added min number of peaks per spectrum

bigbio · Mar 26, 2024 · 6a5e319 · 6a5e319
1 parent a003f4b
commit 6a5e319
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diff --git a/modules/local/openms/thirdparty/searchenginecomet/main.nf b/modules/local/openms/thirdparty/searchenginecomet/main.nf
@@ -102,6 +102,7 @@ process SEARCHENGINECOMET {
         -precursor_error_units $meta.precursormasstoleranceunit \\
         -fragment_mass_tolerance ${bin_tol} \\
         -fragment_bin_offset ${bin_offset} \\
+        -minimum_peaks $params.min_peaks \\
         ${il_equiv} \\
         -PeptideIndexing:unmatched_action ${params.unmatched_action} \\
         -debug $params.db_debug \\

diff --git a/modules/local/openms/thirdparty/searchenginesage/main.nf b/modules/local/openms/thirdparty/searchenginesage/main.nf
@@ -51,6 +51,7 @@ process SEARCHENGINESAGE {
         -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\
         -variable_modifications ${meta.variablemodifications.tokenize(',').collect{ "'${it}'" }.join(" ") } \\
         -charges "$params.min_precursor_charge, $params.max_precursor_charge" \\
+        -min_peaks $params.min_peaks \\
         -max_variable_mods $params.max_mods \\
         -isotope_error_range $params.isotope_error_range \\
         ${il_equiv} \\

diff --git a/nextflow.config b/nextflow.config
@@ -96,6 +96,7 @@ params {
     max_peptide_length            = 40
     num_hits                      = 1
     max_mods                      = 3
+    min_peaks                     = 10 //minimum number of peaks in a spectrum
     min_pr_mz                     = null
     max_pr_mz                     = null
     min_fr_mz                     = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -324,6 +324,13 @@
                     "default": 3,
                     "fa_icon": "fas fa-sliders-h"
                 },
+                "min_peaks": {
+                    "type": "integer",
+                    "description": "Minimum number of peaks in the spectrum to be considered for the search engine. Default: 10",
+                    "default": 10,
+                    "fa_icon": "fas fa-sliders-h"
+                },
+
                 "min_pr_mz": {
                     "type": "number",
                     "description": "The minimum precursor m/z for the in silico library generation or library-free search",