task cufflinks {
    File gtf
    File accepted_hits
    File genome_directory
    String idx_prefix
    String baseout
    String docker

    command {
      cufflinks ${gtf} -p 24 -o ${baseout} ${accepted_hits}

    runtime {
      dockerTag: docker
    }
    
    output {
      File isoforms_count = "${baseout}/isoforms.fpkm_tracking"
      File genes_count = "${baseout}/genes.fpkm_tracking"
      File skipped_gtf = "${baseout}/skipped.gtf"
      File transcripts_gtf = "${baseout}/transcripts.gtf"
    }
}