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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, parameter, or workflow path, update the relevant docs.
  • If plugin declarations changed, update CITATIONS.md, README.md, and agent/context guidance in the same PR.
  • 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>).
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).