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
        mkdir -p /cromwell_root/tmp/bamdst/
        /bamdst/bamdst -p ${bed} -o /cromwell_root/tmp/bamdst/ ${bam}
        cd /cromwell_root/tmp/bamdst/
        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"
    }
}