Workflow output definition (second preview)

docs/reference/cli.md

@@ -1012,6 +1012,11 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-offline`
 : Do not check for remote project updates.
 
+`-o, -output-dir` (`results`)
+: :::{versionadded} 24.10.0
+  :::
+: Directory where workflow outputs are stored.
+
 `-params-file`
 : Load script parameters from a JSON/YAML file.
 

docs/reference/config.md

@@ -18,6 +18,11 @@ This page lists all of the available settings in the {ref}`Nextflow configuratio
 `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`
+: :::{versionadded} 24.10.0
+  :::
+: Defines the pipeline output directory. Equivalent to the `-output-dir` option of the `run` command.
+
 `resume`
 : If `true`, enable the use of previously cached task executions. Equivalent to the `-resume` option of the `run` command.
 
@@ -1584,3 +1589,90 @@ The following settings are available:
 
 `wave.strategy`
 : The strategy to be used when resolving ambiguous Wave container requirements (default: `'container,dockerfile,conda,spack'`).
+
+(config-workflow)=
+
+## `workflow`
+
+:::{versionadded} 24.10.0
+:::
+
+The `workflow` scope provides workflow execution options.
+
+`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` error strategy.
+
+`workflow.output.contentType`
+: *Currently only supported for S3.*
+: Specify the media type a.k.a. [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_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.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.retryPolicy.delay`
+: Delay when retrying a failed publish operation (default: `350ms`).
+
+`workflow.output.retryPolicy.jitter`
+: Jitter value when retrying a failed publish operation (default: `0.25`).
+
+`workflow.output.retryPolicy.maxAttempt`
+: Max attempts when retrying a failed publish operation (default: `5`).
+
+`workflow.output.retryPolicy.maxDelay`
+: Max delay when retrying a failed publish operation (default: `90s`).
+
+`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
+  tags FOO: 'hello', BAR: 'world'
+  ```

docs/reference/stdlib.md

@@ -128,6 +128,11 @@ The following constants are globally available in a Nextflow script:
   `workflow.manifest`
   : Entries of the workflow manifest.
 
+  `workflow.outputDir`
+  : :::{versionadded} 24.10.0
+    :::
+  : Workflow output directory.
+
   `workflow.preview`
   : :::{versionadded} 24.04.0
     :::