Fix paired end.

workflow/main.nf

@@ -127,7 +127,7 @@ 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 {
@@ -250,7 +250,7 @@ process tssEnrich {
   script:
 
   """
-  sregistry pull  bicf/metaseq:0.1.0  
+  sregistry pull  bicf/metaseq:0.1.0
   singularity run $HOME/.singularity/shub/bicf-metaseq:0.1.0.simg $baseDir/scripts/atac_qc.py -b $deduped -p $sampleId -t $tssFile -c $chromSizes
   """