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output files in library subdir where possible#143

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matthdsm merged 12 commits intodevfrom
feature/output_per_library
Dec 4, 2025
Merged

output files in library subdir where possible#143
matthdsm merged 12 commits intodevfrom
feature/output_per_library

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@matthdsm matthdsm commented Dec 4, 2025 •
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fixes #125

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
  • Make sure your code lints (nf-core pipelines 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).

@matthdsm matthdsm requested a review from nvnieuwk December 4, 2025 08:08
nvnieuwk
nvnieuwk approved these changes Dec 4, 2025
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Looks good!

nvnieuwk
nvnieuwk reviewed Dec 4, 2025
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workflows/preprocessing.nf
Comment on lines 475 to 477
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@nvnieuwk nvnieuwk Dec 4, 2025

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These lines should be removed

@matthdsm matthdsm linked an issue Dec 4, 2025 that may be closed by this pull request
output data per library where possible #125
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matthdsm commented Dec 4, 2025

Thanks for the help @nvnieuwk !

@matthdsm matthdsm merged commit 61e6778 into dev Dec 4, 2025
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@matthdsm matthdsm deleted the feature/output_per_library branch December 4, 2025 19:58
@matthdsm matthdsm mentioned this pull request Dec 4, 2025
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output data per library where possible

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@matthdsm @nvnieuwk