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Dev#84

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daichengxin merged 30 commits into
daichengxin:devfrom
bigbio:dev
Jan 20, 2026
Merged

Dev#84
daichengxin merged 30 commits into
daichengxin:devfrom
bigbio:dev

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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).

ypriverol and others added 30 commits January 9, 2026 13:33
Release 1.7.0 - Major changes with quantms-rescoring
Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
…tion

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
Bump version to new release cycle. Add SDRF agent skill
…tandard

Enable ext.args support in GENERATE_CFG module
…nput

Deprecate OpenMS experimental design format, enforce SDRF-only input
@daichengxin daichengxin merged commit 94f5359 into daichengxin:dev Jan 20, 2026
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4 participants