Add SDRF input support with parameter translation

[ypriverol]

Summary

Replace CSV samplesheet input with SDRF. Use sdrf-pipelines convert-relink converter to extract per-file metadata and XL-MS specific columns (crosslinker, enrichment, tolerances). Add parameter translator (bin/generate_engine_config.py) to generate xiSEARCH XML or Scout JSON configs from SDRF-derived parameters.

Tasks

• Create SDRF_PARSING module (modules/local/sdrf_parsing/)
• Create GENERATE_ENGINE_CONFIG module
• Create bin/generate_engine_config.py
• Wire SDRF parsing into pipeline input

Dependencies

• Requires convert-relink in sdrf-pipelines