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update all modules + fix schema_input #1695

Merged
merged 11 commits into from
Oct 28, 2024
Merged

update all modules + fix schema_input #1695

merged 11 commits into from
Oct 28, 2024

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maxulysse
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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).

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github-actions bot commented Oct 25, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6079fcf

+| ✅ 214 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 2024-10-27 21:10:30

@maxulysse maxulysse changed the title update all modules update all modules + fix schema_input Oct 25, 2024
FloWuenne
FloWuenne approved these changes Oct 28, 2024
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LGTM!

@maxulysse maxulysse merged commit c2bb706 into nf-core:dev Oct 28, 2024
29 checks passed
@maxulysse maxulysse deleted the update_all branch October 28, 2024 07:48
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@LouisLeNezet LouisLeNezet LouisLeNezet left review comments

@fellen31 fellen31 fellen31 left review comments

@FloWuenne FloWuenne FloWuenne approved these changes

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

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5 participants
@maxulysse @FloWuenne @FriederikeHanssen @fellen31 @LouisLeNezet