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fix: busco exit and publish dir#1002

Merged
dialvarezs merged 3 commits intonf-core:devfrom
dialvarezs:update-busco
Mar 24, 2026
Merged

fix: busco exit and publish dir#1002
dialvarezs merged 3 commits intonf-core:devfrom
dialvarezs:update-busco

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This PR should fix two issues:

  1. Previously, when a bin fails to classify in a BUSCO run, the module was existing with code 1, even with other bins sucessfully classified.
  2. Include domain and refinement to prevent name clashing on publish when using Das Tool and/or Tiara (this is the same combination CheckM and CheckM2 are using right now).

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/mag 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).

@dialvarezs dialvarezs merged commit efaf6f9 into nf-core:dev Mar 24, 2026
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@dialvarezs dialvarezs mentioned this pull request Mar 28, 2026
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2 participants