changed gene counts merge to use paste instead of csvtk

modules/featureCounts.nf

@@ -48,10 +48,13 @@ process merge_featureCounts {
  path 'merged_gene_counts.tsv.gz'
 
  script:
- //if we only have 1 file, just use cat and pipe output to csvtk. Else join all files first, and then remove unwanted column names.
- def single = input_files instanceof Path ? 1 : input_files.size()
- def merge = (single == 1) ? 'cat' : 'csvtk join -t -f "Geneid,Start,Length,End,Chr,Strand,gene_name"'
  """
- $merge $input_files | csvtk cut -t -f "-Start,-Chr,-End,-Length,-Strand" | sed 's/Aligned.sortedByCoord.out.markDups.bam//g' | sed 's/.sorted.bam//g' | csvtk rename -t -f Geneid -n phenotype_id | csvtk cut -t -f "-gene_name" | gzip -c > merged_gene_counts.tsv.gz
+ paste -d"\t" $input_files > merged_raw_all.tsv
+ 
+ csvtk cut -t -f 1 merged_raw_all.tsv | \
+ csvtk rename -t -f Geneid -n phenotype_id > phenotype_ids_column.tsv
+
+ csvtk cut -t -F -f "*.sorted.bam" merged_raw_all.tsv | sed 's/.sorted.bam//g' > merged_genes_no_phenotype_id.tsv
+ paste -d"\t" phenotype_ids_column.tsv merged_genes_no_phenotype_id.tsv | gzip -c > merged_gene_counts.tsv.gz
  """
 }