diff --git a/workflow/main.nf b/workflow/main.nf
index 444d83f5cc2335b9a11d01ce99731cedd01955b1..a1279d36bf7e1ca43f530da5740e60efc53b8cef 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -151,12 +151,12 @@ process filterReads {
 
   if (pairedEnd) {
     """
-    python3 $baseDir/scripts/map_qc.py -f $mapped -p
+    python3 $baseDir/scripts/map_qc.py -b $mapped -p
     """
   }
   else {
     """
-    python3 $baseDir/scripts/map_qc.py -f $mapped
+    python3 $baseDir/scripts/map_qc.py -b $mapped
     """
   }