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Oncomplete fix #1460

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Oncomplete fix #1460

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robsyme
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@robsyme robsyme commented Nov 29, 2024 •
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Note: This PR is not intended to be merged, it just serves as an executable example of the upstream changes in nf-core/tools and nf-core/modules.

The onComplete handler currently calls the toList() operator on a queue channel, but by the time the onComplete handler is called, the channels have all been emptied, and this operator will hang forever.

This fix moves the transformation of the queue channel into a value channel (which is safe to use inside the onComplete block) and also cleans up the attachMultiqcReport function.

The actual PRs that need to be merged are:

@robsyme robsyme changed the base branch from master to dev November 29, 2024 22:17
@nf-core nf-core deleted a comment from github-actions bot Nov 29, 2024
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github-actions bot commented Nov 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4773e58

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-29 22:17:52

@robsyme robsyme self-assigned this Nov 30, 2024
@robsyme robsyme marked this pull request as draft November 30, 2024 20:01
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We need to fix the subworkflow in nf-core/modules first

@robsyme robsyme mentioned this pull request Dec 5, 2024
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@robsyme robsyme closed this Dec 5, 2024
@robsyme robsyme deleted the oncomplete-fix branch December 5, 2024 23:59
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