battenberg_R2/tasks/battenberg.wdl

task battenberg {
    String sample_id

    String docker
    String cluster
    String disk_size

    command <<<

        set -o pipefail
        set -e
        
        cp /opt/battenberg_reference/battenberg_wgs.R ./${sample_id}.R


    >>>

    runtime {
        docker : docker
        cluster: cluster
        systemDisk: "cloud_ssd 100"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }

    output {
        File subclones = "${sample_id}.R"

    }

}