Dev#87
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daichengxin merged 29 commits intodaichengxin:devfrom Apr 10, 2026
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again using command: nf-core pipelines schema build
- let's hope the next nf-core tools schema builder does not complain
bump quantms-rescoring version - fix bug with quantms-rescoring container permissions
🎨 update schema
🔧 update to fetch SDRF and FASTA files from maintained repo
- create diff for local changes to nf-core module video: https://www.youtube.com/watch?v=7pu6Ikhi1eU docs: https://nf-co.re/docs/nf-core-tools/modules/patch
Use nf-core to point to bigbio modules repo: nf-core modules --git-remote https://github.com/bigbio/nf-modules.git update thermorawfileparser nf-core modules --git-remote https://github.com/bigbio/nf-modules.git patch thermorawfileparser
🚧 Understand how to integrate modules (from nf-core or bigbio)
* Initial plan * fix: correct typo inmermory -> inmemory in openms_peak_picker Co-authored-by: enryH <2833836+enryH@users.noreply.github.com> Agent-Logs-Url: https://github.com/bigbio/quantms/sessions/ef73a74e-d614-4f35-b4af-4c6994dd711d --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: enryH <2833836+enryH@users.noreply.github.com> Co-authored-by: Yasset Perez-Riverol <ypriverol@gmail.com>
Add `fdr_conservative` parameter (default true for backward compatibility) that controls whether the FDR estimation uses the conservative formula (D+1)/T or the tighter (D+1)/(T+D). The conservative formula provides an upper bound on the true FDR but can be overly conservative, especially at low FDR thresholds. Keich & Noble (2025, Nature Methods) showed that (D+1)/T is useful for guaranteeing FDR control but inflates q-values by ~20-40% in the borderline range compared to (D+1)/(T+D). In benchmarking against ProteomeDiscoverer, we found that 429 PD-confirmed peptides with Percolator PEP < 0.01 were filtered out because the conservative FDR formula inflated their q-values above the 1% threshold. Setting fdr_conservative=false may recover a portion of these peptides while maintaining valid FDR control. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…aram feat: expose FDR conservative parameter
Add `lfq_seeding_algorithm` parameter (default 'multiplex') to select the feature detection seeding algorithm in ProteomicsLFQ. The 'biosaur2' option uses the Biosaur2 algorithm recently added to OpenMS (PR #8385), which provides hill-based trace linking with built-in mass calibration. No Biosaur2-specific parameters are exposed since ProteomicsLFQ already tunes the defaults internally (mini=500, minlh=3, pasefminlh=2). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
feat: expose Biosaur2 as alternative feature seeding algorithm for LFQ
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).