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remove consensusid and move to parquet#708

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daichengxin wants to merge 12 commits into
bigbio:devfrom
daichengxin:dev
Open

remove consensusid and move to parquet#708
daichengxin wants to merge 12 commits into
bigbio:devfrom
daichengxin:dev

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@daichengxin

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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 bigbio/quantms 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).

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coderabbitai Bot commented Jun 6, 2026

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codacy-production Bot commented Jun 6, 2026

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Up to standards ✅

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Discussion: replace ConsensusID with a more robust multi-engine rescoring path Implement qpx as output for both TMT and LFQ

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