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fix outdir#342

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matthdsm wants to merge 1 commit into
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fix/gcp
Open

fix outdir#342
matthdsm wants to merge 1 commit into
devfrom
fix/gcp

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@matthdsm

@matthdsm matthdsm commented Jun 16, 2026

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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).

@matthdsm matthdsm requested a review from nvnieuwk June 16, 2026 12:45
@matthdsm matthdsm changed the base branch from main to dev June 16, 2026 12:45
nvnieuwk
nvnieuwk reviewed Jun 16, 2026
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@nvnieuwk nvnieuwk left a comment

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Can you make sure that params.outdir isn't used anywhere where a path is expected?

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@nvnieuwk nvnieuwk nvnieuwk left review comments

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@matthdsm @nvnieuwk