Dev - #98
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Co-Authored-By: Claude <noreply@anthropic.com>
- add qpx/ to output directory trees - drop verbose opt_ column explanations from docs - set best_per_spectrum_only default to true Co-Authored-By: Claude <noreply@anthropic.com>
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).