diff --git a/workflow/main.nf b/workflow/main.nf
index 023d5e775bf5fc086bfce037975f21f7aeb4c303..0b8e0d5589210dfb15a34ad58238085b6456448f 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -239,12 +239,12 @@ process crossReads {
 
   if (pairedEnd) {
     """
-    python3 $baseDir/scripts/xcor.py -b $seTagAlign -p
+    python3 $baseDir/scripts/xcor.py -t $seTagAlign -p
     """
   }
   else {
     """
-    python3 $baseDir/scripts/xcor.py -b $seTagAlign
+    python3 $baseDir/scripts/xcor.py -t $seTagAlign
     """
   }