Merge pull request #694 from ypriverol/feat/biosaur2-seeding

feat: expose Biosaur2 as alternative feature seeding algorithm for LFQ

Author: ypriverol

modules/local/openms/proteomicslfq/main.nf

@@ -48,6 +48,7 @@ process PROTEOMICSLFQ {
         ${feature_with_id_min_score} \\
         ${feature_without_id_min_score} \\
         -mass_recalibration ${params.mass_recalibration} \\
+        -Seeding:algorithm ${params.lfq_seeding_algorithm} \\
         -Seeding:intThreshold ${params.lfq_intensity_threshold} \\
         -protein_quantification ${params.protein_quant} \\
         -alignment_order ${params.alignment_order} \\

nextflow.config

@@ -185,6 +185,7 @@ params {
     protein_inference_method = 'aggregation'
     protein_quant            = 'unique_peptides'
     quantification_method    = 'feature_intensity'
+    lfq_seeding_algorithm    = 'multiplex'  // Feature seeding: 'multiplex' (default) or 'biosaur2'
     mass_recalibration       = false
     alignment_order          = 'star'
     quantify_decoys          = false

nextflow_schema.json

@@ -1064,6 +1064,13 @@
                     "enum": ["feature_intensity", "spectral_counting"],
                     "fa_icon": "fas fa-list-ol"
                 },
+                "lfq_seeding_algorithm": {
+                    "type": "string",
+                    "description": "Feature detection seeding algorithm for ProteomicsLFQ. 'multiplex' uses FeatureFinderMultiplex (default), 'biosaur2' uses the Biosaur2 algorithm.",
+                    "default": "multiplex",
+                    "enum": ["multiplex", "biosaur2"],
+                    "fa_icon": "fas fa-seedling"
+                },
                 "mass_recalibration": {
                     "type": "boolean",
                     "description": "Recalibrates masses based on precursor mass deviations to correct for instrument biases. (default: 'false')",