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ASCAT GC and RT correct#116

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AmberVerhasselt merged 9 commits intoIntGenomicsLab:devfrom
AmberVerhasselt:dev
Dec 23, 2025
Merged

ASCAT GC and RT correct#116
AmberVerhasselt merged 9 commits intoIntGenomicsLab:devfrom
AmberVerhasselt:dev

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@AmberVerhasselt
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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
  • 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).

@robert-a-forsyth robert-a-forsyth self-assigned this Dec 19, 2025
@robert-a-forsyth
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Can you add the updated default values for GC/RT in docs/usage.md?

@robert-a-forsyth robert-a-forsyth self-requested a review December 19, 2025 11:45
@AmberVerhasselt
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The default for both is null and the default values are overwritten by --genome

@AmberVerhasselt AmberVerhasselt merged commit 9eda20b into IntGenomicsLab:dev Dec 23, 2025
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2 participants