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implement rtgtools for somatic small bench #160

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merged 5 commits into from
Mar 4, 2025

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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
  • If necessary, also make a PR on the nf-core/variantbenchmarking 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).

@kubranarci kubranarci merged commit 71c4cda into dev Mar 4, 2025
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@kubranarci kubranarci linked an issue Mar 4, 2025 that may be closed by this pull request
@kubranarci kubranarci deleted the 146-split-output-vcfs-with-rtgtools-vcfeval branch March 4, 2025 15:02
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rtg vcfeval ploidy option for somatic benchmarking
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