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Fix SUMMARIZE_RESULTS crash with --quantify#444

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jonasscheid merged 2 commits intonf-core:devfrom
jonasscheid:fix/summarize-result-quant
Apr 9, 2026
Merged

Fix SUMMARIZE_RESULTS crash with --quantify#444
jonasscheid merged 2 commits intonf-core:devfrom
jonasscheid:fix/summarize-result-quant

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@jonasscheid jonasscheid commented Apr 9, 2026

Description

Fixes the SUMMARIZE_RESULTS process crash when running with --quantify. The crash was caused by an OpenMS 3.5.0 TextExporter bug that writes a phantom -1 column in PEPTIDE/UNASSIGNEDPEPTIDE data rows when exporting consensusXML, but omits the corresponding column from the header — resulting in a ValueError: 123 columns passed, passed data had 124 columns in parse_multiTSV().

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 nf-core/mhcquant 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).

…xporter column mismatch

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Looks good

@jonasscheid jonasscheid merged commit b046949 into nf-core:dev Apr 9, 2026
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@jonasscheid jonasscheid mentioned this pull request Apr 22, 2026
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@jonasscheid jonasscheid deleted the fix/summarize-result-quant branch April 28, 2026 07:27
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3 participants