environment directory.
 
-:::{note}
+:::note
 Spack always installs the software packages in its own directories, regardless of the Nextflow specifications. The Spack environment created by Nextflow only contains symbolic links pointing to the appropriate package locations, and therefore it is relatively small in size.
 :::
 
-You can specify the directory where the Spack environment is stored using the `spack.cacheDir` configuration property (see the {ref}`configuration page <config-spack>` for details). When using a computing cluster, make sure to use a shared file system path accessible from all compute nodes.
+You can specify the directory where the Spack environment is stored using the `spack.cacheDir` configuration property (see [spack][config-spack] for more information). When using a computing cluster, make sure to use a shared file system path accessible from all compute nodes.
 
-:::{warning}
+:::warning
 The Spack environment feature is not supported by executors that use remote object storage as the work directory, e.g. AWS Batch.
 :::
 
 ### Enabling Spack environment
 
-The use of Spack recipes specified using the {ref}`process-spack` directive needs to be enabled explicitly by setting the option shown below in the pipeline configuration file (i.e. `nextflow.config`):
+The use of Spack recipes specified using the [spack][process-spack] directive needs to be enabled explicitly by setting the option shown below in the pipeline configuration file (i.e. `nextflow.config`):
 
 ```groovy
 spack.enabled = true
@@ -60,7 +59,7 @@ Using the above definition, a Spack environment that includes BWA, Samtools, and
 
 The usual Spack package syntax and naming conventions can be used. The version of a package can be specified after the package name like so: `bwa@0.7.15`.
 
-Spack is able to infer the local CPU microarchitecture and optimize the build accordingly. If you really need to customize this option, you can use the {ref}`process-arch` directive.
+Spack is able to infer the local CPU microarchitecture and optimize the build accordingly. If you really need to customize this option, you can use the [arch][process-arch] directive.
 
 Read the Spack documentation for more details about [package specifications](https://spack.readthedocs.io/en/latest/basic_usage.html#specs-dependencies).
 
@@ -80,11 +79,11 @@ spack:
 
 Here, the `concretizer` option is a sensible default for Spack environments.
 
-:::{note}
+:::note
 When creating a Spack environment, Nextflow always enables the corresponding Spack view. This is required by Nextflow to locate executables at pipeline runtime.
 :::
 
-As mentioned above, Spack is able to guess the target CPU microarchitecture and optimize the build accordingly. If you really need to customize this option, we advise to use the {ref}`process-arch` directive rather than the available options for the Spack environment file.
+As mentioned above, Spack is able to guess the target CPU microarchitecture and optimize the build accordingly. If you really need to customize this option, we advise to use the [arch][process-arch] directive rather than the available options for the Spack environment file.
 
 Read the Spack documentation for more details about how to create [environment files](https://spack.readthedocs.io/en/latest/environments.html).
 
@@ -101,7 +100,7 @@ process hello {
 }
 ```
 
-:::{warning}
+:::warning
 The environment file name **must** have a `.yaml` extension or else it won't be properly recognized.
 :::
 
@@ -142,13 +141,13 @@ Spack builds most software package from their source codes, and it does this for
 2. Use the Nextflow stub functionality prior to running the pipeline for production.
    Nextflow will run the stub pipeline, skipping process executions but still setting up the required software packages.
    This option is useful if it is not possible to write a Spack yaml file for the environment.
-   The stub functionality is described in the {ref}`Stub <process-stub>` section of the Processes page.
+   The stub functionality is described in the [Stub][process-stub] section of the Processes page.
 
 ### Configuration file
 
 When the `spack` directive is used in any `process` definition within the pipeline script, Spack is required for the pipeline execution.
 
-Specifying the Spack environments in a separate configuration {ref}`profile <config-profiles>` is therefore
+Specifying the Spack environments in a separate configuration [profile][config-profiles] is therefore
 recommended to allow the execution via a command line option and to enhance the pipeline portability. For example:
 
 ```groovy
@@ -166,10 +165,16 @@ profiles {
 
 The above configuration snippet allows the execution either with Spack or Docker by specifying `-profile spack` or `-profile docker` when running the pipeline script.
 
-:::{note}
+:::note
 Nextflow does not allow for fine-grained configuration of the Spack package manager. Instead, this has to be performed directly on the host Spack installation. For more information see the [Spack documentation](https://spack.readthedocs.io).
 :::
 
 ## Advanced settings
 
-Spack advanced configuration settings are described in the {ref}`Spack <config-spack>` section on the Nextflow configuration page.
+Spack advanced configuration settings are described in the [spack][config-spack] section on the Nextflow configuration page.
+
+[config-profiles]: /nextflow_docs/nextflow_repo/docs/config.mdx#config-profiles
+[config-spack]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#spack
+[process-arch]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#arch
+[process-spack]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#spack
+[process-stub]: /nextflow_docs/nextflow_repo/docs/process.mdx#stub
diff --git a/new-docs/nextflow-docs/sphinx-build.sh b/new-docs/nextflow-docs/sphinx-build.sh
new file mode 100755
index 0000000000..c1709ce5b6
--- /dev/null
+++ b/new-docs/nextflow-docs/sphinx-build.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+docker buildx build \
+    --push \
+    --platform linux/amd64,linux/arm64 \
+    --tag nextflow/sphinx:5.3.0 \
+    .
diff --git a/docs/strict-syntax.md b/new-docs/nextflow-docs/strict-syntax.mdx
similarity index 86%
rename from docs/strict-syntax.md
rename to new-docs/nextflow-docs/strict-syntax.mdx
index 4d72010ad4..6abb9c0137 100644
--- a/docs/strict-syntax.md
+++ b/new-docs/nextflow-docs/strict-syntax.mdx
@@ -1,16 +1,17 @@
-(strict-syntax-page)=
+
 
 # Preparing for strict syntax
 
-This page explains how to update Nextflow scripts and config files to adhere to the {ref}`Nextflow language specification <syntax-page>`, also known as the _strict syntax_.
+This page explains how to update Nextflow scripts and config files to adhere to the [Nextflow language specification][syntax-page], also known as the _strict syntax_.
 
-:::{note}
-If you are still using DSL1, see {ref}`dsl1-page` to learn how to migrate your Nextflow pipelines to DSL2 before consulting this guide.
+:::note
+If you are still using DSL1, see [Migrating from DSL1][dsl1-page] to learn how to migrate your Nextflow pipelines to DSL2 before consulting this guide.
 :::
 
-:::{versionadded} 25.02.0-edge
+<AddedInVersion version="25.02.0-edge">
 The strict syntax can be enabled in Nextflow by setting the environment variable `NXF_SYNTAX_PARSER=v2`.
-:::
+</AddedInVersion>
+
 
 ## Overview
 
@@ -42,11 +43,11 @@ def json = new groovy.json.JsonSlurper().parseText(json_file.text)
 
 Some users use classes in Nextflow to define helper functions or custom types. Helper functions should be defined as standalone functions in Nextflow. Custom types should be moved to the `lib` directory.
 
-:::{note}
+:::note
 Enums, a special type of class, are supported, but they cannot be included across modules at this time.
 :::
 
-:::{note}
+:::note
 Record types will be addressed in a future version of the Nextflow language specification.
 :::
 
@@ -92,7 +93,7 @@ workflow {
 }
 ```
 
-:::{note}
+:::note
 Mixing statements and script declarations was necessary in DSL1 and optional in DSL2. However, it is no longer supported in the strict syntax in order to simplify the language and to ensure that top-level statements are not executed when the script is included as a module.
 :::
 
@@ -222,13 +223,13 @@ In the strict syntax, use `System.getenv()` instead:
 println "PWD = ${System.getenv('PWD')}"
 ```
 
-:::{versionadded} 24.11.0-edge
+<AddedInVersion version="24.11.0-edge">
 The `env()` function should be used instead of `System.getenv()`:
 
 ```nextflow
 println "PWD = ${env('PWD')}"
 ```
-:::
+</AddedInVersion>
 
 ## Restricted syntax
 
@@ -236,7 +237,7 @@ The following patterns are still supported but have been restricted. That is, so
 
 ### Include declarations
 
-In Nextflow DSL2, include declarations can have an `addParams` or `params` clause as described in {ref}`module-params`:
+In Nextflow DSL2, include declarations can have an `addParams` or `params` clause as described in [Module parameters][module-params]:
 
 ```nextflow
 params.message = 'Hola'
@@ -299,8 +300,7 @@ def str = 'hello'
 def meta = [:]
 ```
 
-:::{versionadded} 25.10.0
-:::
+< AddedInVersion version="25.10.0" />
 
 Local variables can be declared with a type annotation:
 
@@ -450,7 +450,7 @@ process greet {
 
 ### Workflow onComplete/onError handlers
 
-{ref}`Workflow handlers <workflow-handlers>` (i.e. `workflow.onComplete` and `workflow.onError`) can be defined in several different ways in a script, but are typically defined as top-level statements and without an equals sign:
+[Workflow handlers][workflow-handlers] (i.e. `workflow.onComplete` and `workflow.onError`) can be defined in several different ways in a script, but are typically defined as top-level statements and without an equals sign:
 
 ```nextflow
 workflow.onComplete {
@@ -472,7 +472,7 @@ workflow {
 }
 ```
 
-:::{note}
+:::note
 A more concise syntax for workflow handlers will be addressed in a future version of the Nextflow language specification.
 :::
 
@@ -532,17 +532,15 @@ workflow {
 
 ### Process when section
 
-The process {ref}`process-when` section is discouraged. As a best practice, conditional logic should be implemented in the calling workflow (e.g. using an `if` statement or {ref}`operator-filter` operator) instead of the process definition.
-
-(updating-config-syntax)=
+The process [when][process-when] section is discouraged. As a best practice, conditional logic should be implemented in the calling workflow (e.g. using an `if` statement or [filter][operator-filter] operator) instead of the process definition.
 
 ## Configuration syntax
 
-:::{versionadded} 25.02.0-edge
+<AddedInVersion version="25.02.0-edge">
 The strict config syntax can be enabled in Nextflow by setting the environment variable `NXF_SYNTAX_PARSER=v2`.
-:::
+</AddedInVersion>
 
-See {ref}`Configuration <config-syntax>` for a comprehensive description of the configuration language.
+See [Configuration][config-syntax] for a comprehensive description of the configuration language.
 
 Currently, Nextflow parses config files as Groovy scripts, allowing the use of scripting constructs like variables, helper functions, try-catch blocks, and conditional logic for dynamic configuration:
 
@@ -594,9 +592,19 @@ params.max_cpus = 32
 
 There are two ways to preserve Groovy code:
 
- - Move the code to the `lib` directory
- - Create a plugin
+- Move the code to the `lib` directory
+- Create a plugin
+
+Any Groovy code can be moved into the `lib` directory, which supports the full Groovy language. This approach is useful for temporarily preserving some Groovy code until it can be updated later and incorporated into a Nextflow script. See [The `lib` directory][lib-directory] for more information.
 
-Any Groovy code can be moved into the `lib` directory, which supports the full Groovy language. This approach is useful for temporarily preserving some Groovy code until it can be updated later and incorporated into a Nextflow script. See {ref}`lib-directory` documentation for more information.
+For Groovy code that is complicated or if it depends on third-party libraries, it may be better to create a plugin. Plugins can define custom functions that can be included by Nextflow scripts like a module. Furthermore, plugins can be easily re-used across different pipelines. See [Developing plugins][plugins-dev-page] for more information on how to develop plugins.
 
-For Groovy code that is complicated or if it depends on third-party libraries, it may be better to create a plugin. Plugins can define custom functions that can be included by Nextflow scripts like a module. Furthermore, plugins can be easily re-used across different pipelines. See {ref}`dev-plugins-page` for more information on how to develop plugins.
+[config-syntax]: /nextflow_docs/nextflow_repo/docs/config.mdx#syntax
+[dsl1-page]: /nextflow_docs/nextflow_repo/docs/migrations/dsl1.mdx
+[lib-directory]: /nextflow_docs/nextflow_repo/docs/sharing.mdx#the-lib-directory
+[module-params]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-parameters
+[operator-filter]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#filter
+[plugins-dev-page]: /nextflow_docs/nextflow_repo/docs/plugins/developing-plugins.mdx
+[process-when]: /nextflow_docs/nextflow_repo/docs/process.mdx#when
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[workflow-handlers]: /nextflow_docs/nextflow_repo/docs/notifications.mdx#workflow-handlers
diff --git a/new-docs/nextflow-docs/tutorials/data-lineage.mdx b/new-docs/nextflow-docs/tutorials/data-lineage.mdx
new file mode 100644
index 0000000000..d5efb3f8e5
--- /dev/null
+++ b/new-docs/nextflow-docs/tutorials/data-lineage.mdx
@@ -0,0 +1,356 @@
+# Getting started with data lineage
+
+Data lineage in Nextflow provides comprehensive tracking of workflow runs, task executions, and output files. This feature helps you verify the integrity and reproducibility of your pipeline results by maintaining a complete history of computations and intermediate data.
+
+:::warning
+Data lineage is an experimental feature added in Nextflow 25.04. The functionality may change in future releases.
+:::
+
+## Overview
+
+Data lineage tracks the complete history of your Nextflow runs, including:
+
+- Workflow runs and their configurations
+- Task executions and their inputs/outputs
+- File outputs and their provenance
+
+Each lineage record has a unique identifier called a *lineage ID* (LID) that you can use to access and query the data.
+
+:::note
+The data model for every lineage record is defined in the Nextflow [source code](https://github.com/nextflow-io/nextflow/tree/master/modules/nf-lineage/src/main/nextflow/lineage/model).
+:::
+
+## Enable data lineage
+
+To enable data lineage tracking, add the following to your Nextflow configuration:
+
+```groovy
+lineage.enabled = true
+```
+
+By default, lineage data is stored in the `.lineage` directory in your current working directory. You can customize this location:
+
+```groovy
+lineage.store.location = '<PATH_TO_STORAGE>'
+```
+
+:::tip
+For global configuration, add these settings to `$HOME/.nextflow/config`.
+:::
+
+See the [lineage][config-lineage] configuration scope for details.
+
+## Generate lineage metadata
+
+Run a Nextflow pipeline to generate some lineage metadata. For example:
+
+```console
+$ nextflow run rnaseq-nf -profile conda
+```
+
+Nextflow will automatically record the workflow run, task executions, and output files in the lineage store.
+
+## Explore lineage
+
+Now that you have generated some lineage metadata, you can explore it from the command line using the [lineage][cli-lineage] command.
+
+First, use the `list` subcommand to list the workflow runs in the lineage store:
+
+```console
+$ nextflow lineage list
+TIMESTAMP               RUN NAME                SESSION ID                              LINEAGE ID
+2025-05-09 13:28:30 CDT peaceful_blackwell      065bdc6b-89b4-42ee-92c1-2a5af37f2c50    lid://16b31030474f2e96c55f4940bca3ab64
+```
+
+The *lineage ID* (LID) is the unique identifier for the workflow run and the entrypoint for exploring the lineage.
+
+Use the `view` subcommand to view the lineage record for the workflow run:
+
+```console
+$ nextflow lineage view lid://16b31030474f2e96c55f4940bca3ab64
+{
+  "version": "lineage/v1beta1",
+  "type": "WorkflowRun",
+  "workflow": {
+    "scriptFiles": [
+      ...
+    ],
+    "repository": "https://github.com/nextflow-io/rnaseq-nf",
+    "commitId": "86165b8c81d43a1f57363964431395152e353e56"
+  },
+  "sessionId": "065bdc6b-89b4-42ee-92c1-2a5af37f2c50",
+  "name": "peaceful_blackwell",
+  "params": [
+    ...
+  ],
+  "config": {
+    ...
+  }
+}
+```
+
+Every workflow run is represented in the lineage store as a `WorkflowRun` record. It includes information such as the pipeline repository, revision, run name, parameters, and resolved config.
+
+The output files of a workflow run can be accessed as `lid://<WORKFLOW_RUN_HASH>/<PATH>`, where `<PATH>` is the file path relative to the workflow output directory.
+
+:::note
+Files must be published to the workflow output directory as defined by the `outputDir` config option (or `-output-dir` command line option) in order to be recorded as workflow outputs in the lineage store.
+:::
+
+List the output directory to see the available files:
+
+```console
+$ find results
+results
+results/fastqc_ggal_gut_logs
+results/fastqc_ggal_gut_logs/ggal_gut_1_fastqc.html
+results/fastqc_ggal_gut_logs/ggal_gut_1_fastqc.zip
+results/fastqc_ggal_gut_logs/ggal_gut_2_fastqc.html
+results/fastqc_ggal_gut_logs/ggal_gut_2_fastqc.zip
+results/multiqc_report.html
+```
+
+Now, use the workflow LID and relative path to view the lineage record for an output file:
+
+```console
+$ nextflow lineage view lid://16b31030474f2e96c55f4940bca3ab64/multiqc_report.html
+{
+  "version": "lineage/v1beta1",
+  "type": "FileOutput",
+  "path": "/results/multiqc_report.html",
+  "checksum": {
+    "value": "03fd5ed150c7862e1fad5efd4f574a47",
+    "algorithm": "nextflow",
+    "mode": "standard"
+  },
+  "source": "lid://862df53160e07cd823c0c3960545e747/multiqc_report.html",
+  "workflowRun": "lid://16b31030474f2e96c55f4940bca3ab64",
+  "taskRun": null,
+  "size": 5079806,
+  "createdAt": "2025-05-09T13:27:34.576590545-05:00",
+  "modifiedAt": "2025-05-09T13:27:34.586590551-05:00",
+  "labels": null
+}
+```
+
+Every output file is represented in the lineage store as a `FileOutput` record. It includes basic file information, such as the real path, checksum, file size and created/modified timestamps, as well as lineage information, such as the workflow run and task run that produced it.
+
+As this record is a workflow output, it is not linked directly to a task run. Instead, it is linked to the original task output.
+
+Any LID in a lineage record can be viewed, allowing you to traverse the lineage metadata interactively. Use the value of `source` to view the original task output:
+
+```console
+$ nextflow lineage view lid://862df53160e07cd823c0c3960545e747/multiqc_report.html
+{
+  "version": "lineage/v1beta1",
+  "type": "FileOutput",
+  "path": "/work/86/2df53160e07cd823c0c3960545e747/multiqc_report.html",
+  "checksum": {
+    "value": "b14f5171a48ce5c22ea27d7b8e57b6c4",
+    "algorithm": "nextflow",
+    "mode": "standard"
+  },
+  "source": "lid://862df53160e07cd823c0c3960545e747",
+  "workflowRun": "lid://16b31030474f2e96c55f4940bca3ab64",
+  "taskRun": "lid://862df53160e07cd823c0c3960545e747",
+  "size": 5079806,
+  "createdAt": "2025-05-09T13:27:34.236590379-05:00",
+  "modifiedAt": "2025-05-09T13:27:34.246590383-05:00",
+  "labels": null
+}
+```
+
+This record is the task output for the same file -- it has a value for `taskRun` which is the same as its `source`.
+
+View the lineage record for the task that produced this file:
+
+```console
+$ nextflow lineage view lid://862df53160e07cd823c0c3960545e747
+{
+  "version": "lineage/v1beta1",
+  "type": "TaskRun",
+  "sessionId": "065bdc6b-89b4-42ee-92c1-2a5af37f2c50",
+  "name": "MULTIQC",
+  "codeChecksum": {
+    "value": "edf2e9f84cd3a18ee9259012b660f2dd",
+    "algorithm": "nextflow",
+    "mode": "standard"
+  },
+  "script": "\n    cp multiqc/* .\n    echo \"custom_logo: $PWD/nextflow_logo.png\" \u003e\u003e multiqc_config.yaml\n    multiqc -n multiqc_report.html .\n    ",
+  "input": [
+    {
+      "type": "path",
+      "name": "*",
+      "value": [
+        "lid://eff8846883b46c5a76f11e7e4480a6c8/ggal_gut",
+        "lid://2d8bd92c69f732605bc99941e60d5319/fastqc_ggal_gut_logs"
+      ]
+    },
+    {
+      "type": "path",
+      "name": "config",
+      "value": [
+        {
+          "path": "https://github.com/nextflow-io/rnaseq-nf/tree/86165b8c81d43a1f57363964431395152e353e56/multiqc",
+          "checksum": {
+            "value": "2aac500cdfb292e961e678433e7dc3d8",
+            "algorithm": "nextflow",
+            "mode": "standard"
+          }
+        }
+      ]
+    }
+  ],
+  "container": null,
+  "conda": "file:///conda/env-4a436c230263dfdbbf4dddd0623505d1",
+  "spack": null,
+  "architecture": null,
+  "globalVars": {},
+  "binEntries": [],
+  "workflowRun": "lid://16b31030474f2e96c55f4940bca3ab64"
+}
+```
+
+Every task run is represented in the lineage store as a `TaskRun`, which includes information such as the name, script, inputs, and software dependencies. From here, you can continue traversing through the file inputs to view upstream tasks.
+
+Finally, use the `render` subcommand to render the entire lineage of the MULTIQC report as an HTML report:
+
+```console
+$ nextflow lineage render lid://16b31030474f2e96c55f4940bca3ab64/multiqc_report.html
+Rendered lineage graph for lid://16b31030474f2e96c55f4940bca3ab64/multiqc_report.html to lineage.html
+```
+
+Open the HTML report in a web browser to view the lineage graph.
+
+## Query lineage records
+
+To find a lineage record, you normally have to know the LID of the record or a downstream record (such as a workflow run) from which you can traverse to the desired record. However, you can also query the entire lineage store by fields to quickly find relevant records and aggregate records from different runs.
+
+Use the `find` subcommand to find all tasks executed by a workflow run:
+
+```console
+$ nextflow lineage find type=TaskRun workflowRun=lid://16b31030474f2e96c55f4940bca3ab64
+[
+  "lid://2d8bd92c69f732605bc99941e60d5319",
+  "lid://eff8846883b46c5a76f11e7e4480a6c8",
+  "lid://862df53160e07cd823c0c3960545e747",
+  "lid://6d3bff36bf2c3c14c2d383384621e8ca"
+]
+```
+
+You can use any field defined in the [lineage data model](https://github.com/nextflow-io/nextflow/tree/master/modules/nf-lineage/src/main/nextflow/lineage/model).
+
+:::tip
+Since the `find` and `view` subcommands always output JSON, you can use JSON processing tools such as [jq](https://jqlang.org/) to further query and transform results.
+:::
+
+## Compare task runs
+
+Task run LIDs are based on the standard [task hash][cache-resume-task-hash], which makes it easy to compare two task runs in the lineage metadata. For example, if a task is unexpectedly re-executed during a resumed run, as long as lineage is enabled for both the initial and resumed runs, the two tasks can be compared without any additional runs.
+
+This section builds on the above [`rnaseq-nf` example](#generate-lineage-metadata) to demonstrate how to compare two task runs in the event of a cache invalidation.
+
+First, modify the pipeline in a way that invalidates the cache for the `MULTIQC` process. For example, modify the process script.
+
+Resume the pipeline. It will re-execute the `MULTIQC` process:
+
+```console
+$ nextflow run rnaseq-nf -profile conda -resume
+
+...
+
+[6d/3bff36] process > RNASEQ:INDEX (ggal_1_48850000_49020000) [100%] 1 of 1, cached: 1 ✔
+[2d/8bd92c] process > RNASEQ:FASTQC (FASTQC on ggal_gut)      [100%] 1 of 1, cached: 1 ✔
+[ef/f88468] process > RNASEQ:QUANT (ggal_gut)                 [100%] 1 of 1, cached: 1 ✔
+[94/33dda7] process > MULTIQC                                 [100%] 1 of 1 ✔
+```
+
+Retrieve the hash of the `MULTIQC` run from the log file or work directory. Compare it to the task hash of the initial run:
+
+```console
+$ nextflow lineage diff lid://862df53160e07cd823c0c3960545e747 lid://9433dda73f2193491f9a26e3e23cd8a1
+diff --git 862df53160e07cd823c0c3960545e747 9433dda73f2193491f9a26e3e23cd8a1
+--- 862df53160e07cd823c0c3960545e747
++++ 9433dda73f2193491f9a26e3e23cd8a1
+@@ -3,11 +3,11 @@
+   "sessionId": "065bdc6b-89b4-42ee-92c1-2a5af37f2c50",
+   "name": "MULTIQC",
+   "codeChecksum": {
+-    "value": "edf2e9f84cd3a18ee9259012b660f2dd",
++    "value": "9615a8da3a3f9e935cfc8e4042cdf5e0",
+     "algorithm": "nextflow",
+     "mode": "standard"
+   },
+-  "script": "\n    cp multiqc/* .\n    echo \"custom_logo: $PWD/nextflow_logo.png\" \u003e\u003e multiqc_config.yaml\n    multiqc -n multiqc_report.html .\n    ",
++  "script": "\n    cp multiqc/* . # hello!\n    echo \"custom_logo: $PWD/nextflow_logo.png\" \u003e\u003e multiqc_config.yaml\n    multiqc -n multiqc_report.html .\n    ",
+   "input": [
+     {
+       "type": "path",
+@@ -38,5 +38,5 @@
+   "architecture": null,
+   "globalVars": {},
+   "binEntries": [],
+-  "workflowRun": "lid://16b31030474f2e96c55f4940bca3ab64"
++  "workflowRun": "lid://65044872aad36f97e42336b9ba0dee57"
+ }
+```
+
+Note the difference between the task scripts, highlighting the change that caused the task to be re-executed.
+
+## Use lineage with workflow outputs
+
+Workflow outputs declared in the `output` block are also recorded in the lineage store. The output of a workflow run is accessible as `lid://<WORKFLOW_RUN_HASH>#output`.
+
+For example, run the `rnaseq-nf` pipeline using the `preview-25-04` branch, which uses the `output` block to publish outputs:
+
+```console
+$ nextflow -r preview-25-04 -profile conda
+```
+
+View the workflow output in the lineage metadata:
+
+```console
+$ nextflow lineage view lid://9410d13abeec617640b5fe9735ba12fc#output
+[
+  {
+    "type": "Collection",
+    "name": "samples",
+    "value": "lid://9410d13abeec617640b5fe9735ba12fc/samples.json"
+  },
+  {
+    "type": "Path",
+    "name": "summary",
+    "value": "lid://9410d13abeec617640b5fe9735ba12fc/multiqc_report.html"
+  }
+]
+```
+
+This view can be used to traverse output files directly instead of inferring LIDs from the workflow output directory.
+
+See [Workflow outputs][workflow-output-def] for more information about the `output` block.
+
+## Use lineage in a Nextflow script
+
+Since lineage IDs are valid URIs, output files in the lineage store can be accessed by their LID in a Nextflow script, like any other path. The LID path returns the *real* path as defined by the `path` field in the `FileOutput` record.
+
+The following script uses the `samples.json` from the previous example as an input samplesheet:
+
+```nextflow
+channel.fromPath('lid://9410d13abeec617640b5fe9735ba12fc/samples.json')
+    .splitJson()
+    .view()
+```
+
+It should produce the following output:
+
+```console
+[id:gut, quant:/results/gut/quant, fastqc:/results/gut/fastqc]
+```
+
+The `fromLineage` channel factory can also be used to query lineage records in a similar manner as the `find` subcommand. See [fromLineage][channel-from-lineage] for details.
+
+[cache-resume-task-hash]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx#task-cache
+[channel-from-lineage]: /nextflow_docs/nextflow_repo/docs/reference/channel.mdx#fromlineage
+[cli-lineage]: /nextflow_docs/nextflow_repo/docs/reference/cli.mdx#lineage
+[config-lineage]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#lineage
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
\ No newline at end of file
diff --git a/docs/tutorials/flux.md b/new-docs/nextflow-docs/tutorials/flux.mdx
similarity index 95%
rename from docs/tutorials/flux.md
rename to new-docs/nextflow-docs/tutorials/flux.mdx
index a72eea95d0..82b28c9e5d 100644
--- a/docs/tutorials/flux.md
+++ b/new-docs/nextflow-docs/tutorials/flux.mdx
@@ -1,9 +1,8 @@
-(flux-page)=
-
 # Using Nextflow with Flux
 
-:::{versionadded} 22.11.0-edge
-:::
+
+
+<AddedInVersion version="22.11.0-edge" />
 
 ## Overview
 
@@ -32,7 +31,7 @@ process {
 }
 ```
 
-For additional Flux settings, see the {ref}`flux-executor` section.
+For additional Flux settings, see the [Flux executor][flux-executor] section.
 
 Here is an example pipeline that we will use:
 
@@ -145,3 +144,5 @@ executor >  flux (5)
 🥑️ for breakfast!
 🥧️ for breakfast!
 ```
+
+[flux-executor]: /nextflow_docs/nextflow_repo/docs/executor.mdx#flux-executor
\ No newline at end of file
diff --git a/new-docs/nextflow-docs/tutorials/metrics.mdx b/new-docs/nextflow-docs/tutorials/metrics.mdx
new file mode 100644
index 0000000000..c2afcced7f
--- /dev/null
+++ b/new-docs/nextflow-docs/tutorials/metrics.mdx
@@ -0,0 +1,309 @@
+# Understanding task resource metrics
+
+This tutorial explains how resource usage metrics are computed from execution reports. See [Execution report][execution-report] for more information about how to enable them.
+
+## CPU Usage
+
+CPU Usage plots report how CPU resources are used by each process.
+
+![CPU usage](../_static/report-resource-cpu-noheader.png)
+
+**Raw Usage** tabs are expected to show 100% core usage if processes perform one task of pure computation. If tasks are distributed over, 2, 3, or 4 CPUs, the raw usage will be 200%, 300%, or 400%, respectively. **% Allocated** tabs rescale raw usage values relative to the number of CPUs that are set with the `cpus` directive. If the `cpus` directive is not set, CPUs are set to `1` and **% Allocated** tabs will show the same values **Raw Usage** tabs.
+
+For example, using the [stress](https://people.seas.harvard.edu/~apw/stress/) program, the following script would report 100% CPU usage in the **Raw Usage** tab and 50% CPU usage in the **% Allocated** tab as the process requested double the number of CPUs that are required:
+
+```nextflow
+process cpu_usage_ex1 {
+    cpus 2
+
+    script:
+    """
+    stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
+    """
+}
+
+workflow{
+    cpu_usage_ex1() // Stress using 1 CPU
+}
+```
+
+:::tip
+See [Linux stress command with examples](https://www.geeksforgeeks.org/linux-stress-command-with-examples/) for more information about the stress command.
+:::
+
+CPU usage decreases if processes spend some time performing pure computation and some time waiting for CPUs. For example, using the `stress` and `sleep` commands, the following script would report 75% CPU usage in the **Raw Usage** tab:
+
+```nextflow
+process cpu_usage_ex2 {
+    cpus 1
+
+    script:
+    """
+    stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
+    stress -c 1 -t 5 # compute square-root of random numbers during 5s using 1 CPU
+    sleep 5 # use no CPU during 5s
+    """
+}
+
+workflow{
+    cpu_usage_ex2() // Stress using 1 CPU and sleep
+}
+```
+
+In the above example, CPU usage is a weighted average that accounts for the percentage of the CPU used and duration of each individual program over the job duration:
+
+$$
+\frac{ 100\% \times 10s + 100\% \times 5s + 0\% \times 5s }{10s+5s+5s} = 75\%
+$$
+
+CPU usage increases if a single step is forked on multiple CPUs:
+
+```nextflow
+process cpu_usage_ex3 {
+    cpus 2
+
+    script:
+    """
+    stress -c 2 -t 10 # compute square-root of random numbers during 10 s using 2 CPUs
+    sleep 10 # use no CPU during 10s
+    """
+}
+
+workflow{
+    cpu_usage_ex3() // Stress using 2 CPUs and sleep
+}
+```
+
+In the above example, the **Raw Usage** tab would report 100%:
+
+$$
+\frac{ 200\% \times 10s + 0\% \times 10s }{10s+10s} = 100\%
+$$
+
+However, the **% Allocated** tab would report 50%. It would not be relevant to change the `cpus` directive from `2` to `1` as the process uses 2 CPUs at it peak load.
+
+## Memory Usage
+
+Memory Usage plots report how memory was used by each process. It has three tabs, **Physical (RAM)**, **Virtual (RAM + Disk swap)**, and **% RAM Allocated**, showing the usage of the physical memory (RAM), the virtual memory (vmem), and the percentage of RAM used by the process relative to the memory that the `memory` directive set, respectively.
+
+Peak usage during process executions is reported for both physical and virtual memories. The total amount of memory used by a process is the `virtual memory (vmem)`. The `vmem` contains all memory areas, including in the physical memory (RAM), in the swap space, on the disk, or shared with other processes. The `resident set size (RSS)` is the amount of `physical memory (RAM)` held by a process.
+
+The relationship is:
+
+
+$$
+vmem \geq RSS + Swap
+$$
+
+The behavior of **Memory Usage** plots can be examined using two programs written in C. The first program allocates a variable of 1 GiB:
+
+```c
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/resource.h>
+#include <sys/time.h>
+#include <sys/types.h>
+#include <unistd.h>
+#include <time.h>
+
+/* Get vmem and rss usage from /proc/<pid>/statm */
+static int mem_used(pid_t pid, unsigned long* vmem, unsigned long* rss) {
+    FILE* file;
+    char path[40];
+    unsigned int page_size;
+
+    snprintf(path, 40, "/proc/%ld/statm", (long) pid);
+    file = fopen(path, "r");
+    // vmem and rss are the first values in the file
+    fscanf(file, "%lu %lu", vmem, rss);
+    // values in statm are in pages so to get bytes we need to know page size
+    page_size = (unsigned) getpagesize();
+    *vmem = *vmem * page_size;
+    *rss = *rss * page_size;
+
+    fclose(file);
+    return 0;
+}
+
+int main(int argc, char **argv) {
+    unsigned char *address;
+    char input;
+    size_t size = 1024*1024*1024;  // 1 GiB
+    unsigned long i;
+    unsigned long vmem = 0;
+    unsigned long rss = 0;
+    pid_t pid;
+
+    pid = getpid();
+    printf("Pid: %ld\n", (long) pid);
+
+    mem_used(pid, &vmem, &rss);
+    printf("VMEM: %lu RSS: %lu\n", vmem, rss);
+
+    address = malloc(size);
+    printf("Allocated %d Bytes of memory\n", (int) size);
+
+    mem_used(pid, &vmem, &rss);
+    printf("VMEM: %lu RSS: %lu\n", vmem, rss);
+
+    // Leave time for nextflow to get information
+    sleep(15);
+
+    free(address);
+    return 0;
+}
+```
+
+The second program allocates a variable of 1 GiB and fills it with data:
+
+```c
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/resource.h>
+#include <sys/time.h>
+#include <sys/types.h>
+#include <unistd.h>
+#include <time.h>
+
+/* Get vmem and rss usage from /proc/<pid>/statm */
+static int mem_used(pid_t pid, unsigned long* vmem, unsigned long* rss) {
+    FILE* file;
+    char path[40];
+    unsigned int page_size;
+
+    snprintf(path, 40, "/proc/%ld/statm", (long) pid);
+    file = fopen(path, "r");
+    // vmem and rss are the first values in the file
+    fscanf(file, "%lu %lu", vmem, rss);
+    // values in statm are in pages so to get bytes we need to know page size
+    page_size = (unsigned) getpagesize();
+    *vmem = *vmem * page_size;
+    *rss = *rss * page_size;
+
+    fclose(file);
+    return 0;
+}
+
+int main(int argc, char **argv) {
+    unsigned char *address;
+    char input;
+    size_t size = 1024*1024*1024;  // 1 GiB
+    unsigned long i;
+    unsigned long vmem = 0;
+    unsigned long rss = 0;
+    pid_t pid;
+
+    pid = getpid();
+    printf("Pid: %ld\n", (long) pid);
+
+    mem_used(pid, &vmem, &rss);
+    printf("VMEM: %lu RSS: %lu\n", vmem, rss);
+
+    address = malloc(size);
+    printf("Allocated %d Bytes of memory\n", (int) size);
+
+    mem_used(pid, &vmem, &rss);
+    printf("VMEM: %lu RSS: %lu\n", vmem, rss);
+
+    printf("Filling memory with data...");
+    fflush(stdout);
+    for (i = 0; i < size; i++) {
+        *(address + i) = 123;
+    }
+
+    mem_used(pid, &vmem, &rss);
+    printf("\nVMEM: %lu RSS: %lu\n", vmem, rss);
+
+    // Leave time for nextflow to get information
+    sleep(15);
+
+    free(address);
+    return 0;
+}
+```
+
+The first and second programs are executed as `malloc` and `malloc_fill`, respectively, in the following script:
+
+```nextflow
+process malloc {
+    memory '1.5 GB'
+
+    script:
+    """
+    memory_vmem_1GiB_ram_0Gib
+    """
+}
+
+process malloc_fill {
+    memory '1.5 GB'
+
+    script:
+    """
+    memory_vmem_1GiB_ram_1Gib
+    """
+}
+
+workflow{
+    malloc() // Allocates a variable of 1 GiB
+    malloc_fill() // Allocates a variable of 1 GiB and fills it with data
+}
+```
+
+The **Virtual (RAM + Disk swap)** tab shows that both `malloc` and `malloc_fill` use the same amount of virtual memory (~1 GiB):
+
+![Memory vmem](../_static/report-resource-memory-vmem.png)
+
+However, the **Physical (RAM)** tab shows that `malloc_fill` uses ~1 GiB of RAM while `malloc` uses ~0 GiB of RAM:
+
+![Memory ram](../_static/report-resource-memory-ram.png)
+
+The **% RAM Allocated** tab shows that `malloc` and `malloc_fill` used 0% and 67% of resources set in the `memory` directive, respectively:
+
+![Memory pctram](../_static/report-resource-memory-pctram.png)
+
+:::warning
+Memory and storage metrics are reported in bytes. For example, 1 KB = $1024$ bytes, 1 MB = $1024^2$ bytes, and 1 GB = $1024^3$ bytes.
+:::
+
+## Job Duration
+
+**Job Duration** plots report how long each process took to run. It has two tabs. The **Raw Usage** tab shows the job duration and the **% Allocated** tab shows the time that was requested relative to what was requested using the `time` directive. Job duration is sometimes known as elapsed real time, real time or wall time.
+
+![Job duration](../_static/report-resource-job-duration.png)
+
+## I/O Usage
+
+I/O Usage plots show how much data was read and written by processes. The amount of data that was read by a process (`rchar` in trace files) is the number of bytes the process read using read-like system calls. The amount of data that was written by a process (`wchar` in trace files) is the number of bytes the process wrote using write-like system call. Read and write data is read from the file `/proc/$pid/io`.
+
+**Read** tabs shows how much data was read and **Write** tabs shows how much data was written by each process. For example, the following script reads and writes different data volumes:
+
+```nextflow
+process io_read_write_1G {
+    script:
+    """
+    dd if=/dev/zero of=/dev/null bs=1G count=1
+    """
+}
+
+process io_read_write_256M {
+    script:
+    """
+    dd if=/dev/zero of=/dev/null bs=256M count=1
+    """
+}
+
+workflow{
+    io_read_write_1G()   // Read and write 1 GiB
+    io_read_write_256M() // Read and write 256 Mb
+}
+```
+
+The **Read** tab shows that ~1 Gib and ~256 Mb are read:
+
+![Resources io read](../_static/report-resource-io-read.png)
+
+The **Write** tab shows that ~1 Gib and ~256 Mb are written:
+
+![Resources io write](../_static/report-resource-io-write.png)
+
+[execution-report]: /nextflow_docs/nextflow_repo/docs/reports.mdx#execution-report
diff --git a/new-docs/nextflow-docs/tutorials/rnaseq-nf.md b/new-docs/nextflow-docs/tutorials/rnaseq-nf.md
new file mode 100644
index 0000000000..e2aae6936d
--- /dev/null
+++ b/new-docs/nextflow-docs/tutorials/rnaseq-nf.md
@@ -0,0 +1,226 @@
+(rnaseq-nf-page)=
+
+# Getting started with rnaseq-nf
+
+[`rnaseq-nf`](https://github.com/nextflow-io/rnaseq-nf) is a basic Nextflow pipeline for RNA-Seq analysis that performs quality control, transcript quantification, and result aggregation. The pipeline processes paired-end FASTQ files, generates quality control reports with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), quantifies transcripts with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html), and produces a unified report with [MultiQC](https://seqera.io/multiqc/).
+
+This tutorial describes the architecture of the [`rnaseq-nf`](https://github.com/nextflow-io/rnaseq-nf) pipeline and provides instructions on how to run it.
+
+## Pipeline architecture
+
+The pipeline is organized into modular workflows and processes that coordinate data flow from input files through analysis steps to final outputs.
+
+### Entry workflow
+
+The [entry workflow](https://github.com/nextflow-io/rnaseq-nf/blob/master/main.nf) orchestrates the entire pipeline by coordinating input parameters and data flow:
+
+```{mermaid}
+flowchart TB
+    subgraph " "
+    subgraph params
+    v0["transcriptome"]
+    v1["reads"]
+    v5["multiqc"]
+    v2["outdir"]
+    end
+    v4([RNASEQ])
+    v6([MULTIQC])
+    v0 --> v4
+    v1 --> v4
+    v4 --> v6
+    v5 --> v6
+    end
+```
+
+Data flow:
+
+- The `transcriptome` and `reads` parameters are passed to the `RNASEQ` subworkflow, which performs indexing, quality control, and quantification.
+
+- The outputs from `RNASEQ`, along with the MultiQC configuration (`multiqc`), are passed to the `MULTIQC` module, which aggregates results into a unified HTML report.
+
+- The `outdir` parameter defines where all results are published.
+
+### `RNASEQ`
+
+The [`RNASEQ`](https://github.com/nextflow-io/rnaseq-nf/blob/master/modules/rnaseq.nf) subworkflow coordinates three processes that run in parallel and sequence:
+
+```{mermaid}
+flowchart TB
+    subgraph RNASEQ
+    subgraph take
+    v0["read_pairs_ch"]
+    v1["transcriptome"]
+    end
+    v2([INDEX])
+    v4([FASTQC])
+    v6([QUANT])
+    subgraph emit
+    v8["fastqc"]
+    v9["quant"]
+    end
+    v1 --> v2
+    v0 --> v4
+    v0 --> v6
+    v2 --> v6
+    v4 --> v8
+    v6 --> v9
+    end
+```
+
+Inputs (`take:`):
+
+- `read_pairs_ch`: A channel of paired-end read files
+- `transcriptome`: A reference transcriptome file
+
+Data flow (`main:`):
+
+- [`INDEX`](https://github.com/nextflow-io/rnaseq-nf/blob/master/modules/index/main.nf) creates a Salmon index from the `transcriptome` input (runs once).
+
+- [`FASTQC`](https://github.com/nextflow-io/rnaseq-nf/blob/master/modules/fastqc/main.nf) analyzes the samples in the `read_pairs_ch` channel in parallel (runs independently for each sample).
+
+- [`QUANT`](https://github.com/nextflow-io/rnaseq-nf/blob/master/modules/quant/main.nf) quantifies transcripts using the index from `INDEX` and the samples in the `read_pairs_ch` channel (runs for each sample after `INDEX` completes).
+
+Outputs (`emit:`):
+
+- `fastqc`: The results from `FASTQC`
+
+- `quant`: The results from `QUANT`
+
+### `MULTIQC`
+
+The [`MULTIQC`](https://github.com/nextflow-io/rnaseq-nf/blob/master/modules/multiqc/main.nf) process aggregates all quality control and quantification outputs into a comprehensive HTML report.
+
+Inputs:
+
+- Input files: All collected outputs from the `RNASEQ` subworkflow (FastQC reports and Salmon quantification files).
+- `config`: MultiQC configuration files and branding (logo, styling).
+
+Process execution:
+
+- `MULTIQC` scans all input files, extracts metrics and statistics, and generates a unified report.
+
+Outputs:
+
+- `multiqc_report.html`: A single consolidated HTML report providing an overview of:
+  - General stats
+  - Salmon fragment length distribution
+  - FastQC quality control
+  - Software versions
+
+## Pipeline parameters
+
+The pipeline behavior can be customized using command-line parameters to specify input data, output locations, and configuration files.
+
+The pipeline accepts the following command-line parameters:
+
+- `--reads`: Path to paired-end FASTQ files (default: `data/ggal/ggal_gut_{1,2}.fq`).
+
+- `--transcriptome`: Path to reference transcriptome FASTA (default: `data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa`).
+
+- `--outdir`: Output directory for results (default: `results`).
+
+- `--multiqc`: Path to MultiQC configuration directory (default: `multiqc`).
+
+## Configuration profiles
+
+Configuration profiles allow you to customize how and where the pipeline runs by specifying the `-profile` flag. Multiple profiles can be specified as a comma-separated list. Profiles are defined in the [`nextflow.config`](https://github.com/nextflow-io/rnaseq-nf/blob/master/nextflow.config) file in the base directory.
+
+<h3>Software profiles</h3>
+
+Software profiles specify how software dependencies for processes should be provisioned:
+
+- `conda`: Provision a Conda environment for each process based on its required Conda packages
+- `docker`: Use a Docker container which contains all required dependencies
+- `singularity`: Use a Singularity container which contains all required dependencies
+- `wave`: Provision a Wave container for each process based on its required Conda packages
+
+:::{note}
+The respective container runtime or package manager must be installed to use these profiles.
+:::
+
+<h3>Execution profiles</h3>
+
+Execution profiles specify the compute and storage environment used by the pipeline:
+
+- `slurm`: Run on a SLURM HPC cluster
+- `batch`: Run on AWS Batch
+- `google-batch`: Run on Google Cloud Batch
+- `azure-batch`: Run on Azure Batch
+
+:::{note}
+Depending on your environment, you may need to configure underlying infrastructure such as resource pools, storage, and credentials.
+:::
+
+## Test data
+
+The pipeline includes test data in the [`data/ggal/`](https://github.com/nextflow-io/rnaseq-nf/tree/master/data/ggal) directory for demonstration and validation purposes:
+
+- Paired-end FASTQ files from four tissue samples (gut, liver, lung, spleen):
+  - `ggal_gut_{1,2}.fq`
+  - `ggal_liver_{1,2}.fq`
+  - `ggal_lung_{1,2}.fq`
+  - `ggal_spleen_{1,2}.fq`
+
+- Reference transcriptome:
+  - `ggal_1_48850000_49020000.Ggal71.500bpflank.fa`
+
+By default, only the `gut` sample is processed. You can use the `all-reads` profile to process all four tissue samples.
+
+## Quick start
+
+The [`rnaseq-nf`](https://github.com/nextflow-io/rnaseq-nf) pipeline is executable out-of-the-box. This section provides examples for running the pipeline with different configurations.
+
+### Basic execution
+
+Run the pipeline with default parameters using Docker:
+
+```bash
+nextflow run nextflow-io/rnaseq-nf -profile docker
+```
+
+### Configuring individual parameters
+
+Override default parameters to use custom input files and output locations:
+
+```bash
+nextflow run nextflow-io/rnaseq-nf \
+  --reads '/path/to/reads/*_{1,2}.fastq.gz' \
+  --transcriptome '/path/to/transcriptome.fa' \
+  --outdir 'my_results' \
+  -profile docker
+```
+
+### Using profiles
+
+Specify configuration profiles to customize runtime environments and data sources:
+
+```bash
+# Use Conda to provision software dependencies
+nextflow run nextflow-io/rnaseq-nf -profile conda
+
+# Run on a SLURM cluster
+nextflow run nextflow-io/rnaseq-nf -profile slurm
+
+# Combine multiple profiles: process all reads using Docker
+nextflow run nextflow-io/rnaseq-nf -profile all-reads,docker
+```
+
+:::{tip}
+See [Configuration profiles](#configuration-profiles) for more information about profiles.
+:::
+
+## Expected outputs
+
+The [`rnaseq-nf`](https://github.com/nextflow-io/rnaseq-nf) pipeline produces the following outputs in the `results` directory:
+
+```
+results/
+├── fastqc_<SAMPLE_ID>_logs/      # FastQC quality reports per sample
+│   ├── <SAMPLE_ID>_1_fastqc.html
+│   ├── <SAMPLE_ID>_1_fastqc.zip
+│   ├── <SAMPLE_ID>_2_fastqc.html
+│   └── <SAMPLE_ID>_2_fastqc.zip
+└── multiqc_report.html           # Aggregated QC and Salmon report
+```
+
+The MultiQC report (`multiqc_report.html`) can be viewed in a web browser.
diff --git a/new-docs/nextflow-docs/tutorials/static-types.md b/new-docs/nextflow-docs/tutorials/static-types.md
new file mode 100644
index 0000000000..ca3357c8c8
--- /dev/null
+++ b/new-docs/nextflow-docs/tutorials/static-types.md
@@ -0,0 +1,353 @@
+(migrating-static-types)=
+
+# Migrating to static types
+
+Nextflow 25.10 introduces the ability to use *static types* in a Nextflow pipeline. This tutorial demonstrates how to migrate to static types using the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline as an example.
+
+:::{note}
+Static types in Nextflow 25.10 are optional. All existing code will continue to work.
+:::
+
+## Overview
+
+Static types allow you to specify the types of variables and parameters in Nextflow code. This language feature serves two purposes:
+
+1. **Better documentation**: Type annotations serve as code documentation, making your code more precise and easier to understand.
+
+2. **Better validation**: The Nextflow language server uses these type annotations to perform *type checking*, which allows it to identify type-related errors during development without requiring code execution.
+
+While Nextflow inherited type annotations from Groovy, types were limited to functions and local variables and weren't supported by Nextflow-specific constructs, such as processes, workflows, and pipeline parameters. Additionally, the Groovy type system is significantly larger and more complex than necessary for Nextflow pipelines.
+
+Nextflow 25.10 provides a native way to specify types at every level of a pipeline, from pipeline parameters to process inputs and outputs, using the {ref}`standard types <stdlib-types>` in the Nextflow standard library.
+
+## Developer tooling
+
+Static types work best with the [Nextflow language server](https://github.com/nextflow-io/language-server) and [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow).
+
+:::{tip}
+See {ref}`devenv-page` for instructions on how to setup VS Code and the Nextflow extension.
+:::
+
+### Type checking
+
+Static type checking is currently available through the language server as an experimental feature.
+
+### Automatic migration
+
+The Nextflow VS Code extension provides a command for automatically migrating Nextflow pipelines to static types. To migrate a script, open the Command Palette, search for **Convert script to static types**, and select it.
+
+:::{note}
+The extension can also convert an entire project using the **Convert pipeline to static types** command.
+:::
+
+The conversion consists of the following steps:
+
+- Legacy parameter declarations are converted to a `params` block. If a `nextflow_schema.json` file is present, it is used to infer parameter types.
+
+- Legacy processes are converted to typed processes.
+
+The language server uses the following rules when attempting to convert a legacy process:
+
+- When input or output types cannot be inferred (e.g., `val` inputs and outputs), the type remains unspecified and the language server reports an error. However, if a process includes an nf-core [meta.yml](https://nf-co.re/docs/guidelines/components/modules#documentation), the language server uses it to infer the appropriate type.
+
+- File inputs (`file` and `path` qualifiers) are converted to `Path` or `Set<Path>` based on (1) the `arity` option or (2) stage name when specified. To ensure accurate conversion, specify the `arity` option in the legacy syntax and review the converted code to verify the correct type is used.
+
+- File outputs (`file` and `path` qualifiers) are converted to `file()` or `files()` based on the `arity` option when specified. To ensure accurate conversion, specify the `arity` option in the legacy syntax and review the converted code to verify the correct output function is used.
+
+## Example: rnaseq-nf
+
+This section demonstrates how to migrate a pipeline to static types using the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline as an example. The completed migration is available in the [preview-25-10](https://github.com/nextflow-io/rnaseq-nf/tree/preview-25-10) branch.
+
+See {ref}`rnaseq-nf-page` for an introduction to the rnaseq-nf pipeline.
+
+:::{tip}
+While much of this migration can be performed automatically by the language server, this example is intended to provide a concrete example of a pipeline that uses static types. Always review generated code for correctness.
+:::
+
+### Migrating pipeline parameters
+
+The pipeline defines the following parameters in the main script using the legacy syntax:
+
+```nextflow
+params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
+params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+params.outdir = "results"
+params.multiqc = "$baseDir/multiqc"
+```
+
+The pipeline also has a `nextflow_schema.json` schema with the following properties:
+
+```json
+"reads": {
+  "type": "string",
+  "description": "The input read-pair files",
+  "default": "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
+},
+"transcriptome": {
+  "type": "string",
+  "format": "file-path",
+  "description": "The input transcriptome file",
+  "default": "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+},
+"outdir": {
+  "type": "string",
+  "format": "directory-path",
+  "description": "The output directory where the results will be saved",
+  "default": "results"
+},
+"multiqc": {
+  "type": "string",
+  "format": "directory-path",
+  "description": "Directory containing the configuration for MultiQC",
+  "default": "${projectDir}/multiqc"
+}
+```
+
+To migrate the pipeline parameters, use the schema and legacy parameters to define the equivalent `params` block:
+
+```nextflow
+params {
+    // The input read-pair files
+    reads: String = "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
+
+    // The input transcriptome file
+    transcriptome: Path = "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+
+    // The output directory where the results will be saved
+    outdir: Path = 'results'
+
+    // Directory containing the configuration for MultiQC
+    multiqc: Path = "${projectDir}/multiqc"
+}
+```
+
+See {ref}`workflow-params-def` for more information about the `params` block.
+
+### Migrating workflows
+
+The type of each workflow input can be inferred by examining how the workflow is called.
+
+```nextflow
+workflow RNASEQ {
+    take:
+    read_pairs_ch
+    transcriptome
+
+    main:
+    // ...
+
+    emit:
+    fastqc = fastqc_ch
+    quant = quant_ch
+}
+```
+
+The `RNASEQ` workflow is called by the entry workflow with the following arguments:
+
+```nextflow
+workflow {
+    read_pairs_ch = channel.fromFilePairs(params.reads, checkIfExists: true, flat: true)
+
+    (fastqc_ch, quant_ch) = RNASEQ(read_pairs_ch, params.transcriptome)
+
+    // ...
+}
+```
+
+You can determine the type of each input as follows:
+
+- The channel `read_pairs_ch` has type `Channel<E>`, where `E` is the type of each value in the channel. The `fromFilePairs()` factory with `flat: true` emits tuples containing a sample ID and two file paths. Therefore the type of `read_pairs_ch` is `Channel<Tuple<String,Path,Path>>`.
+
+- The parameter `params.transcriptome` has type `Path` as defined in the `params` block.
+
+To update the workflow inputs, specify the input types as follows:
+
+```nextflow
+workflow RNASEQ {
+    take:
+    read_pairs_ch: Channel<Tuple<String,Path,Path>>
+    transcriptome: Path
+
+    // ...
+}
+```
+
+:::{note}
+Type annotations can become long for tuples with many elements. Future Nextflow versions will introduce alternative data types (i.e., record types) that have more concise annotations and provide a better overall experience with static types. The focus of Nextflow 25.10 is to enable type checking for existing code with minimal changes.
+:::
+
+You can also specify types for workflow outputs. This is typically not required for type checking, since the output type can usually be inferred from the input types and workflow logic. However, explicit type annotations are still useful as a sanity check -- if the declared output type doesn't match the assigned value's type, the language server can report an error.
+
+You can use the same approach for inputs to determine the type of each output:
+
+- The variable `fastqc_ch` comes from the output of `FASTQC`. This process is called with a channel (`read_pairs_ch`), so it also emits a channel. Each task returns a tuple containing an id and an output file, so the element type is `Tuple<String,Path>`. Therefore, the type of `fastqc_ch` is `Channel<Tuple<String,Path>>`.
+
+- The variable `quant_ch` comes from the output of `QUANT`. THis process is called with a channel (`read_pairs_ch`), so it also emits a channel. Each task returns a tuple containing an id and an output file, so the element type is `Tuple<String,Path>`. Therefore, the type of `quant_ch` is `Channel<Tuple<String,Path>>`.
+
+To update the workflow outputs, specify the output types as follows:
+
+```nextflow
+workflow RNASEQ {
+    take:
+    read_pairs_ch: Channel<Tuple<String,Path,Path>>
+    transcriptome: Path
+
+    main:
+    index = INDEX(transcriptome)
+    fastqc_ch = FASTQC(read_pairs_ch)
+    quant_ch = QUANT(index, read_pairs_ch)
+
+    emit:
+    fastqc: Channel<Tuple<String,Path>> = fastqc_ch
+    quant: Channel<Tuple<String,Path>> = quant_ch
+}
+```
+
+### Migrating processes
+
+See {ref}`process-typed-page` for an overview of typed process inputs and outputs.
+
+<h4>FASTQC</h4>
+
+The `FASTQ` process is defined with the following inputs and outputs:
+
+```nextflow
+process FASTQC {
+    // ...
+
+    input:
+    tuple val(id), path(fastq_1), path(fastq_2)
+
+    output:
+    path "fastqc_${id}_logs"
+
+    // ...
+}
+```
+
+To migrate this process, rewrite the inputs and outputs as follows:
+
+```nextflow
+process FASTQC {
+    // ...
+
+    input:
+    (id, fastq_1, fastq_2): Tuple<String,Path,Path>
+
+    output:
+    file("fastqc_${id}_logs")
+
+    // ...
+}
+```
+
+In the above:
+
+- Inputs of type `Path` are treated like `path` inputs in the legacy syntax. Additionally, if `fastq_1` or `fastq_2` were marked as `Path?`, they could be null, which is not supported by `path` inputs.
+
+- Outputs are normally defined as assignments, similar to workflow emits. In this case, however, the name was omitted since there is only one output.
+
+- Values in the `output:` section can use several specialized functions for {ref}`process outputs <process-reference-typed>`. Here, `file()` is the process output function (not the standard library function).
+
+:::{note}
+Other process sections, such as the directives and the `script:` block, are not shown because they do not require changes. As long as the inputs and outputs declare and reference the same variable names and file patterns, the other process sections will behave the same as before.
+:::
+
+<h4>QUANT</h4>
+
+The `QUANT` process is defined with the following inputs and outputs:
+
+```nextflow
+process QUANT {
+    // ...
+
+    input:
+    tuple val(id), path(fastq_1), path(fastq_2)
+    path index
+
+    output:
+    path "quant_${id}"
+
+    // ...
+}
+```
+
+To migrate this process, rewrite the inputs and outputs as follows:
+
+```nextflow
+process QUANT {
+    // ...
+
+    input:
+    (id, fastq_1, fastq_2): Tuple<String,Path,Path>
+    index: Path
+
+    output:
+    file("quant_${id}")
+
+    // ...
+}
+```
+
+<h4>MULTIQC</h4>
+
+The `MULTIQC` process is defined with the following inputs and outputs:
+
+```nextflow
+process MULTIQC {
+    // ...
+
+    input:
+    path '*'
+    path config
+
+    output:
+    path 'multiqc_report.html'
+
+    // ...
+}
+```
+
+To migrate this process, rewrite the inputs and outputs as follows:
+
+```nextflow
+process MULTIQC {
+    // ...
+
+    input:
+    logs: Set<Path>
+    config: Path
+
+    stage:
+    stageAs logs, '*'
+
+    output:
+    file('multiqc_report.html')
+
+    // ...
+}
+```
+
+In a typed process, file patterns for `path` inputs must be declared using a *stage directive*. In this example, the first input uses the variable name `logs`, and the `stageAs` directive stages the input using the glob pattern `*`.
+
+In this case, you can omit the stage directive because `*` matches Nextflow's default staging behavior. Inputs of type `Path` or a `Path` collection (e.g., `Set<Path>`) are staged by default using the pattern `'*'`.
+
+:::{note}
+In the legacy syntax, you can use the `arity` option to specify whether a `path` qualifier expects a single file or collection of files. When using typed inputs and outputs, the type determines this behavior, i.e., `Path` vs `Set<Path>`.
+:::
+
+:::{note}
+While `List<Path>` and `Bag<Path>` are also valid path collection types, `Set<Path>` is recommended because it most accurately represents an unordered collection of files. You should only use `List<Path>` when you want the collection to be ordered.
+:::
+
+<h4>INDEX</h4>
+
+Apply the same migration principles from the previous processes to migrate `INDEX`.
+
+## Additional resources
+
+See the following links to learn more about static types:
+
+- {ref}`process-typed-page`
+- {ref}`stdlib-types`
+- {ref}`syntax-process-typed`
diff --git a/new-docs/nextflow-docs/tutorials/workflow-outputs.mdx b/new-docs/nextflow-docs/tutorials/workflow-outputs.mdx
new file mode 100644
index 0000000000..bfce516bd3
--- /dev/null
+++ b/new-docs/nextflow-docs/tutorials/workflow-outputs.mdx
@@ -0,0 +1,298 @@
+# Migrating to workflow outputs
+
+The [workflow output definition][workflow-output-def] is a new way to define the top-level outputs of a workflow. It is a replacement for the [publishDir][process-publishdir] directive. This tutorial describes these changes and explains how to migrate from `publishDir` to workflow outputs using the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline as an example.
+
+## Overview
+
+In Nextflow DSL1, pipelines were defined in a single script and there was no concept of workflows. Each process used the `publishDir` directive to publish task outputs, which captured output files with glob patterns and copied them from the work directory to an external location.
+
+Nextflow DSL2 introduced workflows and modules, making it easier to develop large and complex pipelines. However, DSL2 retained the same process-based publishing syntax and became unwieldy for several reasons:
+
+- **Mismatch with reusable modules**: Publishing rules often depend on how a process is used in a pipeline. This made it impractical to set `publishDir` in a reusable way for processes that are shared across many pipelines. Publishing rules could be defined in the configuration, but this approach requires extensive use of [process selectors][config-process-selectors], which are difficult to use for large pipelines.
+
+- **Fragmented outputs**: It is difficult to get a concise view of a workflow's outputs when publishing rules are separated across many different modules.
+
+- **Redundant configuration**: Certain settings, such as the base output directory and publish mode, must be repeated for each `publishDir` declaration, leading to duplicated code.
+
+- **Mismatch with channels**: Channels, the primary data structure in Nextflow, contain files and associated metadata that can be accessed by name. However, `publishDir` uses glob patterns to match files, and cannot publish metadata unless it happens to be in a file. This mismatch makes it difficult to translate channels into pipeline outputs.
+
+Workflow outputs were introduced to address these problems by providing a unified, structured, and flexible way to publish outputs:
+
+- **Unified output definition**: Workflow outputs are declared in an `output` block alongside the entry workflow, ensuring that there is a single comprehensive view of what a pipeline produces.
+
+- **Channel-based publishing**: Instead of publishing files from individual processes, workflow outputs are assigned from channels in the entry workflow. The channel itself can be saved as an *index file*, such as a CSV or JSON file, which provides a structured view of the output directory and can be ingested by downstream pipelines.
+
+- **Flexible file selection**: By default, all files in a published channel are included. However, the published channel can be configured to publish specific files by name, instead of using glob patterns. This approach to publishing files is a natural extension of workflows and channels.
+
+- **Simple configuration**: The base output directory is defined as a global configuration setting, and all files are published into this directory. Publish settings such as the mode are also defined as configuration settings under the `workflow.output` scope, reducing code duplication.
+
+## Timeline
+
+Nextflow [24.04][workflow-outputs-first-preview] introduced the workflow output definition as a preview feature. It has since undergone multiple revisions, with the third preview currently available in Nextflow [25.04][workflow-outputs-third-preview].
+
+Nextflow 25.10 will finalize workflow outputs and bring them out of preview. The `publishDir` directive will continue to be supported, but will be deprecated. It may be removed in a future release.
+
+## Example: rnaseq-nf
+
+This section describes how to migrate from `publishDir` to workflow outputs using the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline as an example. To view the completed migration, see the [`preview-25-04`](https://github.com/nextflow-io/rnaseq-nf/tree/preview-25-04) branch of the rnaseq-nf repository.
+
+See [Getting started with rnaseq-nf][rnaseq-nf-page] for an introduction to the `rnaseq-nf` pipeline.
+
+### Replacing `publishDir` with workflow outputs
+
+Start by removing each `publishDir` directive and publishing the corresponding process output channel in the entry workflow.
+
+Declare an output for each channel in the `output` block and publish the corresponding channel in the `publish:` section of the entry workflow:
+
+```nextflow
+workflow {
+    main:
+    read_pairs_ch = channel.fromFilePairs(params.reads, checkIfExists: true, flat: true)
+
+    (fastqc_ch, quant_ch) = RNASEQ(read_pairs_ch, params.transcriptome)
+
+    multiqc_files_ch = fastqc_ch.mix(quant_ch).collect()
+
+    multiqc_report = MULTIQC(multiqc_files_ch, params.multiqc)
+
+    publish:
+    fastqc_logs = fastqc_ch
+    multiqc_report = multiqc_report
+}
+
+output {
+    fastqc_logs {
+    }
+
+    multiqc_report {
+    }
+}
+```
+
+:::note
+Each output assigned in the `publish:` section must be declared in the `output` block, and vice versa.
+:::
+
+Nextflow copies all files in the published channels into the output directory, which is `results` by default. You can set the output directory using the `outputDir` config setting or the `-output-dir` command-line option.
+
+You can set the publish mode in the config. For example:
+
+```groovy
+workflow.output.mode = 'copy'
+```
+
+Run the pipeline with the `all-reads` profile to verify the published outputs:
+
+```console
+$ nextflow run . -profile conda,all-reads
+```
+
+### Customizing the publish paths
+
+The pipeline runs `FASTQC` and `QUANT` for each input sample. However, the workflow publishes only the `FASTQC` results. The workflow passes the `QUANT` results to `MULTIQC` but doesn't publish them directly.
+
+Improve the workflow outputs by also publishing the outputs of `QUANT`:
+
+```nextflow
+workflow {
+    main:
+    // ...
+
+    publish:
+    fastqc_logs = fastqc_ch
+    quant = quant_ch
+    multiqc_report = multiqc_report
+}
+
+output {
+    fastqc_logs {
+    }
+
+    quant {
+    }
+
+    multiqc_report {
+    }
+}
+```
+
+Running the pipeline with the `all-reads` profile will produce the following output directory:
+
+```console
+results
+├── fastqc_gut_logs
+├── fastqc_liver_logs
+├── fastqc_lung_logs
+├── fastqc_spleen_logs
+├── multiqc_report.html
+├── quant_gut
+├── quant_liver
+├── quant_lung
+└── quant_spleen
+```
+
+This directory will quickly become cluttered as you process more samples. It would be better to group the `FASTQC` and `QUANT` results into separate subdirectories:
+
+```console
+results
+├── fastqc
+│   ├── gut
+│   ├── liver
+│   ├── lung
+│   └── spleen
+├── multiqc_report.html
+└── quant
+    ├── gut
+    ├── liver
+    ├── lung
+    └── spleen
+```
+
+Achieve this directory structure by customizing the `output` block.
+
+First, update the `FASTQC` and `QUANT` processes to also emit the sample ID alongside the output files:
+
+```nextflow
+process FASTQC {
+    // ...
+
+    output:
+    tuple val(id), path("fastqc_${id}")
+
+    // ...
+}
+
+process QUANT {
+    // ...
+
+    output:
+    tuple val(id), path("quant_${id}")
+
+    // ...
+}
+```
+
+Configure the `fastqc_logs` and `quant` outputs in the `output` block to use dynamic publish paths:
+
+```nextflow
+output {
+    fastqc_logs {
+        path { id, fastqc -> "fastqc/${id}" }
+    }
+
+    quant {
+        path { id, quant -> "quant/${id}" }
+    }
+
+    multiqc_report {
+    }
+}
+```
+
+Preserving the sample ID in each output channel allows you to customize the publish path without trying to parse the file name. The dynamic path is applied to each channel value to determine the target name for the given file.
+
+:::note
+The closure parameters for the dynamic publish path must match the structure of the published channel.
+:::
+
+### Generating an index file
+
+An *index file* is a manifest, or *index*, of the published files and their metadata for a workflow output. Nextflow can create an index file for each workflow output by saving the channel as a CSV, JSON, or YAML file.
+
+For example, if you enable the index file for `fastqc_logs`:
+
+```nextflow
+output {
+    fastqc_logs {
+        path { id, fastqc -> "fastqc/${id}" }
+        index {
+            path 'fastqc.csv'
+            header true
+        }
+    }
+}
+```
+
+The workflow produces the following index file:
+
+```console
+$ cat results/fastqc.csv
+"id","fastqc"
+"lung","results/fastqc/lung"
+"spleen","results/fastqc/spleen"
+"gut","results/fastqc/gut"
+"liver","results/fastqc/liver"
+```
+
+The index file mirrors the structure of the published channel, and it provides a structured view of the output directory. Index files are equivalent to samplesheets, and can be used as inputs to downstream pipelines.
+
+You could define two index files for `fastqc_logs` and `quant`. However, since these outputs essentially provide different *slices* of data for the same set of samples, you can also combine them into a single output with one index file.
+
+Use the `join` operator to combine the `FASTQC` and `QUANT` results into a single channel:
+
+```nextflow
+workflow {
+    main:
+    // ...
+
+    samples_ch = fastqc_ch
+        .join(quant_ch)
+        .map { id, fastqc, quant ->
+            [id: id, fastqc: fastqc, quant: quant]
+        }
+
+    multiqc_files_ch = samples_ch
+        .flatMap { sample -> [sample.fastqc, sample.quant] }
+        .collect()
+    multiqc_report = MULTIQC( multiqc_files_ch, params.multiqc )
+
+    publish:
+    samples = samples_ch
+    multiqc_report = multiqc_report
+}
+```
+
+This example uses maps instead of tuples so that you can access fields by name, and so that the index file can use the map keys as column names.
+
+Declare the `samples` output with an index file:
+
+```nextflow
+output {
+    samples {
+        path { sample ->
+            sample.fastqc >> "fastqc/${sample.id}"
+            sample.quant >> "quant/${sample.id}"
+        }
+        index {
+            path 'samples.csv'
+            header true
+        }
+    }
+
+    multiqc_report {
+    }
+}
+```
+
+Since each channel value now contains multiple files that go to different subdirectories, you must use *publish statements* in the `path` directive to route each file to the appropriate location.
+
+Run the pipeline, then verify the index file:
+
+```console
+$ nextflow run . -profile conda,all-reads -resume
+$ cat results/samples.csv
+"id","fastqc","quant"
+"lung","results/fastqc/lung","results/quant/lung"
+"gut","results/fastqc/gut","results/quant/gut"
+"liver","results/fastqc/liver","results/quant/liver"
+"spleen","results/fastqc/spleen","results/quant/spleen"
+```
+
+In the future, if you add a tool with per-sample outputs, you only need to join the tool output into the `samples_ch` channel and update the output `path` directive accordingly. This approach keeps the output definition concise as you add more tools to the pipeline. Additionally, a single unified index file for all per-sample outputs is easier for downstream pipelines to consume, rather than cross-referencing multiple related index files.
+
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[process-publishdir]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#publishdir
+[rnaseq-nf-page]: /nextflow_docs/nextflow_repo/docs/tutorials/rnaseq-nf.mdx
+[workflow-output-def]: /nextflow_docs/nextflow_repo/docs/workflow.mdx#workflow-outputs
+[workflow-outputs-first-preview]: /nextflow_docs/nextflow_repo/docs/migrations/24-04.mdx#workflow-outputs-first-preview
+[workflow-outputs-third-preview]: /nextflow_docs/nextflow_repo/docs/migrations/25-04.mdx
diff --git a/new-docs/nextflow-docs/updating-nextflow.mdx b/new-docs/nextflow-docs/updating-nextflow.mdx
new file mode 100644
index 0000000000..874a99542a
--- /dev/null
+++ b/new-docs/nextflow-docs/updating-nextflow.mdx
@@ -0,0 +1,63 @@
+# Updating Nextflow
+
+This page describes Nextflow release cadence, how to self-update Nextflow, and how select your version of Nextflow.
+
+## Releases
+
+A stable version of Nextflow is released in the 4th and 10th month of each year. An edge version of Nextflow is released on a monthly basis. The edge version can be used to access the latest updates and experimental features.
+
+Nextflow uses [Calendar Versioning](https://calver.org). Versions are numbered as `<year>.<month>.<patch>`. For example, `23.10.1` corresponds to the first patch of the October 2023 stable release.
+
+See [Migration notes][migrations-page] for a list of migration guides for each stable release. See the [changelog](https://github.com/nextflow-io/nextflow/blob/master/changelog.txt) for an exhaustive list of changes across all releases.
+
+## Self-update
+
+To update to the latest stable release of Nextflow, run the `self-update` command:
+
+```bash
+nextflow self-update
+```
+
+To use the latest edge release, set `NXF_EDGE=1` when updating Nextflow:
+
+```bash
+NXF_EDGE=1 nextflow self-update
+```
+
+:::note
+When updating from an edge release to a stable release, you must explicitly set `NXF_EDGE=0`.
+:::
+
+:::warning
+Nextflow will update its executable during the self-update process. The update can fail if the Nextflow executable is in a directory with restricted permissions.
+:::
+
+## Version selection
+
+The `NXF_VER` environment variable can be used to define which version of Nextflow to use. To switch to a specific version of Nextflow for a single run, set the `NXF_VER` environment variable in your execution command. For example:
+
+```bash
+NXF_VER=23.10.0 nextflow info
+```
+
+To set a specific version of Nextflow for a terminal session, export the `NXF_VER` environment variable. For example:
+
+```bash
+export NXF_VER=23.10.0
+```
+
+To set a specific version of Nextflow for your user profile, add the above `NXF_VER` export command to your shell configuration file, such as `~/.bashrc` or `~/.zshrc`, and restart your session.
+
+:::tip
+You can use `NXF_VER` to switch to an edge release. For example:
+
+```bash
+NXF_VER=24.06.0-edge nextflow info
+```
+:::
+
+:::warning
+Nextflow will update its executable during the self-update process. The update can fail if the Nextflow executable is in a directory with restricted permissions.
+:::
+
+[migrations-page]: /nextflow_docs/nextflow_repo/docs/migrations/index.mdx
diff --git a/new-docs/nextflow-docs/updating-spot-retries.mdx b/new-docs/nextflow-docs/updating-spot-retries.mdx
new file mode 100644
index 0000000000..75b0802fd1
--- /dev/null
+++ b/new-docs/nextflow-docs/updating-spot-retries.mdx
@@ -0,0 +1,84 @@
+# Spot Instance failures and retries
+
+This page describes changes in how Nextflow handles Spot Instance failures and retries on AWS and Google Cloud, the impact of those changes, and how to configure spot retry behavior for your pipelines. These changes apply to Nextflow 24.10 and later.
+
+## Retry behavior
+
+Up to version 24.10, Nextflow would silently retry Spot Instance failures up to `5` times when using AWS Batch or Google Batch. These retries were controlled by cloud-specific configuration parameters (e.g., `aws.batch.maxSpotAttempts`) and happened in cloud infrastructure without explicit visibility to Nextflow.
+
+### Before Nextflow 24.10
+
+By default, Nextflow would instruct AWS and Google to automatically retry jobs lost to Spot reclamation up to `5` times. Retries were handled by the cloud provider _within_ a Nextflow task. It was often unclear that tasks were restarted as there was no explicit message. Task runtimes and associated cloud costs were increased because they included the runtime of the reclaimed and retried tasks. Due to the high likelihood of reclamation before completion, long-running tasks running on Spot Instances frequently required retries, leading to inefficient allocation of resources and higher costs.
+
+### After Nextflow 24.10
+
+The default Spot reclamation retry setting changed to `0` on AWS and Google. By default, no _internal_ retries are attempted on these platforms. Spot reclamations lead to an immediate failure, exposed to Nextflow in the same way as other generic failures (for example, returning `exit code 1` on AWS). Nextflow treats these failures like any other job failure, unless a retry strategy is configured.
+
+## Impact on existing workflows
+
+If you rely on silent Spot retries (the previous default behavior), you may now see more tasks fail with the following characteristics:
+
+- **AWS**: Generic failure with `exit code 1`. You may see messages indicating the host machine was terminated.
+
+- **Google**: Spot reclamation typically produces a specific code, but is now surfaced as a recognizable task failure in Nextflow logs.
+
+Since the default for Spot retries is now `0`, you must actively enable a retry strategy if you want Nextflow to handle reclaimed Spot Instances automatically.
+
+## Possible actions
+
+There are four possible actions.
+
+### Do nothing
+
+If you do not configure anything, you will observe more pipeline failures when Spot Instances are reclaimed. This approach provides clearer visibility into failures. Failed tasks can be re-run with the `-resume` option. However, frequent task reclamation may lead to a higher failure rate and each retry requires manual intervention.
+
+:::note
+If you resume the pipeline using the resume option, it will pick up at the point the pipeline was interrupted and start with a retry of that task.
+:::
+
+### Re-enable Spot retries
+
+You can re-enable Spot retries for each provider in your Nextflow config:
+
+```groovy
+aws.batch.maxSpotAttempts = 5
+google.batch.maxSpotAttempts = 5
+```
+
+The above example sets the maximum number of Spot retries to `5` for both AWS and Google.
+
+### Make Spot failures visible and retry them
+
+You can set `maxRetries` to enable Nextflow-level retries for any failure:
+
+```groovy
+process.maxRetries = 5
+```
+
+The above example sets retries to `5` for any failures across all providers.
+
+### Use Fusion Snapshots
+
+*This option is only available for AWS Batch.*
+
+If you have long-running tasks where progress lost due to Spot reclamation is costly, consider [Fusion Snapshots](https://docs.seqera.io/fusion/guide/snapshots) (if supported by your environment). Fusion Snapshots allow you to resume a partially completed task on a new machine if a Spot Instance is reclaimed, thereby reducing wasted compute time.
+
+Key features of Fusion Snapshots:
+
+- Jobs do not need to start from scratch after reclamation.
+- Especially useful for tasks that take many hours or days to complete.
+- May significantly reduce costs and run times in high-reclamation environments.
+
+See [Fusion Snapshots for AWS Batch](https://docs.seqera.io/fusion/guide/snapshots) for more information.
+
+## Best practices
+
+Best practices for Spot Instance failures and retries:
+
+- **Evaluate job duration**: If your tasks are very long (multiple hours or more), Spot Instances can cause repeated interruptions. Consider using on-demand instances or Fusion Snapshots.
+
+- **Set sensible retry limits**: If you enable Spot retries, choose a retry count that balances the cost savings of Spot usage against the overhead of restarting tasks.
+
+- **Monitor logs and exit codes**: Failures due to Spot reclamation will now appear in Nextflow logs. Monitor failures and fine-tune your strategy.
+
+- **Consider partial usage of Spot**: Some workflows may mix on-demand instances for critical or long tasks and Spot Instances for shorter, less critical tasks. This can optimize cost while minimizing wasted compute time.
diff --git a/new-docs/nextflow-docs/vscode.mdx b/new-docs/nextflow-docs/vscode.mdx
new file mode 100644
index 0000000000..a02fefad8b
--- /dev/null
+++ b/new-docs/nextflow-docs/vscode.mdx
@@ -0,0 +1,93 @@
+# VS Code integration
+
+The [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) provides language support for Nextflow pipelines in [VS Code](https://code.visualstudio.com/).
+
+This page describes the [Nextflow language server](https://github.com/nextflow-io/language-server) used by the extension. See the extension README in [GitHub](https://github.com/nextflow-io/vscode-language-nextflow) or the [Visual Studio Marketplace](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) for details on additional extension features.
+
+## Features
+
+### Syntax highlighting
+
+The VS Code extension highlights Nextflow scripts and config files for better readability.
+
+### Diagnostics
+
+The extension highlights source code in red for errors and yellow for warnings.
+
+To view all diagnostics for the workspace, open the **Problems** tab. Here, you can search for diagnostics by diagnostic message, filename, and so on.
+
+:::note
+The language server parses scripts and config files according to the [Nextflow language specification][syntax-page], which is more strict than the Nextflow CLI. See [Preparing for strict syntax][strict-syntax-page] for more information.
+:::
+
+### Hover hints
+
+When you hover over certain source code elements, such as variable names and function calls, the extension provides a tooltip with related information, such as the definition and/or documentation for the element.
+
+If a [Javadoc](https://en.wikipedia.org/wiki/Javadoc) comment is defined above a workflow, process, function, or parameter in a `params` block, the extension will include the contents of the comment in hover hints. The following is an example Javadoc comment:
+
+```nextflow
+/**
+ * Say hello to someone.
+ *
+ * @param name
+ */
+def sayHello(name) {
+    println "Hello, ${name}!"
+}
+```
+
+### Code navigation
+
+The **Outline** section in the Explorer panel lists top-level definitions when you view a script. Include declarations in scripts and config files act as links, and ctrl-clicking them opens the corresponding script or config file.
+
+To view the definition of a symbol (e.g., a workflow, process, function, or variable), right-click the symbol and select **Go to Definition**. Ctrl-click the symbol to view the definition. Ctrl-click the definition to show all references.
+
+### Code completion
+
+The extension suggests auto-completions for variable names, function names, config settings, and other symbols as you type. The extension also provides several snippets for common script declarations, such as processes and workflows.
+
+### Formatting
+
+The extension can format your scripts and config files based on a standard set of formatting rules. Rules can be customized using the **Nextflow > Formatting** extension settings.
+
+Use the **Format Document** command in the command palette to format the current file.
+
+### Renaming symbols
+
+The extension can rename all references of a symbol (e.g., a workflow, process, function, or variable) throughout the code.
+
+To rename a symbol, right-click the symbol, select **Rename Symbol**, and enter a new name.
+
+### Parameter schema
+
+If a `nextflow_schema.json` file exists in the same directory as a script with an entry workflow, the extension uses the schema to provide validation, hover hints, and code completion for params in the entry workflow.
+
+### DAG preview for workflows
+
+The extension can generate a workflow DAG that includes the workflow inputs, outputs, and any processes or workflows that are called by the selected workflow. The workflow DAG is displayed in a new panel to the side.
+
+To preview the DAG of a workflow, select the **Preview DAG** CodeLens above the workflow definition.
+
+## Troubleshooting
+
+In the event of a language server error, you can use the **Nextflow: Restart language server** command in the command palette to restart the language server.
+
+Report issues at [nextflow-io/vscode-language-nextflow](https://github.com/nextflow-io/vscode-language-nextflow) or [nextflow-io/language-server](https://github.com/nextflow-io/language-server). When reporting, include a minimal code snippet that reproduces the issue and any error logs from the server. To view logs, open the **Output** tab and select **Nextflow Language Server** from the dropdown. Enable **Nextflow > Debug** in the extension settings to show additional log messages while debugging.
+
+## Limitations
+
+- The language server does not detect certain filesystem changes, such as changing the current Git branch. Restart the language server from the command palette to sync it with your workspace.
+
+- The language server does not recognize configuration options from third-party plugins and will report "Unrecognized config option" warnings for them.
+
+- The language server provides limited support for Groovy scripts in the `lib` directory. Errors in Groovy scripts are not reported as diagnostics, and changing a Groovy script does not automatically re-compile the Nextflow scripts that reference it. Edit the Nextflow script or close and re-open it to refresh the diagnostics.
+
+## Language server
+
+The Nextflow language server implements the [Language Server Protocol (LSP)](https://microsoft.github.io/language-server-protocol/) for Nextflow scripts and config files. It is distributed as a standalone Java application and can be integrated with any editor that functions as an LSP client.
+
+Currently, only the VS Code integration is officially supported, but community contributions for other editors are welcome. Visit the [GitHub issues](https://github.com/nextflow-io/language-server/issues) page for the latest updates on community-led integrations.
+
+[syntax-page]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
diff --git a/docs/wave.md b/new-docs/nextflow-docs/wave.mdx
similarity index 81%
rename from docs/wave.md
rename to new-docs/nextflow-docs/wave.mdx
index 8b53cfa772..cc76d84951 100644
--- a/docs/wave.md
+++ b/new-docs/nextflow-docs/wave.mdx
@@ -1,9 +1,8 @@
-(wave-page)=
+
 
 # Wave containers
 
-:::{versionadded} 22.10.0
-:::
+<AddedInVersion version="22.10.0" />
 
 [Wave](https://seqera.io/wave/) is a container provisioning service integrated with Nextflow. With Wave, you can build, upload, and manage the container images required by your data analysis workflows automatically and on-demand during pipeline execution.
 
@@ -23,14 +22,12 @@ tower {
 }
 ```
 
-:::{note}
+:::note
 The Seqera Platform access token is not mandatory, but it is recommended in order to access private container repositories and pull public containers without being affected by service rate limits. Credentials should be made available to Wave using the [credentials manager](https://docs.seqera.io/platform/latest/credentials/overview) in Seqera Platform.
 :::
 
 ## Use cases
 
-(wave-authenticate-private-repos)=
-
 ### Authenticate private repositories
 
 Wave allows the use of private repositories in your Nextflow pipelines. The repository access keys must be provided in the form of [Seqera Platform credentials](https://docs.seqera.io/platform/latest/credentials/overview/).
@@ -48,9 +45,9 @@ tower {
 
 Wave can build and provision container images on-demand for your Nextflow pipelines.
 
-To enable this feature, add the Dockerfile of the container to be built in the {ref}`module directory <module-directory>` where the pipeline process is defined. When Wave is enabled, it automatically uses the Dockerfile to build the required container, upload to the registry, and it uses the container to carry out the tasks defined in the module.
+To enable this feature, add the Dockerfile of the container to be built in the [module directory][module-directory] where the pipeline process is defined. When Wave is enabled, it automatically uses the Dockerfile to build the required container, upload to the registry, and it uses the container to carry out the tasks defined in the module.
 
-:::{tip}
+:::tip
 Make sure the process does not declare a `container` directive, otherwise it will take precedence over the Dockerfile definition.
 :::
 
@@ -62,13 +59,13 @@ wave.strategy = ['dockerfile','container']
 
 This setting instructs Wave to prioritize the module Dockerfile over process `container` directives.
 
-:::{warning}
+:::warning
 When building containers, Wave currently does not support `ADD`, `COPY`, or any other Dockerfile commands that access files in the host file system.
 :::
 
 ### Build Conda based containers
 
-Wave allows the provisioning of containers based on the {ref}`process-conda` directive used by the processes in your pipeline. This is a quick alternative to building Conda packages in the local computer. Moreover, this enables the use of Conda packages in your pipeline when deploying to cloud-native platforms such as AWS Batch and Kubernetes, which do not allow the easy use of the Conda package manager.
+Wave allows the provisioning of containers based on the [`conda`][process-conda] directive used by the processes in your pipeline. This is a quick alternative to building Conda packages in the local computer. Moreover, this enables the use of Conda packages in your pipeline when deploying to cloud-native platforms such as AWS Batch and Kubernetes, which do not allow the easy use of the Conda package manager.
 
 With Wave enabled in your pipeline, simply define the `conda` requirements in the pipeline processes, provided the same process does not also specify a `container` directive or a Dockerfile.
 
@@ -80,7 +77,7 @@ wave.strategy = ['conda']
 
 The above setting instructs Wave to use the `conda` directive to provision the pipeline containers and ignore the `container` directive and any Dockerfile(s).
 
-:::{tip}
+:::tip
 Some configuration options in the `conda` scope are used when Wave is used to build Conda-based containers.
 For example, the Conda channels and their priority can be set with `conda.channels`:
 
@@ -90,20 +87,17 @@ conda.channels = 'conda-forge,bioconda'
 ```
 :::
 
-Packages from the [Python Package Index](https://pypi.org/) can also be added to a Conda `environment.yml` file. See {ref}`Conda and PyPI <conda-pypi>` for more information.
-
-(wave-singularity)=
+Packages from the [Python Package Index](https://pypi.org/) can also be added to a Conda `environment.yml` file. See [Conda and PyPI][conda-pypi] for more information.
 
 ### Build Singularity native images
 
-:::{versionadded} 23.09.0-edge
-:::
+<AddedInVersion version="23.09.0-edge" />
 
 Nextflow can build Singularity native images on-demand either using `Singularityfile`,
 Conda packages or Spack packages. The Singularity images are automatically uploaded in a container registry OCI compliant
 of your choice and stored as a [ORAS artefact](https://oras.land/).
 
-:::{note}
+:::note
 This feature requires Singularity (or Apptainer) version supporting the pull of images using the `oras:` pseudo-protocol.
 :::
 
@@ -120,15 +114,14 @@ wave.build.repository = 'docker.io/user/repo'
 In the above configuration replace `docker.io/user/repo` with a repository of your choice where Singularity image files
 should be uploaded.
 
-:::{note}
-When using a private repository, the repository access keys must be provided via the Seqera Platform credentials manager (see {ref}`above <wave-authenticate-private-repos>`).
+:::note
+When using a private repository, the repository access keys must be provided via the Seqera Platform credentials manager (see [Use cases](#use-cases)).
 
-Moreover the access to the repository must be granted in the compute nodes by using the command `singularity remote login <registry>`.
-Please see Singularity documentation for further details.
+Moreover the access to the repository must be granted in the compute nodes by using the command singularity remote login. See Singularity documentation for further details.
 :::
 
-:::{note}
-In order to build Singularity native images, both `singularity.ociAutoPull` and `singularity.ociMode` need to be disabled in the configuration (see the {ref}`config-singularity` section).
+:::note
+In order to build Singularity native images, both `singularity.ociAutoPull` and `singularity.ociMode` need to be disabled in the configuration. See [singularity][config-singularity] for more information.
 :::
 
 ### Push to a private repository
@@ -168,7 +161,7 @@ The container will be copied with the same name, tag, and checksum in the specif
 container is `quay.io/biocontainers/bwa:0.7.13--1` and the build repository setting is `example.com`, the resulting container
 name is `example.com/biocontainers/bwa:0.7.13--1`.
 
-:::{tip}
+:::tip
 When using a path prefix in the target registry name, it will be prepended to the resulting container name. For example,
 having `quay.io/biocontainers/bwa:0.7.13--1` as source container and `example.com/library` as build repository, the resulting
 container will be named `example.com/library/biocontainers/bwa:0.7.13--1`.
@@ -199,18 +192,25 @@ wave.scan.allowedLevels = 'low,medium'
 
 The above setting will allow the use of containers with *low* and *medium* vulnerabilities. Accepted values are `low`, `medium`, `high`, and `critical`. See [common vulnerabilities scoring system](https://en.wikipedia.org/wiki/Common_Vulnerability_Scoring_System) for more information about these levels.
 
-:::{note}
+:::note
 Wave's security scanning applies to any container used in your pipeline, whether it was built by Wave or simply accessed through it. The security scan automatically expires after one week. If a container is accessed again after 7 days or more, the scan will be re-executed.
 :::
 
 ### Run pipelines using Fusion file system
 
-Wave containers allow you to run your containerized workflow with {ref}`fusion-page`.
+Wave containers allow you to run your containerized workflow with [Fusion][fusion-page].
 
 This enables the use of an object storage bucket such as AWS S3 or Google Cloud Storage as your pipeline work directory, simplifying and speeding up many operations on local, AWS Batch, Google Batch or Kubernetes executions.
 
-See {ref}`Fusion <fusion-page>` for more details.
+See [Fusion][fusion-page] for more information.
 
 ## Advanced settings
 
-Wave advanced configuration settings are described in the {ref}`Wave <config-wave>` section on the Nextflow configuration page.
+Wave advanced configuration settings are described in the [Wave][config-wave] section on the Nextflow configuration page.
+
+[conda-pypi]: /nextflow_docs/nextflow_repo/docs/conda.mdx#python-packages-from-pypi
+[config-singularity]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#singularity
+[config-wave]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#wave
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[module-directory]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-directory
+[process-conda]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#conda
diff --git a/docs/workflow.md b/new-docs/nextflow-docs/workflow.mdx
similarity index 74%
rename from docs/workflow.md
rename to new-docs/nextflow-docs/workflow.mdx
index eeb48a175a..bbf025ad38 100644
--- a/docs/workflow.md
+++ b/new-docs/nextflow-docs/workflow.mdx
@@ -1,13 +1,13 @@
-(workflow-page)=
+
 
 # Workflows
 
 In Nextflow, a **workflow** is a function that is specialized for composing processes and dataflow logic (i.e. channels and operators).
 
-See {ref}`syntax-workflow` for a full description of the workflow syntax.
+See [Workflow][syntax-workflow] for a full description of the workflow syntax.
 
-:::{note}
-Workflows were introduced in DSL2. If you are still using DSL1, see {ref}`dsl1-page` for more information about how to migrate your Nextflow pipelines to DSL2.
+:::note
+Workflows were introduced in DSL2. If you are still using DSL1, see [Migrating from DSL1][dsl1-page] for more information about how to migrate your Nextflow pipelines to DSL2.
 :::
 
 ## Entry workflow
@@ -22,19 +22,16 @@ workflow {
 }
 ```
 
-(workflow-params-def)=
-
 ## Parameters
 
 Parameters can be declared in a Nextflow script with the `params` block or with *legacy* parameter declarations.
 
 ### Params block
 
-:::{versionadded} 25.10.0
-:::
+<AddedInVersion version="25.10.0" />
 
-:::{note}
-This feature requires the {ref}`strict syntax <strict-syntax-page>` to be enabled (`NXF_SYNTAX_PARSER=v2`).
+:::note
+This feature requires the [strict syntax][strict-syntax-page] to be enabled (`NXF_SYNTAX_PARSER=v2`).
 :::
 
 A script can declare parameters using the `params` block:
@@ -51,11 +48,11 @@ params {
 
 The following types can be used for parameters:
 
-- {ref}`stdlib-types-boolean`
-- {ref}`stdlib-types-float`
-- {ref}`stdlib-types-integer`
-- {ref}`stdlib-types-path`
-- {ref}`stdlib-types-string`
+- [Boolean][stdlib-types-boolean]
+- [Float][stdlib-types-float]
+- [Integer][stdlib-types-integer]
+- [Path][stdlib-types-path]
+- [String][stdlib-types-string]
 
 Parameters can be used in the entry workflow:
 
@@ -65,16 +62,14 @@ workflow {
 }
 ```
 
-:::{note}
+:::note
 As a best practice, parameters should only be used directly in the entry workflow and passed to workflows and processes as explicit inputs.
 :::
 
-The default value can be overridden by the command line, params file, or config file. Parameters from multiple sources are resolved in the order described in {ref}`cli-params`. Parameters specified on the command line are converted to the appropriate type based on the corresponding type annotation.
+The default value can be overridden by the command line, params file, or config file. Parameters from multiple sources are resolved in the order described in [Pipeline parameters][cli-params]. Parameters specified on the command line are converted to the appropriate type based on the corresponding type annotation.
 
 A parameter that doesn't specify a default value is a *required* param. If a required param is not given a value at runtime, the run will fail.
 
-(workflow-params-legacy)=
-
 ### Legacy parameters
 
 Parameters can be declared by assigning a `params` property to a default value:
@@ -91,7 +86,7 @@ workflow {
 }
 ```
 
-The default value can be overridden by the command line, params file, or config file. Parameters from multiple sources are resolved in the order described in {ref}`cli-params`.
+The default value can be overridden by the command line, params file, or config file. Parameters from multiple sources are resolved in the order described in [Pipeline parameters][cli-params].
 
 ## Named workflows
 
@@ -164,12 +159,10 @@ workflow my_workflow {
 
 The result of the above workflow can be accessed using `my_workflow.out.my_data`.
 
-:::{note}
+:::note
 Every output must be assigned to a name when multiple outputs are declared.
 :::
 
-(workflow-process-invocation)=
-
 ## Calling processes and workflows
 
 Processes and workflows are called like functions, passing their inputs as arguments:
@@ -217,7 +210,7 @@ Processes and workflows have a few extra rules for how they can be called:
 
 - Processes and workflows can only be called by workflows
 
-- A given process or workflow can only be called once in a given workflow. To use a process or workflow multiple times in the same workflow, use {ref}`module-aliases`.
+- A given process or workflow can only be called once in a given workflow. To use a process or workflow multiple times in the same workflow, use [Module aliases][module-aliases].
 
 The "return value" of a process or workflow call is the process outputs or workflow emits, respectively. The return value can be assigned to a variable or passed into another call:
 
@@ -283,11 +276,11 @@ workflow {
 }
 ```
 
-:::{note}
-Process named outputs are defined using the `emit` option on a process output. See {ref}`naming process outputs <process-naming-outputs>` for more information.
+:::note
+Process named outputs are defined using the `emit` option on a process output. See [naming process outputs][process-naming-outputs] for more information.
 :::
 
-:::{note}
+:::note
 Process and workflow outputs can also be accessed by index (e.g., `hello.out[0]`, `hello.out[1]`, etc.). As a best practice, multiple outputs should be accessed by name.
 :::
 
@@ -325,12 +318,12 @@ workflow {
 }
 ```
 
-:::{note}
+:::note
 The same process can be called in different workflows without using an alias, like `tick` in the above example, which is used in both `flow1` and `flow2`. The workflow call stack determines the *fully qualified process name*, which is used to distinguish the different process calls, i.e. `flow1:tick` and `flow2:tick` in the above example.
 :::
 
-:::{tip}
-The fully qualified process name can be used as a {ref}`process selector <config-process-selectors>` in a Nextflow configuration file, and it takes priority over the simple process name.
+:::tip
+The fully qualified process name can be used as a [process selector][config-process-selectors] in a Nextflow configuration file, and it takes priority over the simple process name.
 :::
 
 ## Special operators
@@ -361,7 +354,7 @@ workflow {
 }
 ```
 
-The above snippet defines a process named `greet` and invokes it with the input channel. The result is then piped to the {ref}`operator-map` operator, which converts each string to uppercase, and finally to the {ref}`operator-view` operator which prints it.
+The above snippet defines a process named `greet` and invokes it with the input channel. The result is then piped to the [map][operator-map] operator, which converts each string to uppercase, and finally to the [view operator][operator-view] operator which prints it.
 
 The same code can also be written as:
 
@@ -409,7 +402,7 @@ workflow {
 }
 ```
 
-In the above snippet, the initial channel is piped to the {ref}`operator-map` operator, which reverses the string value. Then, the result is passed to the processes `greet` and `to_upper`, which are executed in parallel. Each process outputs a channel, and the two channels are combined using the {ref}`operator-mix` operator. Finally, the result is printed using the {ref}`operator-view` operator.
+In the above snippet, the initial channel is piped to the [map][operator-map] operator, which reverses the string value. Then, the result is passed to the processes `greet` and `to_upper`, which are executed in parallel. Each process outputs a channel, and the two channels are combined using the [mix][operator-mix] operator. Finally, the result is printed using the [view][operator-view] operator.
 
 The same code can also be written as:
 
@@ -422,25 +415,20 @@ workflow {
 }
 ```
 
-(workflow-recursion)=
-
 ## Process and workflow recursion
 
-:::{versionadded} 21.11.0-edge
-:::
+<AddedInVersion version="21.11.0-edge" />
 
-:::{note}
+:::note
 This feature requires the `nextflow.preview.recursion` feature flag to be enabled.
 :::
 
 Processes can be invoked recursively using the `recurse` method.
 
-```{literalinclude} snippets/recurse-process.nf
-:language: nextflow
+```nextflow file=./snippets/recurse-process.nf
 ```
 
-```{literalinclude} snippets/recurse-process.out
-:language: console
+```nextflow file=./snippets/recurse-process.out
 ```
 
 In the above example, the `count_down` process is first invoked with the value `params.start`. On each subsequent iteration, the process is invoked again using the output from the previous iteration. The recursion continues until the specified condition is satisfied, as defined by the `until` method, which terminates the recursion.
@@ -456,12 +444,10 @@ count_down
 
 Workflows can also be invoked recursively:
 
-```{literalinclude} snippets/recurse-workflow.nf
-:language: nextflow
+```nextflow file=./snippets/recurse-workflow.nf
 ```
 
-```{literalinclude} snippets/recurse-workflow.out
-:language: console
+```console file=./snippets/recurse-workflow.out
 ```
 
 **Limitations**
@@ -470,15 +456,13 @@ Workflows can also be invoked recursively:
 
 - Recursive workflows cannot use *reduction* operators such as `collect`, `reduce`, and `toList`, because these operators cause the recursion to hang indefinitely after the initial iteration.
 
-(workflow-output-def)=
-
 ## Workflow outputs
 
-:::{versionadded} 25.10.0
-This feature is available as a preview in Nextflow {ref}`24.04 <workflow-outputs-first-preview>`, {ref}`24.10 <workflow-outputs-second-preview>`, and {ref}`25.04 <workflow-outputs-third-preview>`.
-:::
+<AddedInVersion version="24.04.0">
+This feature is available as a preview in Nextflow [24.04][workflow-outputs-first-preview], [24.10][workflow-outputs-second-preview], and [25.04][workflow-outputs-third-preview].
+</AddedInVersion>
 
-A script can define an *output block* which declares the top-level outputs of the workflow. Each output should be assigned in the `publish` section of the entry workflow. Any channel in the workflow can be assigned to an output, including process and subworkflow outputs. This approach is intended to replace the {ref}`publishDir <process-publishdir>` directive.
+A script can define an *output block* which declares the top-level outputs of the workflow. Each output should be assigned in the `publish` section of the entry workflow. Any channel in the workflow can be assigned to an output, including process and subworkflow outputs. This approach is intended to replace the [publishDir][process-publishdir] directive.
 
 Here is a basic example:
 
@@ -509,8 +493,6 @@ output {
 
 In the above example, the output of process `fetch` is assigned to the `samples` workflow output. How this output is published to a directory structure is described in the next section.
 
-(workflow-publishing-files)=
-
 ### Publishing files
 
 The top-level output directory of a workflow run can be set using the `-output-dir` command-line option or the `outputDir` config option:
@@ -610,7 +592,7 @@ output {
 
 Each `>>` specifies a *source file* and *publish target*. The source file should be a file or collection of files, and the publish target should be a directory or file name. If the publish target ends with a slash, it is treated as the directory in which source files are published. Otherwise, it is treated as the target filename of a source file. Only files that are published with the `>>` operator are saved to the output directory.
 
-:::{note}
+:::note
 Files that do not originate from the work directory are not published.
 :::
 
@@ -670,7 +652,7 @@ This example will produce the following index file:
 "3"|"sample 3"|"results/fastq/3a.fastq"|""
 ```
 
-:::{note}
+:::note
 Files that do not originate from the work directory are not published, but are included in the index file.
 :::
 
@@ -680,27 +662,40 @@ See [Output directives](#output-directives) for the list of available index dire
 
 The following directives are available for each output in the output block:
 
-`index`
-: Create an index file which will contain a record of each published value.
+##### `index`
+
+Create an index file which will contain a record of each published value.
 
-  The following directives are available in an index definition:
+The following directives are available in an index definition:
 
-  `header`
-  : When `true`, the keys of the first record are used as the column names (default: `false`). Can also be a list of column names. Only used for CSV files.
+######
 
-  `path`
-  : The name of the index file relative to the base output directory (required). Can be a CSV, JSON, or YAML file.
+`header`
 
-  `sep`
-  : The character used to separate values (default: `','`). Only used for CSV files.
+When `true`, the keys of the first record are used as the column names (default: `false`). Can also be a list of column names. Only used for CSV files.
 
-`label`
-: Specify a label to be applied to every published file. Can be specified multiple times.
+######
 
 `path`
-: Specify the publish path relative to the output directory (default: `'.'`). Can be a path, a closure that defines a custom directory for each published value, or a closure that publishes individual files using the `>>` operator.
 
-Additionally, the following options from the {ref}`workflow <config-workflow>` config scope can be specified as directives:
+The name of the index file relative to the base output directory (required). Can be a CSV, JSON, or YAML file.
+
+##### `sep`
+
+The character used to separate values (default: `','`). Only used for CSV files.
+
+##### `label`
+
+Specify a label to be applied to every published file. Can be specified multiple times.
+
+##### `path`
+
+Specify the publish path relative to the output directory (default: `'.'`). Can be a path, a closure that defines a custom directory for each published value, or a closure that publishes individual files using the `>>` operator.
+
+#
+
+Additionally, the following options from the [workflow][config-workflow] config scope can be specified as directives:
+
 - `contentType`
 - `enabled`
 - `ignoreErrors`
@@ -718,3 +713,23 @@ output {
     }
 }
 ```
+
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[config-process-selectors]: /nextflow_docs/nextflow_repo/docs/config.mdx#process-selectors
+[config-workflow]: /nextflow_docs/nextflow_repo/docs/reference/config.mdx#workflow
+[dsl1-page]: /nextflow_docs/nextflow_repo/docs/migrations/dsl1.mdx
+[module-aliases]: /nextflow_docs/nextflow_repo/docs/module.mdx#module-aliases
+[process-naming-outputs]: /nextflow_docs/nextflow_repo/docs/process.mdx#naming-outputs
+[operator-map]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#map
+[operator-mix]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#mix
+[operator-view]: /nextflow_docs/nextflow_repo/docs/reference/operator.mdx#view
+[process-publishdir]: /nextflow_docs/nextflow_repo/docs/reference/process.mdx#publishdir
+[stdlib-types-boolean]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#boolean
+[stdlib-types-float]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#float
+[stdlib-types-integer]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#integer
+[stdlib-types-path]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#path
+[stdlib-types-string]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#string
+[strict-syntax-page]: /nextflow_docs/nextflow_repo/docs/strict-syntax.mdx
+[workflow-outputs-first-preview]: /nextflow_docs/nextflow_repo/docs/reference/syntax.mdx#workflow
+[workflow-outputs-second-preview]: /nextflow_docs/nextflow_repo/docs/migrations/24-10.mdx#workflow-outputs-second-preview
+[workflow-outputs-third-preview]: /nextflow_docs/nextflow_repo/docs/migrations/25-04.mdx#workflow-outputs-third-preview
diff --git a/new-docs/nextflow-docs/working-with-files.mdx b/new-docs/nextflow-docs/working-with-files.mdx
new file mode 100644
index 0000000000..3ce81d4bb2
--- /dev/null
+++ b/new-docs/nextflow-docs/working-with-files.mdx
@@ -0,0 +1,271 @@
+# Working with files
+
+## Opening files
+
+To access and work with files, use the `file()` method, which returns a file system object given a file path string:
+
+```nextflow
+myFile = file('some/path/to/my_file.file')
+```
+
+The `file()` method can reference both files and directories, depending on what the string path refers to in the file system.
+
+When using the wildcard characters `*`, `?`, `[]` and `{}`, the argument is interpreted as a [glob](http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob) path matcher and the `file()` method returns a list object holding the paths of files whose names match the specified pattern, or an empty list if no match is found:
+
+```nextflow
+listOfFiles = file('some/path/*.fa')
+```
+
+:::note
+The `file()` method does not return a list if only one file is matched. Use the `files()` method to always return a list.
+:::
+
+:::note
+A double asterisk (`**`) in a glob pattern works like `*` but also searches through subdirectories.
+:::
+
+By default, wildcard characters do not match directories or hidden files. For example, if you want to include hidden files in the result list, enable the `hidden` option:
+
+```nextflow
+listWithHidden = file('some/path/*.fa', hidden: true)
+```
+
+:::note
+To compose paths, instead of string interpolation, use the `resolve()` method or the `/` operator:
+
+```nextflow
+def dir = file('s3://bucket/some/data/path')
+def sample1 = dir.resolve('sample.bam')         // correct
+def sample2 = dir / 'sample.bam'
+def sample3 = file("$dir/sample.bam")           // correct (but verbose)
+def sample4 = "$dir/sample.bam"                 // incorrect
+```
+:::
+
+## Getting file attributes
+
+The `file()` method returns a [Path](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/Path.html), which has several methods for retrieving metadata about the file:
+
+```nextflow
+def path = file('/some/path/file.txt')
+
+assert path.baseName == 'file'
+assert path.extension == 'txt'
+assert path.name == 'file.txt'
+assert path.parent == '/some/path'
+```
+
+:::tip
+When calling an object method, any method that looks like `get*()` can also be accessed as a field. For example, `path.getName()` is equivalent to `path.name`, `path.getBaseName()` is equivalent to `path.baseName`, and so on.
+:::
+
+See the [Path][stdlib-types-path] reference for the list of available methods.
+
+## Reading and writing
+
+### Reading and writing an entire file
+
+Given a file variable, created with the `file()` method as shown previously, reading a file is as easy as getting the file's `text` property, which returns the file content as a string:
+
+```nextflow
+print myFile.text
+```
+
+Similarly, you can save a string to a file by assigning it to the file's `text` property:
+
+```nextflow
+myFile.text = 'Hello world!'
+```
+
+Binary data can be managed in the same way, just using the file property `bytes` instead of `text`. Thus, the following example reads the file and returns its content as a byte array:
+
+```nextflow
+binaryContent = myFile.bytes
+```
+
+Or you can save a byte array to a file:
+
+```nextflow
+myFile.bytes = binaryContent
+```
+
+:::note
+The above assignment overwrites any existing file contents, and implicitly creates the file if it doesn't exist.
+:::
+
+:::warning
+The above methods read and write the **entire** file contents at once, in a single variable or buffer. For this reason, when dealing with large files it is recommended that you use a more memory efficient approach, such as reading/writing a file line by line or using a fixed size buffer.
+:::
+
+### Appending to a file
+
+In order to append a string value to a file without erasing existing content, you can use the `append()` method:
+
+```nextflow
+myFile.append('Add this line\n')
+```
+
+Or use the left shift operator, a more idiomatic way to append text content to a file:
+
+```nextflow
+myFile << 'Add a line more\n'
+```
+
+### Reading a file line by line
+
+In order to read a text file line by line you can use the method `readLines()` provided by the file object, which returns the file content as a list of strings:
+
+```nextflow
+myFile = file('some/my_file.txt')
+allLines = myFile.readLines()
+for( line : allLines ) {
+    println line
+}
+```
+
+This can also be written in a more idiomatic syntax:
+
+```nextflow
+file('some/my_file.txt')
+    .readLines()
+    .each { println it }
+```
+
+:::warning
+The method `readLines()` reads the **entire** file at once and returns a list containing all the lines. For this reason, do not use it to read big files.
+:::
+
+To process a big file, use the method `eachLine()`, which reads only a single line at a time into memory:
+
+```nextflow
+count = 0
+myFile.eachLine { str ->
+    println "line ${count++}: $str"
+}
+```
+
+### Advanced file reading
+
+The classes `Reader` and `InputStream` provide fine-grained control for reading text and binary files, respectively.
+
+The method `newReader()` creates a [Reader](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Reader.html) object for the given file that allows you to read the content as single characters, lines or arrays of characters:
+
+```nextflow
+myReader = myFile.newReader()
+String line
+while( line = myReader.readLine() ) {
+    println line
+}
+myReader.close()
+```
+
+The method `withReader()` works similarly, but automatically calls the `close()` method for you when you have finished processing the file. So, the previous example can be written more simply as:
+
+```nextflow
+myFile.withReader {
+    String line
+    while( line = it.readLine() ) {
+        println line
+    }
+}
+```
+
+The methods `newInputStream()` and `withInputStream()` work similarly. The main difference is that they create an [InputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/InputStream.html) object useful for writing binary data.
+
+See the [Path][stdlib-types-path] reference for the list of available methods.
+
+### Advanced file writing
+
+The `Writer` and `OutputStream` classes provide fine-grained control for writing text and binary files, respectively, including low-level operations for single characters or bytes, and support for big files.
+
+For example, given two file objects `sourceFile` and `targetFile`, the following code copies the first file's content into the second file, replacing all `U` characters with `X`:
+
+```nextflow
+sourceFile.withReader { source ->
+    targetFile.withWriter { target ->
+        String line
+        while( line=source.readLine() ) {
+            target << line.replaceAll('U','X')
+        }
+    }
+}
+```
+
+See the [Path][stdlib-types-path] reference for the list of available methods.
+
+## Filesystem operations
+
+Methods for performing filesystem operations such as copying, deleting, and directory listing are documented in the [Path][stdlib-types-path] reference.
+
+### Listing directories
+
+The simplest way to list a directory is to use `list()` or `listFiles()`, which return a collection of first-level elements (files and directories) of a directory:
+
+```nextflow
+for( def file : file('any/path').list() ) {
+    println file
+}
+```
+
+Additionally, the `eachFile()` method allows you to iterate through the first-level elements only (just like `listFiles()`). As with other `each*()` methods, `eachFile()` takes a closure as a parameter:
+
+```nextflow
+myDir.eachFile { item ->
+    if( item.isFile() ) {
+        println "${item.getName()} - size: ${item.size()}"
+    }
+    else if( item.isDirectory() ) {
+        println "${item.getName()} - DIR"
+    }
+}
+```
+
+### Copying files
+
+In general, you should not need to manually copy files, because Nextflow will automatically stage files in and out of the task environment based on the definition of process inputs and outputs. Ideally, any operation which transforms files should be encapsulated in a process, in order to leverage Nextflow's staging capabilities as much as possible.
+
+## Remote files
+
+Nextflow works with many types of remote files and objects using the same interface as for local files. The following protocols are supported:
+
+- HTTP(S)/FTP (`http://`, `https://`, `ftp://`)
+- Amazon S3 (`s3://`)
+- Azure Blob Storage (`az://`)
+- Google Cloud Storage (`gs://`)
+
+To reference a remote file, simply specify the URL when opening the file:
+
+```nextflow
+pdb = file('http://files.rcsb.org/header/5FID.pdb')
+```
+
+It can then be used in the same way as a local file:
+
+```nextflow
+println pdb.text
+```
+
+:::note
+Not all operations are supported for all protocols. For example, writing and directory listing is not supported for HTTP(S) and FTP paths.
+:::
+
+:::note
+Additional configuration may be necessary for cloud object storage, such as authenticating with a private bucket. See the documentation for each cloud storage provider for further details.
+:::
+
+### Remote file staging
+
+When a process input file resides on a different file system than the work directory, Nextflow copies the file into the work directory using an appropriate Java SDK.
+
+Remote files are staged in a subdirectory of the work directory with the form `stage-<session-id>/<hash>/<filename>`, where `<hash>` is determined by the remote file path. If multiple tasks request the same remote file, the file will be downloaded once and reused by each task. These files can be reused by resumed runs with the same session ID.
+
+:::note
+Remote file staging can be a bottleneck during large-scale runs, particularly when input files are stored in object storage but need to be staged in a shared filesystem work directory. This bottleneck occurs because Nextflow handles all of these file transfers.
+
+To mitigate this, you can implement a custom process to download the required files, allowing you to stage multiple files efficiently through parallel jobs. Files should be given as a `val` input instead of a `path` input to bypass Nextflow's built-in remote file staging.
+
+Alternatively, use [Fusion][fusion-page] with the work directory set to object storage. In this case, tasks can access remote files directly without any prior staging, eliminating the bottleneck.
+:::
+
+[fusion-page]: /nextflow_docs/nextflow_repo/docs/fusion.mdx
+[stdlib-types-path]: /nextflow_docs/nextflow_repo/docs/reference/stdlib-types.mdx#path
diff --git a/new-docs/nextflow-docs/your-first-script.mdx b/new-docs/nextflow-docs/your-first-script.mdx
new file mode 100644
index 0000000000..15ce849187
--- /dev/null
+++ b/new-docs/nextflow-docs/your-first-script.mdx
@@ -0,0 +1,200 @@
+# Your first script
+
+This guide details fundamental skills to run a basic Nextflow pipeline. It includes:
+
+- Running a pipeline
+- Modifying and resuming a pipeline
+- Configuring a pipeline parameter
+
+:::info[**Prerequisites**]
+You will need the following to get started:
+
+- Nextflow installed locally
+:::
+
+## Run a pipeline
+
+You will run a basic Nextflow pipeline that splits a string of text into two files and then converts lowercase letters to uppercase letters. You can see the pipeline here:
+
+```groovy
+// Default parameter input
+params.str = "Hello world!"
+
+// split process
+process split {
+    publishDir "results/lower"
+
+    input:
+    val x
+
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf '${x}' | split -b 6 - chunk_
+    """
+}
+
+// convert_to_upper process
+process convert_to_upper {
+    publishDir "results/upper"
+    tag "$y"
+
+    input:
+    path y
+
+    output:
+    path 'upper_*'
+
+    script:
+    """
+    cat $y | tr '[a-z]' '[A-Z]' > upper_${y}
+    """
+}
+
+// Workflow block
+workflow {
+    ch_str = channel.of(params.str)       // Create a channel using parameter input
+    ch_chunks = split(ch_str)             // Split string into chunks and create a named channel
+    convert_to_upper(ch_chunks.flatten()) // Convert lowercase letters to uppercase letters
+}
+```
+
+This script defines two processes:
+
+- `split`: takes a string input, splits it into 6-character chunks, and writes the chunks to files with the prefix `chunk_`.
+- `convert_to_upper`: takes files as input, transforms their contents to uppercase letters, and writes the uppercase strings to files with the prefix `upper_`.
+
+The `split` output is emitted as a single element. The `flatten` operator splits this combined element so that each file is treated as a sole element.
+
+The outputs from both processes are published in subdirectories (`lower` and `upper`) in the `results` directory.
+
+To run your pipeline:
+
+1. Create a new file named `main.nf` in your current directory.
+2. Copy and save the above pipeline to your new file.
+3. Run your pipeline using the following command:
+
+    ```bash
+    nextflow run main.nf
+    ```
+
+You will see output similar to the following:
+
+```console
+N E X T F L O W   ~  version 24.10.3
+
+Launching `main.nf` [big_wegener] DSL2 - revision: 13a41a8946
+
+executor >  local (3)
+[82/457482] split (1)                   | 1 of 1 ✔
+[2f/056a98] convert_to_upper (chunk_aa) | 2 of 2 ✔
+```
+
+Nextflow creates a `work` directory to store files used during a pipeline run. Each execution of a process is run as a separate task. The `split` process is run as one task and the `convert_to_upper` process is run as two tasks. The hexadecimal string, for example, `82/457482`, is the beginning of a unique hash. It is a prefix used to identify the task directory where the script was executed.
+
+:::tip
+Run your pipeline with `-ansi-log false` to see each task printed on a separate line:
+
+```bash
+nextflow run main.nf -ansi-log false
+```
+
+You will see output similar to the following:
+
+```console
+N E X T F L O W  ~  version 24.10.3
+Launching `main.nf` [peaceful_watson] DSL2 - revision: 13a41a8946
+[43/f1f8b5] Submitted process > split (1)
+[a2/5aa4b1] Submitted process > convert_to_upper (chunk_ab)
+[30/ba7de0] Submitted process > convert_to_upper (chunk_aa)
+```
+
+:::
+
+## Modify and resume
+
+Nextflow tracks task executions in a task cache, a key-value store of previously executed tasks. The task cache is used in conjunction with the work directory to recover cached tasks. If you modify and resume your pipeline, only the processes that are changed will be re-executed. The cached results will be used for tasks that don't change.
+
+You can enable resumability using the `-resume` flag when running a pipeline. To modify and resume your pipeline:
+
+1. Open `main.nf`.
+2. Replace the `convert_to_upper` process with the following:
+
+    ```groovy
+    process convert_to_upper {
+        publishDir "results/upper"
+        tag "$y"
+
+        input:
+        path y
+
+        output:
+        path 'upper_*'
+
+        script:
+        """
+        rev $y > upper_${y}
+        """
+    }
+    ```
+
+3. Save your changes.
+4. Run your updated pipeline using the following command:
+
+    ```bash
+    nextflow run main.nf -resume
+    ```
+
+You will see output similar to the following:
+
+```console
+ N E X T F L O W   ~  version 24.10.3
+
+Launching `main.nf` [furious_curie] DSL2 - revision: 5490f13c43
+
+executor >  local (2)
+[82/457482] split (1)                   | 1 of 1, cached: 1 ✔
+[02/9db40b] convert_to_upper (chunk_aa) | 2 of 2 ✔
+```
+
+Nextflow skips the execution of the `split` process and retrieves the results from the cache. The `convert_to_upper` process is executed twice.
+
+See [Caching and resuming][cache-resume-page] for more information about Nextflow cache and resume functionality.
+
+## Pipeline parameters
+
+Parameters are used to control the inputs to a pipeline. They are declared by prepending a variable name to the prefix `params`, separated by dot character. Parameters can be specified on the command line by prefixing the parameter name with a double dash character, for example, `--paramName`. Parameters specified on the command line override parameters specified in a main script.
+
+You can configure the `str` parameter in your pipeline. To modify your `str` parameter:
+
+1. Run your pipeline using the following command:
+
+    ```bash
+    nextflow run main.nf --str 'Bonjour le monde'
+    ```
+
+You will see output similar to the following:
+
+```console
+ N E X T F L O W   ~  version 24.10.3
+
+Launching `main.nf` [distracted_kalam] DSL2 - revision: 082867d4d6
+
+executor >  local (4)
+[55/a3a700] process > split (1)           [100%] 1 of 1 ✔
+[f4/af5ddd] process > convert_to_upper (chunk_ac) [100%] 3 of 3 ✔
+```
+
+The input string is now longer and the `split` process splits it into three chunks. The `convert_to_upper` process is run three times.
+
+See [Pipeline parameters][cli-params] for more information about modifying pipeline parameters.
+
+## Next steps
+
+Your first script is a brief introduction to running pipelines, modifying and resuming pipelines, and pipeline parameters. See [training.nextflow.io](https://training.nextflow.io/) for further Nextflow training modules.
+
+[cache-resume-page]: /nextflow_docs/nextflow_repo/docs/cache-and-resume.mdx
+[cli-params]: /nextflow_docs/nextflow_repo/docs/cli.mdx#pipeline-parameters
+[install-page]: /nextflow_docs/nextflow_repo/docs/install.mdx
diff --git a/new-docs/package-lock.json b/new-docs/package-lock.json
new file mode 100644
index 0000000000..0b397c2117
--- /dev/null
+++ b/new-docs/package-lock.json
@@ -0,0 +1,18000 @@
+{
+  "name": "new-docs",
+  "version": "0.0.0",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "new-docs",
+      "version": "0.0.0",
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+        "clsx": "^2.0.0",
+        "prism-react-renderer": "^2.3.0",
+        "react": "^19.0.0",
+        "react-dom": "^19.0.0"
+      },
+      "devDependencies": {
+        "@docusaurus/module-type-aliases": "3.9.2",
+        "@docusaurus/tsconfig": "3.9.2",
+        "@docusaurus/types": "3.9.2",
+        "typescript": "~5.6.2"
+      },
+      "engines": {
+        "node": ">=20.0"
+      }
+    },
+    "node_modules/@ai-sdk/gateway": {
+      "version": "2.0.7",
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+      "license": "Apache-2.0",
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+      },
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+      },
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+      "resolved": "https://registry.npmjs.org/@ai-sdk/provider/-/provider-2.0.0.tgz",
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+      "license": "Apache-2.0",
+      "dependencies": {
+        "json-schema": "^0.4.0"
+      },
+      "engines": {
+        "node": ">=18"
+      }
+    },
+    "node_modules/@ai-sdk/provider-utils": {
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+      "peerDependencies": {
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+      "license": "Apache-2.0",
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+        "swr": "^2.2.5",
+        "throttleit": "2.1.0"
+      },
+      "engines": {
+        "node": ">=18"
+      },
+      "peerDependencies": {
+        "react": "^18 || ^19 || ^19.0.0-rc",
+        "zod": "^3.25.76 || ^4.1.8"
+      },
+      "peerDependenciesMeta": {
+        "zod": {
+          "optional": true
+        }
+      }
+    },
+    "node_modules/@algolia/abtesting": {
+      "version": "1.8.0",
+      "resolved": "https://registry.npmjs.org/@algolia/abtesting/-/abtesting-1.8.0.tgz",
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+        "@algolia/requester-node-http": "5.42.0"
+      },
+      "engines": {
+        "node": ">= 14.0.0"
+      }
+    },
+    "node_modules/@algolia/autocomplete-core": {
+      "version": "1.19.2",
+      "resolved": "https://registry.npmjs.org/@algolia/autocomplete-core/-/autocomplete-core-1.19.2.tgz",
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+      "license": "MIT",
+      "dependencies": {
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+        "@algolia/autocomplete-shared": "1.19.2"
+      }
+    },
+    "node_modules/@algolia/autocomplete-plugin-algolia-insights": {
+      "version": "1.19.2",
+      "resolved": "https://registry.npmjs.org/@algolia/autocomplete-plugin-algolia-insights/-/autocomplete-plugin-algolia-insights-1.19.2.tgz",
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+      "dependencies": {
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+      },
+      "peerDependencies": {
+        "search-insights": ">= 1 < 3"
+      }
+    },
+    "node_modules/@algolia/autocomplete-shared": {
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+      "license": "MIT",
+      "peerDependencies": {
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+        "algoliasearch": ">= 4.9.1 < 6"
+      }
+    },
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+      "engines": {
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+    },
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+      "engines": {
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+      }
+    },
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+      }
+    },
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+      },
+      "engines": {
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+    },
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+      "engines": {
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+      }
+    },
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+        "node": ">=8.3.0"
+      },
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+        "is-wsl": "^3.1.0"
+      },
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+      },
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+      },
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+        "xml-js": "bin/cli.js"
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diff --git a/new-docs/package.json b/new-docs/package.json
new file mode 100644
index 0000000000..73b7fcfd04
--- /dev/null
+++ b/new-docs/package.json
@@ -0,0 +1,47 @@
+{
+  "name": "new-docs",
+  "version": "0.0.0",
+  "private": true,
+  "scripts": {
+    "docusaurus": "docusaurus",
+    "start": "docusaurus start",
+    "build": "docusaurus build",
+    "swizzle": "docusaurus swizzle",
+    "deploy": "docusaurus deploy",
+    "clear": "docusaurus clear",
+    "serve": "docusaurus serve",
+    "write-translations": "docusaurus write-translations",
+    "write-heading-ids": "docusaurus write-heading-ids",
+    "typecheck": "tsc"
+  },
+  "dependencies": {
+    "@docusaurus/core": "3.9.2",
+    "@docusaurus/preset-classic": "3.9.2",
+    "@mdx-js/react": "^3.0.0",
+    "clsx": "^2.0.0",
+    "prism-react-renderer": "^2.3.0",
+    "react": "^19.0.0",
+    "react-dom": "^19.0.0"
+  },
+  "devDependencies": {
+    "@docusaurus/module-type-aliases": "3.9.2",
+    "@docusaurus/tsconfig": "3.9.2",
+    "@docusaurus/types": "3.9.2",
+    "typescript": "~5.6.2"
+  },
+  "browserslist": {
+    "production": [
+      ">0.5%",
+      "not dead",
+      "not op_mini all"
+    ],
+    "development": [
+      "last 3 chrome version",
+      "last 3 firefox version",
+      "last 5 safari version"
+    ]
+  },
+  "engines": {
+    "node": ">=20.0"
+  }
+}
diff --git a/new-docs/sidebars.ts b/new-docs/sidebars.ts
new file mode 100644
index 0000000000..289713975c
--- /dev/null
+++ b/new-docs/sidebars.ts
@@ -0,0 +1,33 @@
+import type {SidebarsConfig} from '@docusaurus/plugin-content-docs';
+
+// This runs in Node.js - Don't use client-side code here (browser APIs, JSX...)
+
+/**
+ * Creating a sidebar enables you to:
+ - create an ordered group of docs
+ - render a sidebar for each doc of that group
+ - provide next/previous navigation
+
+ The sidebars can be generated from the filesystem, or explicitly defined here.
+
+ Create as many sidebars as you want.
+ */
+const sidebars: SidebarsConfig = {
+  // By default, Docusaurus generates a sidebar from the docs folder structure
+  tutorialSidebar: [{type: 'autogenerated', dirName: '.'}],
+
+  // But you can create a sidebar manually
+  /*
+  tutorialSidebar: [
+    'intro',
+    'hello',
+    {
+      type: 'category',
+      label: 'Tutorial',
+      items: ['tutorial-basics/create-a-document'],
+    },
+  ],
+   */
+};
+
+export default sidebars;
diff --git a/new-docs/src/components/HomepageFeatures/index.tsx b/new-docs/src/components/HomepageFeatures/index.tsx
new file mode 100644
index 0000000000..c2551fb9b8
--- /dev/null
+++ b/new-docs/src/components/HomepageFeatures/index.tsx
@@ -0,0 +1,71 @@
+import type {ReactNode} from 'react';
+import clsx from 'clsx';
+import Heading from '@theme/Heading';
+import styles from './styles.module.css';
+
+type FeatureItem = {
+  title: string;
+  Svg: React.ComponentType<React.ComponentProps<'svg'>>;
+  description: ReactNode;
+};
+
+const FeatureList: FeatureItem[] = [
+  {
+    title: 'Easy to Use',
+    Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default,
+    description: (
+      <>
+        Docusaurus was designed from the ground up to be easily installed and
+        used to get your website up and running quickly.
+      </>
+    ),
+  },
+  {
+    title: 'Focus on What Matters',
+    Svg: require('@site/static/img/undraw_docusaurus_tree.svg').default,
+    description: (
+      <>
+        Docusaurus lets you focus on your docs, and we&apos;ll do the chores. Go
+        ahead and move your docs into the <code>docs</code> directory.
+      </>
+    ),
+  },
+  {
+    title: 'Powered by React',
+    Svg: require('@site/static/img/undraw_docusaurus_react.svg').default,
+    description: (
+      <>
+        Extend or customize your website layout by reusing React. Docusaurus can
+        be extended while reusing the same header and footer.
+      </>
+    ),
+  },
+];
+
+function Feature({title, Svg, description}: FeatureItem) {
+  return (
+    <div className={clsx('col col--4')}>
+      <div className="text--center">
+        <Svg className={styles.featureSvg} role="img" />
+      </div>
+      <div className="text--center padding-horiz--md">
+        <Heading as="h3">{title}</Heading>
+        <p>{description}</p>
+      </div>
+    </div>
+  );
+}
+
+export default function HomepageFeatures(): ReactNode {
+  return (
+    <section className={styles.features}>
+      <div className="container">
+        <div className="row">
+          {FeatureList.map((props, idx) => (
+            <Feature key={idx} {...props} />
+          ))}
+        </div>
+      </div>
+    </section>
+  );
+}
diff --git a/new-docs/src/components/HomepageFeatures/styles.module.css b/new-docs/src/components/HomepageFeatures/styles.module.css
new file mode 100644
index 0000000000..b248eb2e5d
--- /dev/null
+++ b/new-docs/src/components/HomepageFeatures/styles.module.css
@@ -0,0 +1,11 @@
+.features {
+  display: flex;
+  align-items: center;
+  padding: 2rem 0;
+  width: 100%;
+}
+
+.featureSvg {
+  height: 200px;
+  width: 200px;
+}
diff --git a/new-docs/src/css/custom.css b/new-docs/src/css/custom.css
new file mode 100644
index 0000000000..2bc6a4cfde
--- /dev/null
+++ b/new-docs/src/css/custom.css
@@ -0,0 +1,30 @@
+/**
+ * Any CSS included here will be global. The classic template
+ * bundles Infima by default. Infima is a CSS framework designed to
+ * work well for content-centric websites.
+ */
+
+/* You can override the default Infima variables here. */
+:root {
+  --ifm-color-primary: #2e8555;
+  --ifm-color-primary-dark: #29784c;
+  --ifm-color-primary-darker: #277148;
+  --ifm-color-primary-darkest: #205d3b;
+  --ifm-color-primary-light: #33925d;
+  --ifm-color-primary-lighter: #359962;
+  --ifm-color-primary-lightest: #3cad6e;
+  --ifm-code-font-size: 95%;
+  --docusaurus-highlighted-code-line-bg: rgba(0, 0, 0, 0.1);
+}
+
+/* For readability concerns, you should choose a lighter palette in dark mode. */
+[data-theme='dark'] {
+  --ifm-color-primary: #25c2a0;
+  --ifm-color-primary-dark: #21af90;
+  --ifm-color-primary-darker: #1fa588;
+  --ifm-color-primary-darkest: #1a8870;
+  --ifm-color-primary-light: #29d5b0;
+  --ifm-color-primary-lighter: #32d8b4;
+  --ifm-color-primary-lightest: #4fddbf;
+  --docusaurus-highlighted-code-line-bg: rgba(0, 0, 0, 0.3);
+}
diff --git a/new-docs/src/pages/index.module.css b/new-docs/src/pages/index.module.css
new file mode 100644
index 0000000000..9f71a5da77
--- /dev/null
+++ b/new-docs/src/pages/index.module.css
@@ -0,0 +1,23 @@
+/**
+ * CSS files with the .module.css suffix will be treated as CSS modules
+ * and scoped locally.
+ */
+
+.heroBanner {
+  padding: 4rem 0;
+  text-align: center;
+  position: relative;
+  overflow: hidden;
+}
+
+@media screen and (max-width: 996px) {
+  .heroBanner {
+    padding: 2rem;
+  }
+}
+
+.buttons {
+  display: flex;
+  align-items: center;
+  justify-content: center;
+}
diff --git a/new-docs/src/pages/index.tsx b/new-docs/src/pages/index.tsx
new file mode 100644
index 0000000000..2e006d153b
--- /dev/null
+++ b/new-docs/src/pages/index.tsx
@@ -0,0 +1,44 @@
+import type {ReactNode} from 'react';
+import clsx from 'clsx';
+import Link from '@docusaurus/Link';
+import useDocusaurusContext from '@docusaurus/useDocusaurusContext';
+import Layout from '@theme/Layout';
+import HomepageFeatures from '@site/src/components/HomepageFeatures';
+import Heading from '@theme/Heading';
+
+import styles from './index.module.css';
+
+function HomepageHeader() {
+  const {siteConfig} = useDocusaurusContext();
+  return (
+    <header className={clsx('hero hero--primary', styles.heroBanner)}>
+      <div className="container">
+        <Heading as="h1" className="hero__title">
+          {siteConfig.title}
+        </Heading>
+        <p className="hero__subtitle">{siteConfig.tagline}</p>
+        <div className={styles.buttons}>
+          <Link
+            className="button button--secondary button--lg"
+            to="/docs/intro">
+            Docusaurus Tutorial - 5min ⏱️
+          </Link>
+        </div>
+      </div>
+    </header>
+  );
+}
+
+export default function Home(): ReactNode {
+  const {siteConfig} = useDocusaurusContext();
+  return (
+    <Layout
+      title={`Hello from ${siteConfig.title}`}
+      description="Description will go into a meta tag in <head />">
+      <HomepageHeader />
+      <main>
+        <HomepageFeatures />
+      </main>
+    </Layout>
+  );
+}
diff --git a/new-docs/src/pages/markdown-page.md b/new-docs/src/pages/markdown-page.md
new file mode 100644
index 0000000000..9756c5b668
--- /dev/null
+++ b/new-docs/src/pages/markdown-page.md
@@ -0,0 +1,7 @@
+---
+title: Markdown page example
+---
+
+# Markdown page example
+
+You don't need React to write simple standalone pages.
diff --git a/new-docs/static/.nojekyll b/new-docs/static/.nojekyll
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/new-docs/static/img/docusaurus-social-card.jpg b/new-docs/static/img/docusaurus-social-card.jpg
new file mode 100644
index 0000000000..ffcb448210
Binary files /dev/null and b/new-docs/static/img/docusaurus-social-card.jpg differ
diff --git a/new-docs/static/img/docusaurus.png b/new-docs/static/img/docusaurus.png
new file mode 100644
index 0000000000..f458149e3c
Binary files /dev/null and b/new-docs/static/img/docusaurus.png differ
diff --git a/new-docs/static/img/favicon.ico b/new-docs/static/img/favicon.ico
new file mode 100644
index 0000000000..c01d54bcd3
Binary files /dev/null and b/new-docs/static/img/favicon.ico differ
diff --git a/new-docs/static/img/logo.svg b/new-docs/static/img/logo.svg
new file mode 100644
index 0000000000..9db6d0d066
--- /dev/null
+++ b/new-docs/static/img/logo.svg
@@ -0,0 +1 @@
+<svg width="200" height="200" viewBox="0 0 200 200" xmlns="http://www.w3.org/2000/svg"><g fill="none" fill-rule="evenodd"><path fill="#FFF" d="M99 52h84v34H99z"/><path d="M23 163c-7.398 0-13.843-4.027-17.303-10A19.886 19.886 0 0 0 3 163c0 11.046 8.954 20 20 20h20v-20H23z" fill="#3ECC5F"/><path d="M112.98 57.376L183 53V43c0-11.046-8.954-20-20-20H73l-2.5-4.33c-1.112-1.925-3.889-1.925-5 0L63 23l-2.5-4.33c-1.111-1.925-3.889-1.925-5 0L53 23l-2.5-4.33c-1.111-1.925-3.889-1.925-5 0L43 23c-.022 0-.042.003-.065.003l-4.142-4.141c-1.57-1.571-4.252-.853-4.828 1.294l-1.369 5.104-5.192-1.392c-2.148-.575-4.111 1.389-3.535 3.536l1.39 5.193-5.102 1.367c-2.148.576-2.867 3.259-1.296 4.83l4.142 4.142c0 .021-.003.042-.003.064l-4.33 2.5c-1.925 1.111-1.925 3.889 0 5L23 53l-4.33 2.5c-1.925 1.111-1.925 3.889 0 5L23 63l-4.33 2.5c-1.925 1.111-1.925 3.889 0 5L23 73l-4.33 2.5c-1.925 1.111-1.925 3.889 0 5L23 83l-4.33 2.5c-1.925 1.111-1.925 3.889 0 5L23 93l-4.33 2.5c-1.925 1.111-1.925 3.889 0 5L23 103l-4.33 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new file mode 100644
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new file mode 100644
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diff --git a/new-docs/static/img/undraw_docusaurus_tree.svg b/new-docs/static/img/undraw_docusaurus_tree.svg
new file mode 100644
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diff --git a/new-docs/tsconfig.json b/new-docs/tsconfig.json
new file mode 100644
index 0000000000..920d7a6523
--- /dev/null
+++ b/new-docs/tsconfig.json
@@ -0,0 +1,8 @@
+{
+  // This file is not used in compilation. It is here just for a nice editor experience.
+  "extends": "@docusaurus/tsconfig",
+  "compilerOptions": {
+    "baseUrl": "."
+  },
+  "exclude": [".docusaurus", "build"]
+}