lohhla_test/tasks/lohhla.wdl

task lohhla {
    String sample_id
    File normBAM
    File normBAM_bai
    File tumorBAM
    File tumorBAM_bai
    File hlas
    File ascat

    String docker
    String cluster
    String disk_size

    command <<<

        set -o pipefail
        set -e

        echo ${sample_id} >a.txt
        ls ${normBAM}
        ls ${normBAM_bai}
        ls ${tumorBAM}
        ls ${tumorBAM_bai}
        ls ${hlas}
        ls ${ascat}
        
    >>>

    runtime {
        docker : docker
        cluster: cluster
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }

    output {
        Array[File] lohhla_xls = glob("*.txt")
    }

}