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fix: read Rfam GA cutoff from CM section so non-rRNA hits aren't dropped#7

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Rfam:bugfix/ga-score-thresholds
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fix: read Rfam GA cutoff from CM section so non-rRNA hits aren't dropped#7
pmb59 wants to merge 1 commit into
nf-core:devfrom
Rfam:bugfix/ga-score-thresholds

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@pmb59

@pmb59 pmb59 commented Jun 9, 2026

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bin/parse_rfam_results.pyextract_rfam_metrics now tracks whether it's inside the INFERNAL covariance‑model section vs. the HMMER3 filter section, and only reads metrics from the CM section. Previously the GA‑less filter section overwrote each model's real GA cutoff, so downstream filtering dropped every non‑rRNA hit.

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!
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@pmb59 pmb59 marked this pull request as draft June 9, 2026 23:18
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