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Exclude sample groups from quantification when MapAlignerIdentification doesn't finds shared feature maps - #474

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jonasscheid merged 2 commits into
nf-core:devfrom
jonasscheid:fix/mapaligner-zero-landmarks
Sep 11, 2026
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Exclude sample groups from quantification when MapAlignerIdentification doesn't finds shared feature maps#474
jonasscheid merged 2 commits into
nf-core:devfrom
jonasscheid:fix/mapaligner-zero-landmarks

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@jonasscheid

@jonasscheid jonasscheid commented Sep 8, 2026 •
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MapAlignerIdentification aborts (exit 8, no data points for 'linear' model) when one LC-MS run of a sample+condition shares no FDR-filtered peptide IDs with its replicates within --max_rt_alignment_shift, so no RT anchor pairs exist for the linear fit. Seen in PRIDE reprocessing (RCC replicate with 3 PSMs; PXD037270 QE vs QE2 runs beyond the shift window). The tool has no option to skip such runs.

flowchart TD
    R1[Replicate 1<br/>2063 shared peptides] --> A
    R2[Replicate 2<br/>1872 shared peptides] --> A
    R3[Replicate 3<br/>2038 shared peptides] --> A
    R4[Replicate 4<br/>3 PSMs, 0 shared peptides] --> A
    A[RT alignment, MapAlignerIdentification<br/>no RT anchors for replicate 4, exit 8]
    A -- dev --> X[Pipeline aborts]
    A -- this PR --> S[Sample excluded from LFQ<br/>peptide IDs exported, warning logged]
    style R4 fill:#fde2dc,stroke:#c2410c,color:#7c2d12
    style X fill:#fde2dc,stroke:#c2410c,color:#7c2d12
    style S fill:#d5f0ec,stroke:#0f766e,color:#134e4a
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  • Exit 8 ignored via errorStrategy for OPENMS_MAPALIGNERIDENTIFICATION; MAP_ALIGNMENT detects groups without trafoXMLs (join(remainder: true) + branch), warns once per sample, and the main workflow exports them identification-only like empty-FDR samples
  • Also disables faims:merge_features in FeatureFinderIdentification: OpenMS 3.5.0 drops all peptide IDs from features on FAIMS data (upstream issue to follow)
  • Verified on the failing RCC group, a healthy 3-run group and a FAIMS sample (PXD037270 Liv32)

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!
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nf-test test --profile +docker).
  • Usage/Output documentation updated.
  • CHANGELOG.md is updated.

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github-actions Bot commented Sep 8, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eb4121a

+| ✅ 318 tests passed       |+
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config manifest.version should end in dev: 3.2.0
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • schema_lint - Input mimetype is missing or empty

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-09-10 11:41:31

@jonasscheid
jonasscheid marked this pull request as draft September 8, 2026 12:13
@jonasscheid
jonasscheid force-pushed the fix/mapaligner-zero-landmarks branch 2 times, most recently from 167f807 to 93947bb Compare September 9, 2026 11:41
@jonasscheid jonasscheid changed the title Fall back to identity RT transformation for runs without alignment landmarks Exclude sample groups from quantification when MapAlignerIdentification finds no shared RT landmarks Sep 9, 2026
@github-actions

github-actions Bot commented Sep 9, 2026 •
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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 3/7

See the full run for details.

jonasscheid
jonasscheid commented Sep 9, 2026
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Comment thread docs/output.md
@jonasscheid
Exclude sample groups from quantification instead of crashing when Ma…
091c4ce 
…pAlignerIdentification finds no shared RT landmarks
@jonasscheid
jonasscheid force-pushed the fix/mapaligner-zero-landmarks branch 2 times, most recently from 93947bb to 091c4ce Compare September 9, 2026 12:49
@jonasscheid jonasscheid changed the title Exclude sample groups from quantification when MapAlignerIdentification finds no shared RT landmarks Exclude sample groups from quantification when MapAlignerIdentification doesn't finds shared feature maps Sep 9, 2026
@jonasscheid
jonasscheid marked this pull request as ready for review September 9, 2026 20:27
@jonasscheid
jonasscheid merged commit 9ec6a90 into nf-core:dev Sep 11, 2026
57 of 69 checks passed
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@steffenlem steffenlem steffenlem approved these changes
@marissaDubbelaar marissaDubbelaar Awaiting requested review from marissaDubbelaar marissaDubbelaar is a code owner

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@jonasscheid @steffenlem