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Bump OpenMS to 3.6.0 - #494
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Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…penMS 3.6.0 Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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…ET:xcorr becomes Comet:xcorr) Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…en CPU types Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…ucible CI peptide set for PBMC009_A Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…XML and spectrum alignment APIs Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…es it Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…shot the CI peptide sets without them Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…, without the .mzML extension and only for Thermo scan numbers Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
6 tasks done
… of the idXML line count Generated by Claude Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…e system order does not change the snapshot Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Ngarciar24
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Looks good, CI green with some nitpicks from claude.
…olator as 3.9.0 Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <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: 4.1.0. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
…line parameter Generated by Claude (Opus 5.5) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Updates all OpenMS and pyOpenMS modules to 3.6.0 (nf-core/modules#13126) and adapts the pipeline to it.
COMET:xcorrno longer exists in OpenMS 3.6.0 (Remove duplicate Comet score metavalues in PepXMLFile parser OpenMS/OpenMS#9089); The quantificationIDScoreSwitchernow usesMS:1002252.summarize_results.pynames every PSI-MS accession column by its CV term, so the result TSV columnCOMET:xcorrbecomesComet:xcorr.openmsthirdparty/percolatoradapterandfeaturelinkerunlabeledkdalso move toopenms-thirdparty3.6.0 (percolator 3.9).IDMassAccuracystays on 3.4.1 (removed in OpenMS 3.5.0).get_ion_annotations.pyadapts to the new API (strinstead ofbytes,getSpectrumAlignmentreturns the alignment,IdXMLFile().load(path)returns the IDs); OpenMS 3.6.0 renames immonium ions (iHtoiH+) and one precursor ion inmatching_ions.tsv.summarize_results.pydrops the TextExporter phantom-column workaround (fixed in 3.6.0).USIcolumn in the result TSV fromTextExporter -id:add_usi(feat: Add USI support and consolidate ProForma files OpenMS/OpenMS#8684), with datasetlocal; a ProteomeXchange accession can be set via-id:usi_dataset_idin theOPENMS_TEXTEXPORTERext.args.summarize_results.pyremoves the.mzMLextension from the run name. For timsTOF, OpenMS writesscan:<n>from the tdf2mzmlindex=native ID, which is the spectrum position in the converted mzML, not a Bruker frame/scan ID (USI: msRun keeps the .mzML extension, and non-Thermo native IDs become scan numbers OpenMS/OpenMS#10591); kept for now and to be revised. Checked ontest_full: all 10,257 USIs resolve to a spectrum with matching precursor m/z and charge, and sampled USIs resolve at ProteomeCentral with PXD011628.--remove_precursor_peakwas parsed withtype=bool, sofalseenabled it in the ion annotator; it is now a flag.--quantify: they are detected by their PSMs instead of the idXML line count.std::to_chars. This changes the MS²Rescore DeepLC features slightly and the peptide counts by +3 (HepG2_A, 252 to 255) and -57 (PBMC007_B, 2206 to 2149).devreproduces the old counts on the same machine.PBMC007_Bis CPU-dependent: CI (m7i-flex) gives 2149 in repeated runs, a Xeon Gold 6140 gives 2138; the snapshot holds the CI value. With the same input, the 3.6.0 Percolator step gives the same scores and q-values as 3.5.0.test_single_quant:MapAlignerIdentificationnow writes an identity transformation for a single run, so the aligned-residuals MultiQC plot is not produced for single-run groups.Generated by Claude (Opus 5.5)
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nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.