diff --git a/src/nf_modules/flexi_splitter/main.nf b/src/nf_modules/flexi_splitter/main.nf
index d7a87b94a28fdb48131c0edcdc7afcd4d47c9319..42d405af8a2a776dffbbdf4bb82233763923439f 100644
--- a/src/nf_modules/flexi_splitter/main.nf
+++ b/src/nf_modules/flexi_splitter/main.nf
@@ -30,7 +30,7 @@ process split {
 
   if (reads.size() == 2)
   """
-  flexi_splitter ${params.split} -n 2 -f ${reads[0]} ${reads[1]} -o split -c ${config}
+  flexi_splitter ${params.split} -n 2 -f ${reads[0]},${reads[1]} -o split -c ${config}
   """
   else
   """