…plesheet

# Conflicts:
#	modules.json
#	modules/local/easypqp/convert/main.nf
#	modules/local/easypqp/library/main.nf
#	modules/local/epicore/main.nf
#	modules/local/ms2rescore/main.nf
#	modules/local/openms/featurefinderidentification/main.nf
#	modules/local/openms/idconflictresolver/main.nf
#	modules/local/openms/idmassaccuracy/main.nf
#	modules/local/openms/mapaligneridentification/main.nf
#	modules/local/openms/maprttransformer/main.nf
#	modules/local/openms/mztabexporter/main.nf
#	modules/local/openms/psmfeatureextractor/main.nf
#	modules/local/openms/textexporter/main.nf
#	modules/local/openmsthirdparty/featurelinkerunlabeledkd/main.nf
#	modules/local/openmsthirdparty/percolatoradapter/main.nf
#	modules/local/pyopenms/chromatogramextractor/main.nf
#	modules/local/pyopenms/ionannotator/main.nf
#	modules/local/tdf2mzml/main.nf
#	modules/local/untar/main.nf
#	modules/local/unzip/main.nf
#	modules/nf-core/openms/idmassaccuracy/tests/main.nf.test
#	subworkflows/local/map_alignment/main.nf
#	subworkflows/local/prepare_spectra/main.nf
#	subworkflows/local/process_feature/main.nf
#	subworkflows/local/rescore/main.nf
#	subworkflows/local/speclib/main.nf

- Add 12 optional search parameter columns to schema_input.json (SearchPreset,
  PeptideMinLength, PeptideMaxLength, PrecursorMassRange, PrecursorCharge, etc.)
- Add resolveSearchParams() with priority: individual column > preset > global params
- Add search_presets.config with 8 presets (lumos/qe/timstof/xl x class1/class2)
- Convert Sample/Condition integers to strings during samplesheet parsing
- Add test_search_params profile to nextflow.config

- Apply meta.X ?: params.X pattern for per-sample parameter override in
  CometAdapter, IDFilter, MS2Rescore, IDMassAccuracy, and IonAnnotator
- Add -weights flag to PERCOLATORADAPTER_GLOBAL to avoid filename collisions

- Carry search_preset through ch_rescore_in in mhcquant.nf
- Group by preset in RESCORE for IDMERGER_GLOBAL and backfilter via combine(by:0)
- Fix EASYPQP_LIBRARY multi-include syntax in speclib subworkflow

- Change Channel.empty() to channel.empty() (lowercase)
- Replace implicit 'it' with explicit closure parameter in EPICORE call

- Update test_search_params.config to use nf-core/test-datasets samplesheet
- Add tests/search_params.nf.test with snapshot
- Remove local samplesheets folder (now using test-datasets)

…ile directive

- Rename config, test file, and profile from search_params to search_presets
- Add profile directive to nf-test file matching other test patterns
- Use test-datasets samplesheet URL, remove local samplesheet
- Use string concatenation for fasta path matching test.config pattern

…sheet

…commented lines

- Restore nf-core modules to match upstream/dev
- Remove emit declarations from version topic outputs in local modules
- Remove version emit metadata from local module meta.yml files
- Add peptidoform content check to search_presets nf-test

…napshot

- Format schema_input.json with prettier
- Add search_presets to schema_params lint ignore (nested config map)
- Update ionannotator snapshot for topic channel version deduplication

…ence

…search params

…ded defaults

…ation on NF 25.04

…ce type, update snapshots

…put schema

…1, make test robust