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Workflow outputs (third preview) #5909

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@bentsherman bentsherman commented Mar 20, 2025

This PR implements the third preview of the workflow output definition for Nextflow 25.04.

Changes are described in the docs, copied here for convenience:

  • The publish: section can only be specified in the entry workflow.

  • Workflow outputs in the publish: section are assigned instead of using the >> operator. The output name must be a valid identifier.

  • By default, output files are published to the base output directory, rather than a subdirectory corresponding to the output name.

  • The syntax for dynamic publish paths has changed. Instead of defining a closure that returns a closure with the path directive, the outer closure should use the >> operator to publish individual files.

  • The mapper index directive has been removed. Use a map operator in the workflow body instead.

Changes not described in the docs:

  • The onWorkflowPublish trace event has been modified to include the output name. It is emitted once for each output, rather than once for each channel value, and it is emitted regardless of whether the index file is enabled.

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
@bentsherman bentsherman requested review from a team as code owners March 20, 2025 21:44
@bentsherman bentsherman requested a review from pditommaso March 20, 2025 21:44
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Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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Successfully merging this pull request may close these issues.

In a channel that is directed to a publish target, Files listed inside a Map object are not published.
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