add support for changing cascadia score threshold

Author: mriffle

modules/cascadia.nf

@@ -38,7 +38,7 @@ process CASCADIA_SEARCH {
 
         """
         ${extra_command}
-        cascadia sequence ${ms_file} /usr/local/bin/cascadia.ckpt --out ${ms_file.baseName}
+        cascadia sequence ${ms_file} /usr/local/bin/cascadia.ckpt --score_threshold ${params.cascadia.score_threshold} --out ${ms_file.baseName}
             > >(tee "${ms_file.baseName}.stdout") 2> >(tee "${ms_file.baseName}.stderr" >&2)
 
         echo "${params.images.cascadia}" | egrep -o '[0-9]+\\.[0-9]+\\.[0-9]+' | xargs printf "cascadia_version=%s\n" > cascadia_version.txt

nextflow.config

@@ -55,7 +55,8 @@ params {
 
     // options for Cascadia (de novo DIA search)
     cascadia.use_gpu = false;       // whether or not to use available GPU, must be set to false if no GPU is available
-
+    cascadia.score_threshold = 0.8  // score threshold applied to predictions. (default: 0.8)
+    
     // optional user-supplied parameters
     email = null                    // email to notify of workflow outcome, leave null to send no email
     skyline.template_file = null    // the skyline template, if null use default_skyline_template_file