Add Scout as switchable search engine (params.search_engine)

[ypriverol]

Summary

Add SCOUT_SEARCH and SCOUT_FILTER Nextflow modules. Scout v2.1 supports -no_filter for per-sample parallel search and -filter for aggregated FDR computation across all samples.

Architecture

• params.search_engine = 'xisearch' (default): existing xiSEARCH + xiFDR path
• params.search_engine = 'scout': SCOUT_SEARCH (per sample, parallel) -> SCOUT_FILTER (collect all *.buf, single FDR)
• FDR tied to engine: xiSEARCH uses xiFDR, Scout uses Scout -filter

Tasks

• Create SCOUT_SEARCH module (modules/local/scout_search/)
• Create SCOUT_FILTER module (modules/local/scout_filter/)
• Add engine branching logic in workflows/relink.nf
• Add Scout process configs in conf/modules.config
• Add search_engine parameter to nextflow.config

Dependencies

• Requires Scout 2.1 in container (quantms-containers)
• Requires mzML migration (Switch spectral format from MGF to mzML #5)