input:
    file input_files from featureCounts_to_merge.collect()

    output:
    file 'merged_gene_counts.txt'

    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' > merged_gene_counts.txt
    """