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Fix bug and bump pmultiqc version - #714

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ypriverol merged 5 commits into
bigbio:devfrom
yueqixuan:dev
Jul 28, 2026
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Fix bug and bump pmultiqc version#714
ypriverol merged 5 commits into
bigbio:devfrom
yueqixuan:dev

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@yueqixuan

@yueqixuan yueqixuan commented Jul 16, 2026 •
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Need to release pmultiqc (0.0.46) first.

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.
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  • 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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@yueqixuan
yueqixuan marked this pull request as draft July 16, 2026 05:06
@yueqixuan
yueqixuan marked this pull request as ready for review July 18, 2026 13:41
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@yueqixuan yueqixuan closed this Jul 18, 2026
@yueqixuan yueqixuan reopened this Jul 18, 2026
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@yueqixuan
yueqixuan marked this pull request as draft July 18, 2026 15:59
@ypriverol ypriverol mentioned this pull request Jul 27, 2026
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ypriverol added a commit that referenced this pull request Jul 27, 2026
@ypriverol
Merge pull request #719 from bigbio/feat/pmultiqc-0.0.46-rescoring-0.…
8da57e9 
…0.22

chore: pmultiqc 0.0.46 and quantms-rescoring 0.0.22 (incorporates #714)
ypriverol added a commit to yueqixuan/quantms that referenced this pull request Jul 27, 2026
@ypriverol
chore: pmultiqc 0.0.46 and quantms-rescoring 0.0.22
69b2ba7 
pmultiqc 0.0.45 -> 0.0.46
  bigbio#714 bumped to 0.0.45, which fails every test_dda_id_* profile:

    ValueError: No pmultiqc plugin selected; skipping.
    AttributeError: module 'rich' has no attribute 'panel'

  Those profiles do not export an mzTab, so `--quantms-plugin` is never added
  and 0.0.45 raises instead of degrading. pmultiqc 0.0.46 is exactly the fix:
  "Allow successful execution without mzTab file" (bigbio/pmultiqc#688),
  "gracefully handle plugin execution errors" (bigbio#689) and "Support pmultiqc
  without mzTab" (bigbio#690).

quantms-rescoring 0.0.21 -> 0.0.22 (8 references: 4 docker, 4 singularity)
  0.0.21 is broken for multi-engine runs. On a comet+msgf merge it collapsed
  the Percolator feature table to four raw scores with a single global
  imputation constant; ~80% of PSMs in such a run are single-engine and those
  are ~45% decoy, so protein-level FDR never cleared 1% and EPIFANY returned
  "No proteins left after FDR filtering" (exit 8).

  0.0.22 feeds Percolator the union of every engine's features with
  orientation-aware per-feature imputation and engine-source indicators.
  Validated on MSV000085836 (552 TMT fractions): ISOBARIC_WORKFLOW merged
  41,391 proteins where 0.0.21 produced zero, and the full run yields +4.4%
  peptides / +0.6% protein groups at 1% FDR vs the comet-only reference. It
  also generalises to SAGE (comet+sage, msgf+sage, comet+msgf+sage), with the
  Sage feature set verified against a real SageAdapter idparquet.

  Single-engine runs are unchanged: the consensus path only activates for
  multi-engine merges, and the default remains search_engines=comet.

CAVEAT: multi-engine consensus feeds Percolator explicit engine-source
indicators, and engine source correlates strongly with decoy status. There is
no stratified or entrapment calibration evidence yet that protein-level FDR
stays calibrated under that mixture, so multi-engine should stay opt-in and be
validated per dataset. This bump does not change any default.
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ypriverol marked this pull request as ready for review July 28, 2026 08:57
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@ypriverol
ypriverol merged commit 5db1314 into bigbio:dev Jul 28, 2026
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