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Update samtools to 1.19.2 in local module CHECK_IF_PAIRED_END #93

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Merged
merged 5 commits into from
May 15, 2024
Merged

Update samtools to 1.19.2 in local module CHECK_IF_PAIRED_END #93

merged 5 commits into from
May 15, 2024

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@asp8200 asp8200 commented May 14, 2024 •
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Issue #92

Updating samtools to 1.19.2 in local module CHECK_IF_PAIRED_END.

I the following commands successfully :

nextflow run main.nf -profile test,conda --outdir results
nextflow run main.nf -profile test,singularity --outdir results
nextflow run main.nf -profile test,docker --outdir results

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/bamtofastq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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 May 14, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e62fab4

+| ✅ 194 tests passed       |+
!| ❗   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 passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-14 19:11:24

@asp8200 asp8200 marked this pull request as ready for review May 14, 2024 19:06
@maxulysse maxulysse merged commit 34c06a7 into nf-core:dev May 15, 2024
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@maxulysse maxulysse maxulysse approved these changes

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@asp8200 @maxulysse