Workflow output definition (#4784)

Signed-off-by: Ben Sherman <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]> Co-authored-by: Paolo Di Tommaso <[email protected]>
nextflow-io · May 17, 2024 · cf0546b · cf0546b
1 parent 935bb1e
commit cf0546b
Show file tree

Hide file tree

Showing 31 changed files with 1,919 additions and 839 deletions.
diff --git a/docs/channel.md b/docs/channel.md
@@ -398,7 +398,7 @@ 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`, {ref}`operator-timeout`, 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 {ref}`operator-take` or {ref}`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:
 

diff --git a/docs/cli.md b/docs/cli.md
@@ -1109,6 +1109,8 @@ Checking nextflow-io/hello ...
 checkout-out at AnyObjectId[1c3e9e7404127514d69369cd87f8036830f5cf64] - revision: 1c3e9e7404 [v1.1]
 ```
 
+(cli-run)=
+
 ### run
 
 Execute a pipeline.

diff --git a/docs/config.md b/docs/config.md
@@ -2101,6 +2101,15 @@ Some features can be enabled using the `nextflow.enable` and `nextflow.preview`
 
   - 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
+  :::
+
+: *Experimental: may change in a future release.*
+
+: When `true`, enables the use of the {ref}`workflow output definition <workflow-output-def>`.
+
 `nextflow.preview.recursion`
 
 : :::{versionadded} 21.11.0-edge

diff --git a/docs/operator.md b/docs/operator.md
@@ -1472,6 +1472,8 @@ An optional {ref}`closure <script-closure>` can be used to transform each item b
 :language: console
 ```
 
+(operator-take)=
+
 ## take
 
 *Returns: queue channel*
@@ -1675,6 +1677,8 @@ The difference between `unique` and `distinct` is that `unique` removes *all* du
 
 See also: [distinct](#distinct)
 
+(operator-until)=
+
 ## until
 
 *Returns: queue channel or value channel, matching the source type*

diff --git a/docs/process.md b/docs/process.md
@@ -1008,7 +1008,7 @@ Some caveats on glob pattern behavior:
 Although the input files matching a glob output declaration are not included in the resulting output channel, 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?][what is a glob?]
+Read more about glob syntax at the following link [What is a glob?][glob]
 
 ### Dynamic output file names
 
@@ -2791,4 +2791,3 @@ process foo {
 ```
 
 [glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
-[what is a glob?]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob