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

run:
pip install pre-commit
pre-commit install
pre-commit run --all-files

🚧 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