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Fix bug where workflow can hang if the email parameter is set. #1745

Merged
merged 2 commits into from
Dec 9, 2024
Merged

Fix bug where workflow can hang if the email parameter is set. #1745

merged 2 commits into from
Dec 9, 2024

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robsyme
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@robsyme robsyme commented Dec 6, 2024

This fix moves all queue channel operations out of the onComplete block and into the main workflow.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@robsyme
Fix bug where workflow can hang if the email parameter is set.
8fc4a7b 
This fix moves all queue channel operations out of the onComplete block and into the main workflow.
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github-actions bot commented Dec 6, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e68b414

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-06 00:08:37

@FriederikeHanssen FriederikeHanssen merged commit 9569c93 into dev Dec 9, 2024
38 checks passed
@FriederikeHanssen FriederikeHanssen deleted the oncomplete-fix branch December 9, 2024 10:24
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@robsyme @FriederikeHanssen