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Make task.ext assigments closures #96

Merged
merged 2 commits into from
Jun 17, 2024
Merged

Make task.ext assigments closures #96

merged 2 commits into from
Jun 17, 2024

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fbdtemme
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Description

Make all task.ext assigments closures.
When people pass params in seperate config files the results can be very unintuitive and depends on the order of config file evaluation. Delaying the creation of additional commandline options with closures works around this.

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/pixelator 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).

@fbdtemme fbdtemme requested a review from ambarrio June 14, 2024 14:17
@fbdtemme fbdtemme changed the title Fix/make task ext closures Make task.ext assigments closures Jun 14, 2024
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github-actions bot commented Jun 14, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ccb35d0

+| ✅ 202 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   3 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-14 14:18:26

ambarrio
ambarrio approved these changes Jun 14, 2024
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@ambarrio ambarrio left a comment

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LGTM, just a small comment. I guess we set up date when we merge to main.

CHANGELOG.md Show resolved Hide resolved
@fbdtemme fbdtemme merged commit 27c8743 into nf-core:dev Jun 17, 2024
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@fbdtemme fbdtemme mentioned this pull request Jul 15, 2024
Merged
@fbdtemme fbdtemme deleted the fix/make-task-ext-closures branch December 10, 2024 14:15
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@ambarrio ambarrio ambarrio approved these changes

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@fbdtemme @ambarrio