rnaseq-engineering/tasks/ballgown.wdl

task ballgown {
  File gene_abundance
  String base=basename(gene_abundance, ".gene.abundance.txt")
  String docker
  String cluster
  String disk_size
  Array[File] ballgown

  command <<<
    mkdir -p /cromwell_root/tmp/${base}
    cp -r ${sep=" " ballgown} /cromwell_root/tmp/${base}
    ballgown /cromwell_root/tmp/${base} ${base}.txt
    sed -i 's/"//g' ${base}.txt
    sed -i '1s/FPKM./gene_id\t/g' ${base}.txt
  >>>
  
  runtime {
    docker: docker
    cluster: cluster
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }
  
  output {
    File mat_expression="${base}.txt"
  }
}