CNVkit/tasks/access.wdl

task access {
	  File ref_dir
	  String fasta
    String docker
    String cluster_config
    String disk_size

    command <<<
        cnvkit.py access -s 5000 -o access-5kb-mappable.hg38.bed ${ref_dir}/${fasta}
    >>>

    runtime {
        docker: docker
        cluster: cluster_config
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }
    
    output {
        File access_bed = "access-5kb-mappable.hg38.bed"
    }
}