docs: Add output labels use cases and details (nextflow-io#6986)

Co-authored-by: Ben Sherman <bentshermann@gmail.com>

Author: christopher-hakkaart

docs/module.md

@@ -277,7 +277,7 @@ Those scripts will be made accessible like any other command in the task environ
 This feature requires the use of a local or shared file system for the pipeline work directory, or {ref}`wave-page` when using cloud-based executors.
 :::
 
-:::{info}
+:::{note}
 When {ref}`wave-page` is enabled, the contents of the module `resources/` directory are automatically included in the provisioned container. Wave treats the `resources/` directory as the container root. For example, `resources/some/data/file.txt` becomes `/some/data/file.txt` in the container.
 :::
 

docs/tutorials/data-lineage.md

@@ -139,6 +139,10 @@ Every output file is represented in the lineage store as a `FileOutput` record.
 
 As this record is a workflow output, it is not linked directly to a task run. Instead, it is linked to the original task output.
 
+:::{note}
+The `labels` field is `null` because no labels were assigned to this file. Labels are set using the `label` directive in the `output` block. See {ref}`workflow-output-labels` for more information.
+:::
+
 Any LID in a lineage record can be viewed, allowing you to traverse the lineage metadata interactively. Use the value of `source` to view the original task output:
 
 ```console
@@ -303,10 +307,10 @@ Note the difference between the task scripts, highlighting the change that cause
 
 Workflow outputs declared in the `output` block are also recorded in the lineage store. The output of a workflow run is accessible as `lid://<WORKFLOW_RUN_HASH>#output`.
 
-For example, run the `rnaseq-nf` pipeline using the `preview-25-04` branch, which uses the `output` block to publish outputs:
+For example, run the `rnaseq-nf` pipeline with the `preview-25-04` branch, which uses the `output` block to publish outputs:
 
 ```console
-$ nextflow -r preview-25-04 -profile conda
+$ nextflow run rnaseq-nf -r preview-25-04 -profile conda
 ```
 
 View the workflow output in the lineage metadata:
@@ -337,7 +341,20 @@ The following types are used in workflow output lineage records:
 | `Map`        | object                      | `Map`, `Record` |
 | `Path`       | string with `lid://` prefix | `Path` |
 
-See {ref}`workflow-output-def` for more information about the `output` block.
+When labels are assigned to a workflow output with the `label` directive, they appear in the `labels` field of each corresponding `FileOutput` record:
+
+```console
+$ nextflow lineage view lid://9410d13abeec617640b5fe9735ba12fc/multiqc_report.html
+{
+  "version": "lineage/v1beta1",
+  "type": "FileOutput",
+  "path": "/results/multiqc_report.html",
+  ...
+  "labels": ["qc", "summary"]
+}
+```
+
+Labels can be used to filter files when querying lineage records with the `nextflow lineage find` command. See {ref}`workflow-output-labels` for details on assigning labels to workflow outputs.
 
 ## Use lineage in a Nextflow script
 

docs/wave.md

@@ -62,7 +62,7 @@ wave.strategy = ['dockerfile','container']
 
 This setting instructs Wave to prioritize the module Dockerfile over process `container` directives.
 
-:::{info}
+:::{note}
 When building containers, Wave does not support `ADD`, `COPY`, or any other Dockerfile commands that access files in the host file system. To include custom scripts or files, use the module `resources/` directory instead. Wave automatically includes its contents in the container build context. See {ref}`module-binaries` for more details.
 :::
 

docs/workflow.md

@@ -337,6 +337,23 @@ Files that do not originate from the work directory are not published, but are i
 
 See [Output directives](#output-directives) for the list of available index directives.
 
+(workflow-output-labels)=
+
+### Labels
+
+You can apply labels to each workflow output using the `label` directive:
+
+```nextflow
+output {
+    multiqc_report {
+        label 'qc'
+        label 'summary'
+    }
+}
+```
+
+Labels can be used to find and filter output files across workflow runs with data lineage. They are stored in the `labels` field of each `FileOutput` record published by the workflow output in the lineage store. See {ref}`data-lineage-page` for details on how to query output files by label.
+
 ### Output directives
 
 The following directives are available for each output in the output block:

docs/your-first-script.md

@@ -12,7 +12,7 @@ This guide details fundamental skills to run a basic Nextflow pipeline. It inclu
 
 You will need the following to get started:
 
-- Nextflow version 25.10 or later. See {ref}`install-page` for installation instructions. If you have an older version, see {ref}`updating-nextflow` to update.
+- Nextflow version 25.10 or later. See {ref}`install-page` for installation instructions. If you have an older version, see {ref}`updating-nextflow-page` to update.
 
 ## Run a pipeline