threshold added to xcos nextflow workflow

Author: tdudgeon

src/nextflow/xchem/xcos.nf

@@ -2,9 +2,10 @@
 
 params.inputs = 'data/mpro/poses.sdf.gz'
 params.fragments = 'data/mpro/hits-17.sdf.gz'
-params.chunk = 500
-params.limit = 0
-params.digits = 4
+params.threshold = 0.4 // XCos score theshold
+params.chunk = 500     // chunk size to split input into
+params.limit = 0       // max number of molecules to process
+params.digits = 4      // number of digits for the split file name number
 
 inputs = file(params.inputs)
 fragments = file(params.fragments)
@@ -36,7 +37,7 @@ process xcos {
     file 'scored_part*.sdf' into scored_parts
 
     """
-    python -m pipelines.xchem.xcos -i '$part' -f '$fragments' -o '${part.name.replace('inputs', 'scored')[0..-8]}' -of sdf --no-gzip
+    python -m pipelines.xchem.xcos -i '$part' -f '$fragments' -t $params.threshold -o '${part.name.replace('inputs', 'scored')[0..-8]}' -of sdf --no-gzip
     """
 }