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Fix saving of samtools output #178

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erikrikarddaniel merged 8 commits into from
Dec 9, 2025
Merged

Fix saving of samtools output #178

erikrikarddaniel merged 8 commits into from
Dec 9, 2025

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@erikrikarddaniel erikrikarddaniel commented Dec 5, 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/magmap 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).

danilodileo
danilodileo approved these changes Dec 5, 2025
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LGTM

@erikrikarddaniel erikrikarddaniel merged commit e045d60 into nf-core:dev Dec 9, 2025
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@erikrikarddaniel erikrikarddaniel deleted the fix-samtools branch December 9, 2025 06:02
@erikrikarddaniel erikrikarddaniel mentioned this pull request Dec 10, 2025
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@danilodileo danilodileo danilodileo approved these changes

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@erikrikarddaniel @danilodileo