Bump docs 22.10.2

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

Author: pditommaso

assets/docs/latest/.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: fdbdef3fba1ce98e7aa920e375e9caf6
+config: 15e369f31649ef6891b0e6925783b56f
 tags: 645f666f9bcd5a90fca523b33c5a78b7

assets/docs/latest/_sources/config.rst.txt

@@ -244,15 +244,16 @@ useMicromamba       uses the ``micromamba`` binary instead of ``conda`` to creat
 Scope `dag`
 -------------
 
-The ``dag`` scope allows you to control the layout of the execution graph file generated by Nextflow.
+The ``dag`` scope allows you to control the layout of the execution graph diagram generated by Nextflow.
 
 The following settings are available:
 
 ================== ================
 Name                Description
 ================== ================
-enabled             When ``true`` turns on the generation of the execution graph report file (default: ``false``).
-file                Graph file name (default: ``dag.dot``).
+enabled             When ``true`` turns on the generation of the DAG file (default: ``false``).
+file                Graph file name (default: ``dag-<timestamp>.dot``).
+overwrite           When ``true`` overwrites any existing DAG file with the same name.
 ================== ================
 
 The above options can be used by prefixing them with the ``dag`` scope or surrounding them by curly
@@ -730,8 +731,8 @@ The ``report`` scope allows you to define configuration setting of the workflow
 Name                Description
 ================== ================
 enabled             If ``true`` it create the workflow execution report.
-file                The path of the created execution report file (default: ``report.html``).
-overwrite           When ``true`` overwrites existing report file instead of rolling it.
+file                The path of the created execution report file (default: ``report-<timestamp>.html``).
+overwrite           When ``true`` overwrites any existing report file with the same name.
 ================== ================
 
 
@@ -793,8 +794,8 @@ The following settings are available:
 Name                Description
 ================== ================
 enabled             When ``true`` turns on the generation of the timeline report file (default: ``false``).
-file                Timeline file name (default: ``timeline.html``).
-overwrite           When ``true`` overwrites an existing timeline file instead of rolling it.
+file                Timeline file name (default: ``timeline-<timestamp>.html``).
+overwrite           When ``true`` overwrites any existing timeline file with the same name.
 ================== ================
 
 
@@ -846,10 +847,10 @@ Name                Description
 ================== ================
 enabled             When ``true`` turns on the generation of the execution trace report file (default: ``false``).
 fields              Comma separated list of fields to be included in the report. The available fields are listed at :ref:`this page <trace-fields>`
-file                Trace file name (default: ``trace.txt``).
+file                Trace file name (default: ``trace-<timestamp>.txt``).
 sep                 Character used to separate values in each row (default: ``\t``).
 raw                 When ``true`` turns on raw number report generation i.e. date and time are reported as milliseconds and memory as number of bytes
-overwrite           When ``true`` overwrites an existing trace file instead of rolling it.
+overwrite           When ``true`` overwrites any existing trace file with the same name.
 ================== ================
 
 The above options can be used by prefixing them with the ``trace`` scope or surrounding them by curly

assets/docs/latest/_sources/process.rst.txt

@@ -632,6 +632,9 @@ with the current execution context.
   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.
 
+  An example of when you may have to deal with that is when you have many input files in a task,
+  and some of these files may have the same filename. In this case, a solution would be to use
+  the option ``stageAs``.
 
 Input type ``env``
 ------------------
@@ -1092,6 +1095,11 @@ on the actual value of the ``species`` input.
   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.
 
+  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.
 
@@ -1974,7 +1982,7 @@ saveAs          A closure which, given the name of the file being published, ret
 enabled         Enable or disable the publish rule depending on the boolean value specified (default: ``true``).
 failOnError     When ``true`` abort the execution if some file can't be published to the specified target directory or bucket for any cause (default: ``false``)
 contentType     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 the boolean value ``true`` is specified the content type is inferred from the file extension (EXPERIMENTAL. Currently only supported by files stored on AWS S3. Default: ``false``, requires `22.10.0`` or later).
-tags            Allow the association of arbitrary tags with the published file e.g. ``tag: [FOO: 'Hello world']`` (EXPERIMENTAL. Currently only supported by files stored on AWS S3. Requires version ``21.12.0-edge`` or later).
+tags            Allow the association of arbitrary tags with the published file e.g. ``tags: [FOO: 'Hello world']`` (EXPERIMENTAL. Currently only supported by files stored on AWS S3. Requires version ``21.12.0-edge`` or later).
 =============== =================
 
 Table of publish modes:

assets/docs/latest/_sources/script.rst.txt

@@ -251,11 +251,11 @@ The following variables are implicitly defined in the ``task`` object of each pr
 Name            Description
 =============== ========================
 ``attempt``     The current task attempt
-``hash``        The task unique hash Id
+``hash``        The task unique hash Id. NOTE: This is only available for processes that run native code via ``exec:``.
 ``index``       The task index (corresponds to ``task_id`` in the execution trace)
-``name``        The current task name
+``name``        The current task name. NOTE: This is only available for processes that run native code via ``exec:``.
 ``process``     The current process name
-``workDir``     The task unique directory. NOTE: This is only available for processes that run native code via the ``exec:`` statement.
+``workDir``     The task unique directory. NOTE: This is only available for processes that run native code via ``exec:``.
 =============== ========================
 
 The ``task`` object also contains the values of all process directives for the given task,

assets/docs/latest/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '22.10.1',
+    VERSION: '22.10.2',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

assets/docs/latest/amazons3.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Amazon S3 storage &mdash; Nextflow 22.10.1 documentation</title>
+  <title>Amazon S3 storage &mdash; Nextflow 22.10.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/theme.css" type="text/css" />

assets/docs/latest/aws.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Amazon Cloud &mdash; Nextflow 22.10.1 documentation</title>
+  <title>Amazon Cloud &mdash; Nextflow 22.10.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/theme.css" type="text/css" />

assets/docs/latest/azure.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Azure Cloud &mdash; Nextflow 22.10.1 documentation</title>
+  <title>Azure Cloud &mdash; Nextflow 22.10.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/theme.css" type="text/css" />

assets/docs/latest/basic.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Basic concepts &mdash; Nextflow 22.10.1 documentation</title>
+  <title>Basic concepts &mdash; Nextflow 22.10.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/theme.css" type="text/css" />

assets/docs/latest/channel.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Channels &mdash; Nextflow 22.10.1 documentation</title>
+  <title>Channels &mdash; Nextflow 22.10.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/theme.css" type="text/css" />