Fix paired end issu.e

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 {