Update docs to version 22.12.0-edge

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

assets/docs/edge/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: d8a475bdae6146a78a7e69d8a4a55a7b
+config: 44c7db84bcca4445fa0fd1670e4e5d03
 tags: 645f666f9bcd5a90fca523b33c5a78b7

assets/docs/edge/_sources/aws.rst.txt

@@ -152,6 +152,12 @@ AWS CLI
 Nextflow requires to access the `AWS command line tool <https://aws.amazon.com/cli/>`_ (``aws``) from the container in
 which the job runs in order to stage the required input files and to copy back the resulting output files in the S3 storage.
 
+.. tip::
+  When using :ref:`wave-page` and :ref:`fusion-page` there is no need to configure the AWS command line tool in
+  the task containers or the host Ec2 instances for the deployment of Nextflow pipeline with AWS Batch.
+  You can ignore this requirement when using the Fusion file system feature. See the :ref:`fusion-page` documentation
+  for further details.
+
 The ``aws`` tool can be made available in the container in two ways:
 
 1. installed in the Docker image(s) used during the pipeline execution,
@@ -299,6 +305,12 @@ AWS CLI installation
 .. warning:: The `AWS CLI tool <https://aws.amazon.com/cli>`_ must to be installed in your custom AMI
   by using a self-contained package manager such as `Conda <https://conda.io>`_.
 
+.. tip::
+  When using :ref:`wave-page` and :ref:`fusion-page` there is no need to configure the AWS command line tool in
+  the task containers or the host Ec2 instances for the deployment of Nextflow pipeline with AWS Batch.
+  You can ignore this requirement when using the Fusion file system feature. See the :ref:`fusion-page` documentation
+  for further details.
+
 The reason is that when the AWS CLI tool executes using Conda it will use the version of python supplied by Conda.
 If you don't use Conda and install the AWS CLI using something like `pip <https://pypi.org/project/pip/>`_ the ``aws``
 command will attempt to run using the version of python found in the running container which won't be able to find
@@ -335,8 +347,9 @@ Replace the path above with the one matching the location where ``aws`` tool is
 .. note:: Using a version of Nextflow prior 19.07.x the config setting `executor.awscli` should be used
   instead of `aws.batch.cliPath`.
 
+
 Docker installation
----------------------------------------
+-------------------
 Docker is required by Nextflow to execute tasks on AWS Batch. `Amazon ECS-Optimized Amazon Linux 2 AMI` has Docker installed,
 however if you create your AMI starting from a different AMI that does not have Docker installed, you need to do it manually.
 
@@ -392,7 +405,7 @@ of a specific job e.g. to define custom mount paths or other Batch Job special s
 
 To do that first create a *Job Definition* in the AWS Console (or with 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 specifing, in place of the container image name, the Job definition name prefixed by the
+directive and specifying, in place of the container image name, the Job definition name prefixed by the
 ``job-definition://`` string, as shown below::
 
   process.container = 'job-definition://your-job-definition-name'
@@ -411,13 +424,13 @@ The pipeline execution must specifies a AWS Storage bucket where jobs intermedia
 
 .. warning::
   The bucket path should include at least a top level directory name e.g. use ``s3://my-bucket/work``
-  not just ``s3://my-bucket``. 
+  not just ``s3://my-bucket``.
 
 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 execute in the local computer or local computing cluster and
+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 service.
 
 To enable this feature use one or more :ref:`config-process-selectors` in your Nextflow configuration file to apply

assets/docs/edge/_sources/azure.rst.txt

@@ -308,13 +308,13 @@ Together, these settings determine the Operating System and version installed on
 By default, Nextflow creates CentOS 8-based pool nodes, but this behavior can be customised in the pool configuration.
 Below the configurations for image reference/SKU combinations to select two popular systems.
 
-* Ubuntu 20.04::
+* Ubuntu 20.04 (default)::
 
 	azure.batch.pools.<name>.sku = "batch.node.ubuntu 20.04"
 	azure.batch.pools.<name>.offer = "ubuntu-server-container"
 	azure.batch.pools.<name>.publisher = "microsoft-azure-batch"
 
-* CentOS 8 (default)::
+* CentOS 8::
 
 	azure.batch.pools.<name>.sku = "batch.node.centos 8"
 	azure.batch.pools.<name>.offer = "centos-container"
@@ -345,6 +345,42 @@ Public images from other registries are still pulled (if requested by a Task) wh
   specified via the :ref:`container <process-container>` directive using the format: ``[server]/[your-organization]/[your-image]:[tag]``.
   Read more about image fully qualified image names in the `Docker documentation <https://docs.docker.com/engine/reference/commandline/pull/#pull-from-a-different-registry>`_.
 
+Active Directory Authentication
+===============================
+
+As of version ``22.11.0-edge``, `Service Principal <https://learn.microsoft.com/en-us/azure/active-directory/develop/howto-create-service-principal-portal>`_ credentials can optionally be used instead of Shared Keys for Azure Batch and Storage accounts. 
+
+The Service Principal should have the at least the following role assignments :
+
+1. Contributor
+
+2. Storage Blob Data Reader
+
+3. Storage Blob Data Contributor
+
+.. note::
+  To assign the necessary roles to the Service Principal refer to the `official Azure documentation <https://learn.microsoft.com/en-us/azure/role-based-access-control/role-assignments-portal?tabs=current>`_.
+
+The credentials for Service Principal can be specified as follows::
+
+    azure {
+        activeDirectory {
+            servicePrincipalId = '<YOUR SERVICE PRINCIPAL CLIENT ID>'
+            servicePrincipalSecret = '<YOUR SERVICE PRINCIPAL CLIENT SECRET>'
+            tenantId = '<YOUR TENANT ID>'
+          }
+
+        storage {
+            accountName = '<YOUR STORAGE ACCOUNT NAME>'
+          }
+
+        batch {
+            accountName = '<YOUR BATCH ACCOUNT NAME>'
+            location = '<YOUR BATCH ACCOUNT LOCATION>'
+          }
+    }
+
+
 Advanced settings
 ==================
 
@@ -353,10 +389,13 @@ The following configuration options are available:
 ============================================== =================
 Name                                           Description
 ============================================== =================
+azure.activeDirectory.servicePrincipalId        The service principal client ID
+azure.activeDirectory.servicePrincipalSecret    The service principal client secret
+azure.activeDirectory.tenantId                  The Azure tenant ID
 azure.storage.accountName                       The blob storage account name
 azure.storage.accountKey                        The blob storage account key
 azure.storage.sasToken                          The blob storage shared access signature token. This can be provided as an alternative to the ``accountKey`` setting.
-azure.storage.tokenDuration                     The duration of the shared access signature token created by Nextflow when the ``sasToken`` option is *not* specified (default: ``12h``).
+azure.storage.tokenDuration                     The duration of the shared access signature token created by Nextflow when the ``sasToken`` option is *not* specified (default: ``48h``).
 azure.batch.accountName                         The batch service account name.
 azure.batch.accountKey                          The batch service account key.
 azure.batch.endpoint                            The batch service endpoint e.g. ``https://nfbatch1.westeurope.batch.azure.com``.

assets/docs/edge/_sources/basic.rst.txt

@@ -96,6 +96,7 @@ The following batch schedulers are supported:
 * `Univa grid engine <http://www.univa.com/>`_
 * `Platform LSF <http://www.ibm.com/systems/technicalcomputing/platformcomputing/products/lsf/>`_
 * `Linux SLURM <https://computing.llnl.gov/linux/slurm/>`_
+* `Flux Framework <https://flux-framework.org/>`_
 * `PBS Works <http://www.pbsworks.com/gridengine/>`_
 * `Torque <http://www.adaptivecomputing.com/products/open-source/torque/>`_
 * `HTCondor <https://research.cs.wisc.edu/htcondor/>`_
@@ -133,15 +134,15 @@ Read the :ref:`script-page` section to learn about the Nextflow scripting langua
 Configuration options
 ---------------------
 
-Pipeline configuration properties are defined in a file named ``nextflow.config`` in the pipeline execution directory. 
+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. 
+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::
 
-	process { 
+	process {
 	  executor='sge'
-	  queue = 'cn-el6' 
+	  queue = 'cn-el6'
 	}
 
 

assets/docs/edge/_sources/channel.rst.txt

@@ -88,19 +88,6 @@ Channels may be created explicitly using the following channel factory methods.
   methods can be specified either as ``channel.of()`` or ``Channel.of()``, and so on.
 
 
-.. _channel-create:
-
-create
-------
-
-.. warning::
-    The ``create`` method is no longer available in DSL2 syntax.
-
-Creates a new channel, as shown below::
-
-    channelObj = Channel.create()
-
-
 .. _channel-empty:
 
 empty
@@ -476,36 +463,6 @@ See also: `fromPath`_ factory method.
 Channel methods
 ===============
 
-.. _channel-bind1:
-
-bind
-----
-
-.. warning::
-    The ``bind`` method is no longer available in DSL2 syntax.
-
-Channel objects provide a `bind( )` method which is the basic operation to send a message over the channel.
-For example::
-
-    myChannel = Channel.create()
-    myChannel.bind( 'Hello world' )
-
-
-.. _channel-bind2:
-
-operator <<
------------
-
-.. warning::
-    The ``<<`` operator is no longer available in DSL2 syntax.
-
-The operator ``<<`` is just a syntax sugar for the ``bind`` method. Thus, the following example produces
-an identical result as the previous one::
-
-    myChannel = Channel.create()
-    myChannel << 'Hello world'
-
-
 .. _channel-subscribe:
 
 subscribe