CNVkit/tasks/export.wdl

task export{
    String sample_id
    Array[File] results
    String docker
    String cluster_config
    String disk_size

    command <<<
        # mkdir -p /cromwell_root/tmp/cnvkit
        cp -r ${sep=" " results} .
        # cd /cromwell_root/tmp/cnvkit
        # this version app just provides seg
        cnvkit.py export seg *.cns -o ${sample_id}.seg
    >>>
   
    runtime { 
        docker: docker
        cluster: cluster_config
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }

    output {
        File seg = "${sample_id}.seg"
    }
}