Add per-sample search parameter support via samplesheet#439

Merged

jonasscheid merged 37 commits intonf-core:devfrom

jonasscheid:search-params-samplesheet

Feb 27, 2026

Commits on Jan 23, 2026

Update openms and openmsthirdparty nf-core modules
jonasscheid
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Update local modules to use topic channels for versions
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Remove redundant version parsing and channel creation from subworkflows
jonasscheid
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Commits on Feb 5, 2026

Commits on Feb 6, 2026

Merge remote-tracking branch 'upstream/topics' into search-params-samplesheet
jonasscheid
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Add per-sample search parameter support via samplesheet and presets
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Use meta-based search parameters in module configs
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Group global FDR by search preset instead of merging all samples
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Add test profile and samplesheet for search params feature
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Fix deprecated Nextflow syntax for strict mode compliance
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Update CHANGELOG for per-sample search parameters feature
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Add nf-test for search params and use test-datasets samplesheet
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Rename test_search_params to test_search_presets and add nf-test profile directive
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Merge remote-tracking branch 'upstream/dev' into search-params-samplesheet
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Remove redundant emit declarations from version outputs and clean up commented lines
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Fix CI failures: prettier formatting, lint ignore, and ionannotator snapshot
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Add search_presets as hidden param in nextflow_schema.json to fix lint
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Document per-sample search parameters and fix stale ch_versions reference
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Align search preset fragment_mass_tolerance with recommended settings
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Commits on Feb 10, 2026

Commits on Feb 11, 2026

Fix ion annotator join key mismatch and rename XL preset comment
jonasscheid
committed

Commits on Feb 13, 2026

Commits on Feb 21, 2026

Merge branch 'dev' into search-params-samplesheet
jonasscheid
authored