Merge pull request #1078 from nf-core/nf-core-template-merge-2.10

Important! Template update for nf-core/tools v2.10

Author: drpatelh

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.github/workflows/release-announcments.yml

@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/[email protected]
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #

CHANGELOG.md

@@ -23,10 +23,23 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9
 - [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation
 - [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module
+- [PR #1078](https://github.com/nf-core/rnaseq/pull/1078) - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
 - [PR #1083](https://github.com/nf-core/rnaseq/pull/1083) - Move local modules and subworkflows to subfolders
 - [PR #1088](https://github.com/nf-core/rnaseq/pull/1088) - Updates contributing and code of conduct documents with nf-core template 2.10
 - [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability
 
+### Software dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `fastqc`   | 0.11.9      | 0.12.1      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02
 
 ### Credits

CITATIONS.md

@@ -22,7 +22,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)
 

README.md

@@ -1,6 +1,7 @@
 # ![nf-core/rnaseq](docs/images/nf-core-rnaseq_logo_light.png#gh-light-mode-only) ![nf-core/rnaseq](docs/images/nf-core-rnaseq_logo_dark.png#gh-dark-mode-only)
 
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)
+[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -49,10 +50,11 @@
 
 ## Usage
 
-> **Note**
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
-> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
-> with `-profile test` before running the workflow on actual data.
+:::note
+If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
+to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
+with `-profile test` before running the workflow on actual data.
+:::
 
 First, prepare a samplesheet with your input data that looks as follows:
 
@@ -82,10 +84,11 @@ nextflow run nf-core/rnaseq \
     -profile <docker/singularity/.../institute>
 ```
 
-> **Warning:**
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+:::warning
+Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+:::
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnaseq" target="_blank">nf-core/rnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/dev" target="_blank">nf-core/rnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/rnaseq/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/rnaseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-rnaseq-methods-description":
     order: -1000

docs/output.md

@@ -742,6 +742,7 @@ A number of genome-specific files are generated by the pipeline because they are
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+  - Parameters used by the pipeline run: `params.json`.
 
 </details>
 

docs/usage.md

@@ -187,7 +187,9 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::warning
+Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -224,19 +226,25 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::tip
+If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::
 
 ## Core Nextflow arguments
 
-> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::note
+These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::
 
 ### `-profile`
 
 Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::info
+We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::
 
 The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 

lib/NfcoreTemplate.groovy

@@ -3,6 +3,7 @@
 //
 
 import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
 
 class NfcoreTemplate {
 
@@ -245,6 +246,21 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Dump pipeline parameters in a json file
+    //
+    public static void dump_parameters(workflow, params) {
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+
+        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+        def output_pf  = new File(output_d, "params_${timestamp}.json")
+        def jsonStr    = JsonOutput.toJson(params)
+        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+    }
+
     //
     // Print pipeline summary on completion
     //

lib/WorkflowRnaseq.groovy

@@ -276,7 +276,7 @@ class WorkflowRnaseq {
     // Generate methods description for MultiQC
     //
     public static String toolCitationText(params) {
-        // TODO Optionally add in-text citation tools to this list.
+        // TODO nf-core: Optionally add in-text citation tools to this list.
         // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
         // Uncomment function in methodsDescriptionText to render in MultiQC report
         def citation_text = [