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Fixed kmerfinder subworkflow to use winner assembly for reference matching - #324

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victor5lm merged 2 commits into
nf-core:devfrom
victor5lm:update_kmerfinder_subworkflow
Aug 31, 2026
Merged

Fixed kmerfinder subworkflow to use winner assembly for reference matching#324
victor5lm merged 2 commits into
nf-core:devfrom
victor5lm:update_kmerfinder_subworkflow

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@victor5lm

@victor5lm victor5lm commented Aug 27, 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
  • If necessary, also make a PR on the nf-core/bacass 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).

PR checklist

Closes #323.

@victor5lm victor5lm added this to the Release 2.7.0 milestone Aug 27, 2026
@victor5lm victor5lm self-assigned this Aug 27, 2026
@victor5lm victor5lm linked an issue Aug 27, 2026 that may be closed by this pull request
Assemblies are not consistently associated with the selected winner reference by KmerFinder #323
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@victor5lm
victor5lm marked this pull request as ready for review August 28, 2026 06:07
@Daniel-VM
Daniel-VM self-requested a review August 31, 2026 06:50
Daniel-VM
Daniel-VM approved these changes Aug 31, 2026
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LGTM!

@victor5lm
victor5lm merged commit 1bb1007 into nf-core:dev Aug 31, 2026
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@Daniel-VM Daniel-VM Daniel-VM approved these changes

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Assemblies are not consistently associated with the selected winner reference by KmerFinder

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@victor5lm @Daniel-VM