Dev#85
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Remove 9 parameters that are now exclusively read from SDRF files: - acquisition_method - labelling_type - enzyme - precursor_mass_tolerance - precursor_mass_tolerance_unit - fragment_mass_tolerance - fragment_mass_tolerance_unit - fixed_mods - variable_mods These parameters were redundant as SDRF already contains all this metadata. The pipeline now requires proper SDRF annotation for these values, making the configuration simpler and reducing confusion. Updated files: - nextflow.config: Removed default parameter definitions - nextflow_schema.json: Removed schema entries and updated help text - conf/tests/test_lfq.config: Removed deprecated test params - conf/tests/test_lfq_sage.config: Removed deprecated test params Fixes #650
Since parameters like enzyme, tolerances, and modifications are now exclusively read from SDRF files (removed from config in previous commit), add explicit validation to ensure these required columns are present and valid: - Check all required columns are present and non-empty: Label, Enzyme, PrecursorMassTolerance, PrecursorMassToleranceUnit, FragmentMassTolerance, FragmentMassToleranceUnit, FixedModifications, VariableModifications - Validate tolerance values are valid numbers - Validate tolerance units are 'ppm' or 'Da' Provides clear error messages indicating which columns are missing or invalid, helping users fix their SDRF annotation. Part of #650
Per review feedback, only these 4 parameters should be exclusively read from SDRF (no command-line override): - acquisition_method - labelling_type - enzyme - fixed_mods The following parameters are restored and can be overridden via command line (with SDRF as default if present): - precursor_mass_tolerance - precursor_mass_tolerance_unit - fragment_mass_tolerance - fragment_mass_tolerance_unit - variable_mods Updated create_input_channel validation to: - Only require Label, Enzyme, FixedModifications columns - Use SDRF values for tolerances/variable_mods if present - Fall back to params values if SDRF columns are empty Part of #650
Resolve quantms issue 650 - remove unnecesary params, present in SDRF
fix everything
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).