diff --git a/workflow/main.nf b/workflow/main.nf
index 31ab992f591a7a44acffee356c42915babcd86f9..9cd780d8e67558b3a86e833c5dbdf31e8da52a84 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -126,7 +126,7 @@ process alignReads {
 
   if (pairedEnd) {
     """
-    python3 $baseDir/scripts/map_reads.py -f $reads -r ${index}/genome.fa -p
+    python3 $baseDir/scripts/map_reads.py -f ${reads[0]} ${reads[1]} -r ${index}/genome.fa -p
     """
   }
   else {