rnaseq-engineering/tasks/ballgown.wdl

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

    command <<<
      mkdir /cromwell_root/tmp/
      cp -r ${sep=" " ballgown} /cromwell_root/tmp/ballgown
      Rscript /usr/bin/ballgown.R /cromwell_root/tmp/ballgown/${base} ${base}.txt
    >>>
    
    runtime {
      docker: docker
      cluster: cluster
      systemDisk: "cloud_ssd 40"
      dataDisk: "cloud_ssd 150 /cromwell_root/"
    }
    
    output {
      File mat_expression = "${base}.txt"
    }
}