Workflow runs through OK

workflow/main.nf

@@ -22,7 +22,7 @@ index_name = "genome"
 // which is covered by the GNU General Public License v3
 // https://github.com/nextflow-io/rnatoy/blob/master/main.nf
 Channel
-    .fromPath( "{" + fastqs + "}, " )
+    .fromPath( fastqs )
     .ifEmpty { error "Cannot find any files matching: ${fastqs}" }
     .map { path ->
        def prefix = readPrefix(path, '*{1,2}.{fastq,fq}{,.gz}')
@@ -168,7 +168,7 @@ process featurect {
   set pair_id, file(dbam) from deduped1
   file gtf_file
   output:
-  set pair_id, file("${pair_id}.cts") into counts
+  file("${pair_id}.cts")  into counts
   """
   module load module subread/1.5.0-intel
   featureCounts -T 4 -p -g gene_name -a ${gtf_file} -o ${pair_id}.cts ${dbam}
@@ -212,14 +212,15 @@ process genenames {
 }
 
 process statanal {
-   publishDir "$basDir/output", mode: 'copy'
+   publishDir "$baseDir/output", mode: 'copy'
    input:
    file count_file from counts.toList()
    file design_file name 'design.txt'
    file genenames_file name 'genenames.txt' from genenames
    output:
    """
-   perl $baseDir/scripts/concat_cts.pl -g $refDir -o ./ *.cts
+   module load R/3.2.1-intel
+   perl $baseDir/scripts/concat_cts.pl -g genenames.txt -o ./ *.cts
    Rscript  $baseDir/scripts/DEA_htseq.R
  """
 }