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Don't convert input bam files that are supplied in post-alignment steps, it's not necessary. #1728

Merged
merged 10 commits into from
Nov 12, 2024
Merged

Don't convert input bam files that are supplied in post-alignment steps, it's not necessary. #1728

merged 10 commits into from
Nov 12, 2024

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FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Nov 8, 2024 •
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Thank you to @SPPearce for chatting with me again to finally remove this wasteful step.

Closes #1162

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 Nov 8, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e8639d0

+| ✅ 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 2024-11-12 09:12:27

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review November 9, 2024 14:51
maxulysse
maxulysse reviewed Nov 11, 2024
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tests/.nftignore
variant_calling/**/*.vcf.{gz,gz.tbi}
.DS_Store
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That should not be produce by Nextflow

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it ended up in my nf-test test files repeatedly

maxulysse
maxulysse previously approved these changes Nov 11, 2024
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@maxulysse maxulysse merged commit 79d749e into nf-core:dev Nov 12, 2024
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@maxulysse maxulysse maxulysse approved these changes

@SPPearce SPPearce Awaiting requested review from SPPearce

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@FriederikeHanssen @maxulysse