SAAV/tasks/stringtie.wdl

task stringtie {
    File bam
    File anno_gtf
    String docker
    String sample_id
    String cluster

    command <<<
      nt=$(nproc)
      /opt/conda/bin/stringtie -p $nt -G ${anno_gtf} -o ${sample_id}.gtf -l CUFF ${bam}
    >>>
    
    runtime {
      docker: docker
      cluster: cluster
      systemDisk: "cloud_ssd 40"
      dataDisk: "cloud_ssd 150 /cromwell_root/"
    }
    
    output {
      File gtf = "${sample_id}.gtf"
    }
}