diff --git a/workflow/main.nf b/workflow/main.nf
index 7cbe553d4b95e00d553d08dc9fb4db473d990560..aa758a8656dfddd010f782b57296458c5edabdf4 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -297,12 +297,12 @@ process poolAndPsuedoReads {
 
   if (pairedEnd) {
     """
-    python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -p -c cutoffRatio
+    python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -c $cutoffRatio -p
     """
   }
   else {
     """
-    python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -c cutoffRatio
+    python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -c $cutoffRatio
     """
   }