revert params.remove_precursor_peak to boolean for backwards compatib…

…ility
nf-core · Jan 22, 2025 · b3e9846 · b3e9846
1 parent a7c890a
commit b3e9846
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -114,7 +114,7 @@ process {
             "-use_A_ions ${params.use_a_ions}",
             "-use_C_ions ${params.use_c_ions}",
             "-use_NL_ions ${params.use_NL_ions}",
-            "-remove_precursor_peak ${params.remove_precursor_peak}"
+            params.remove_precursor_peak ? "-remove_precursor_peak yes" : "",
         ].join(' ').trim() }
         publishDir = [
             path: {"${params.outdir}/intermediate_results/comet"},

diff --git a/nextflow.config b/nextflow.config
@@ -40,7 +40,7 @@ params {
     use_a_ions                      = false
     use_c_ions                      = false
     use_NL_ions                     = false
-    remove_precursor_peak           = 'no'
+    remove_precursor_peak           = false
     spectrum_batch_size             = 0
 
     // Preprocessing settings

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -228,10 +228,10 @@
                     "description": "Include NL ions into the peptide spectrum matching"
                 },
                 "remove_precursor_peak": {
-                    "type": "string",
+                    "type": "boolean",
                     "fa_icon": "fas fa-pipe",
                     "description": "Include if you want to remove all peaks around precursor m/z",
-                    "default": "no"
+                    "default": "false"
                 },
                 "spectrum_batch_size": {
                     "type": "integer",