rnaseq-engineering/tasks/stringtie.wdl

task stringtie {
  File bam
  File gtf
  String docker
  String base=basename(bam, ".sorted.bam")
  String cluster
  String disk_size

  command <<<
    nt=$(nproc)
    mkdir ballgown
    /opt/conda/bin/stringtie -e -B -p $nt -G ${gtf} -o ballgown/${base}/${base}.gtf -C ${base}.cov.ref.gtf -A ${base}.gene.abundance.txt ${bam}
  >>>
  
  runtime {
    docker: docker
    cluster: cluster
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }
  
  output {
    File covered_transcripts="${base}.cov.ref.gtf"
    File gene_abundance="${base}.gene.abundance.txt"
    Array[File] ballgown=["ballgown/${base}/${base}.gtf", "ballgown/${base}/e2t.ctab", "ballgown/${base}/e_data.ctab", "ballgown/${base}/i2t.ctab", "ballgown/${base}/i_data.ctab", "ballgown/${base}/t_data.ctab"]
  }
}