ASCAT_pipeline/tasks/ASCAT.wdl

task ASCAT{
    String sample
    File tumor_bam
    File tumor_bam_index
    File? normal_bam
    File? normal_bam_index
    String gender
    String ref_genome
    String docker
    String cluster_config
    String disk_size

    command <<<
        set -o pipefail
        set -e
        
        out_dir='./'
         /root/miniconda3/envs/hrd/bin/Rscript /home/ASCAT/ascat.r tumor_bam normal_bam ${sample}+'_T' ${sample}+'_N' ${sample} WGS ${out_dir} ${gender} ${ref_genome}

        ls ./

        tar cvf ${sample}.tar ./

    >>>

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

    output{
        File out_file = "${sample}.tar"
    }

}