diff --git a/workflow/main.nf b/workflow/main.nf
index 04866eb3929d46658f50af560b3c7c1ae9cbe812..1d1d6afd96ab9e1e3285a9e05cdcbf8265e89f12 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -56,12 +56,12 @@ process checkDesignFile {
 
   if (pairedEnd) {
     """
-    python3 $baseDir/scripts/check_design.py -d $designFile -f $readsList -p
+    python3 $baseDir/scripts/check_design.py -d $designFile -f $readsList -p -a
     """
   }
   else {
     """
-    python $baseDir/scripts/check_design.py -d $designFile -f $readsList
+    python $baseDir/scripts/check_design.py -d $designFile -f $readsList -a
     """
   }
 
@@ -75,7 +75,7 @@ if (pairedEnd) {
 } else {
 rawReads = designFilePaths
   .splitCsv(sep: '\t', header: true)
-  .map { row -> [ row.sample_id, [row.fastq_read1], row.experiment_id, row.biosample, row.factor, row.treatment, row.replicate, ] }
+  .map { row -> [ row.sample_id, [row.fastq_read1], row.experiment_id, row.biosample, row.factor, row.treatment, row.replicate ] }
 }
 
 // Trim raw reads using trimgalore
@@ -116,12 +116,12 @@ process alignReads {
 
   input:
 
-  set sampleId, reads, experimentId, biosample, factor, treatment, replicate, from trimmedReads
+  set sampleId, reads, experimentId, biosample, factor, treatment, replicate from trimmedReads
   file index from bwaIndex.first()
 
   output:
 
-  set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, into mappedReads
+  set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate into mappedReads
   file '*.srt.bam.flagstat.qc' into mappedReadsStats