chore: remove ms2features_range modes and IDRipper

[ypriverol]

Summary

• Drop the by_sample and by_project branches of ms2features_range and collapse the three-way switch in psm_rescoring, dda_id, and peptide_database_search to a single per-file Percolator path.
• Delete the IDRipper Nextflow module (no remaining caller). The IDRipper binary stays available inside the OpenMS container — Sage's module still invokes it internally to split multi-file search output.
• Delete the GET_SAMPLE / extract_sample module (only used by the removed by_sample branch).
• Remove ms2features_range from nextflow.config and nextflow_schema.json. ms2features_enable remains as the sole rescoring gate.
• Tidy IDMerger's ms2features_range-keyed prefix logic (module kept for future reuse).

Net: 10 files changed, 7 insertions(+), 296 deletions(-).

Why

by_sample / by_project merge per-file idXMLs into one and run a single Percolator over the merged pool, then IDRipper splits the result back per-run for CONSENSUSID. The pooled-Percolator step has two problems: (a) it is not backed by a project-specific benchmark at 1000+ file scale, and (b) PercolatorAdapter refuses multi-engine input natively, so the whole point of the merge-then-split dance depends on CONSENSUSID — which is itself under discussion for replacement (see follow-up issue).

Dropping these modes now leaves only the independent_run topology (per-file Percolator), which is both the default today and the conservative choice for correctness. Users of the removed modes see a schema error and must adjust their config; this is an intentional hard break rather than a silent behaviour change.

The CONSENSUSID replacement strategy is a bigger design decision with its own trade-offs and is tracked separately. This PR is the pure-deletion prerequisite that removes code those discussions would otherwise have to reason around.

Test plan

• nf-test LFQ default run still passes (single-engine, independent_run, ms2features_enable=false).
• nf-test LFQ with ms2features_enable=true (single-engine rescoring path) still passes.
• nf-test TMT default run still passes.
• nf-test multi-engine (Comet + MSGF+) path still passes (goes through CONSENSUSID — unchanged).
• Schema validation rejects any config that still sets ms2features_range (parameter no longer exists).
• Verify Sage's internal IDRipper invocation (modules/local/openms/sage/main.nf:63) still works — the binary stays in the OpenMS container.

Breaking change

Yes, intentional. Any config setting ms2features_range = by_sample or by_project must be updated (or removed — independent_run is the only supported value, and it's now implicit).

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[codacy-production]

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[Copilot]

Pull request overview

This PR removes the ms2features_range modes (by_sample, by_project) and the associated merge/split rescoring topology, standardizing rescoring to a single per-file Percolator path, and deletes now-unused Nextflow modules (IDRipper, GET_SAMPLE / extract_sample).

Changes:

• Collapse rescoring logic in psm_rescoring, dda_id, and peptide_database_search to always use per-file Percolator outputs.
• Remove ms2features_range from nextflow.config and nextflow_schema.json (intentional breaking change).
• Delete unused modules (modules/local/openms/id_ripper/*, modules/local/utils/extract_sample/*) and simplify IDMerger prefix logic.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
subworkflows/local/psm_rescoring/main.nf	Removes ms2features_range branching and ID_RIPPER usage; always emits Percolator results.
subworkflows/local/peptide_database_search/main.nf	Removes sample/project grouping paths (GET_SAMPLE, ID_MERGER); always mixes per-engine per-file IDs.
subworkflows/local/dda_id/main.nf	Removes ID_RIPPER branching; always uses per-file Percolator results prior to downstream steps.
nextflow_schema.json	Deletes ms2features_range parameter from schema to enforce the breaking change.
nextflow.config	Removes default ms2features_range parameter.
modules/local/utils/extract_sample/meta.yml	Deletes metadata for removed GET_SAMPLE / extract_sample module.
modules/local/utils/extract_sample/main.nf	Deletes the GET_SAMPLE process implementation.
modules/local/openms/id_ripper/meta.yml	Deletes metadata for removed ID_RIPPER module.
modules/local/openms/id_ripper/main.nf	Deletes the ID_RIPPER process implementation.
modules/local/openms/id_merger/main.nf	Removes ms2features_range-keyed prefix branching.

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