bamdst/tasks/bamdst.wdl

task bamdst {

    File bam
    File bai
    File bed
    String sample
    String docker
    String cluster_config
    String disk_size

    command <<<
        set -o pipefail
        set -e
        nt=$(nproc)
        bamdst -p ${bed} -o ./ ${bam}
        cp ./chromosomes.report ./${sample}_chromosomes.report
        cp ./coverage.report ./${sample}_coverage.report
        cp ./depth_distribution.plot ./${sample}_depth_distribution.plot
        cp ./insertsize.plot ./${sample}_insertsize.plot
        cp ./region.tsv.gz ./${sample}_region.tsv.gz
        cp ./uncover.bed ./${sample}_uncover.bed
    >>>

    runtime {
        docker: docker
        cluster: cluster_config
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }
    
    output {
        File chromosomes.report = "${sample}_chromosomes.report"
        File coverage.report = "${sample}_coverage.report"
        File depth_distribution.plot = "${sample}_depth_distribution.plot"
        File depth.tsv.gz = "${sample}_depth.tsv.gz"
        File insertsize.plot = "${sample}_insertsize.plot"
        File region.tsv.gz = "${sample}_region.tsv.gz"
        File uncover.bed = "${sample}_uncover.bed"
    }
}