bam-readcount/tasks/Count.wdl

task Count {

    String sample_id
    File readcount
    File bed
    String docker
    String cluster_config
    String disk_size

    command <<<
        python /count.py -s ${sample_id} -i ${readcount} -c ${bed} -o ${sample_id}.coverage
    >>>

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

    output {
        File Count = "${sample_id}.coverage"
    }
}