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feat!(PCGR): move sample params to samplesheet#96

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feat!(PCGR): move sample params to samplesheet#96
HomoPolyethylen wants to merge 5 commits into
nf-core:devfrom
HomoPolyethylen:feat/87_move-sample-params-to-samplesheet

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@HomoPolyethylen

@HomoPolyethylen HomoPolyethylen commented Jun 3, 2026

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this PR moves sample-specific parameters for PCGR to the samplesheet.
Params moved:

  • tumor_site
  • tumor_purity
  • tumor_ploidy

This is a breaking, backwards-incompatible change, as the moved params are no longer supported as pipeline parameters (via CLI or params file).

closes #87


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/variantprioritization branch on the nf-core/test-datasets repository.
  • 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).

@HomoPolyethylen HomoPolyethylen changed the title Feat!(PCGR): move sample params to samplesheet feat!(PCGR): move sample params to samplesheet Jun 3, 2026
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Considering moving the sample-specific parameters to samplesheet

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