Merge pull request #275 from steffenlem/dev

Fixed extra flag setting for ms2pip
nf-core · Aug 18, 2023 · 013dc25 · 013dc25
2 parents 5ac3e94 + 047c8d8
commit 013dc25
Showing 1 changed file with 6 additions and 4 deletions.
diff --git a/modules/local/openms_psmfeatureextractor.nf b/modules/local/openms_psmfeatureextractor.nf
@@ -21,15 +21,17 @@ process OPENMS_PSMFEATUREEXTRACTOR {
         def prefix           = task.ext.prefix ?: "${merged.baseName}_psm"
         def args             = task.ext.args ?: ''
         def extra_features = ""
-        if(params.use_deeplc){
+        if(params.use_deeplc || params.use_ms2pip){
             extra_features = "-extra"
-            if(params.add_abs_rt_error){
+        }
+        if(params.use_deeplc){
+            if(params.deeplc_add_abs_rt_error){
                 extra_features = "${extra_features} deeplc_abs_error"
             }
-            if(params.add_log_rt_error){
+            if(params.deeplc_add_log_rt_error){
                 extra_features = "${extra_features} deeplc_log_error"
             }
-            if(params.add_sqr_rt_error || (!params.add_sqr_rt_error && !params.add_abs_rt_error && !params.add_log_rt_error)){
+            if(params.deeplc_add_sqr_rt_error || (!params.deeplc_add_sqr_rt_error && !params.deeplc_add_abs_rt_error && !params.deeplc_add_log_rt_error)){
                 extra_features = "${extra_features} deeplc_sqr_error"
             }
         }