battenberg_R/tasks/battenberg.wdl

task battenberg {
    String sample_id
    File tumor_bam
    File tumor_bam_bai
    String normal_id
    File normal_bam
    File normal_bam_bai

    String docker
    String cluster
    String disk_size

    command <<<

        set -o pipefail
        set -e
        cp ${normal_bam} ./${normal_id}.bam
        cp ${tumor_bam} ./${sample_id}.bam
        
        cp ${normal_bam_bai} ./${normal_id}.bam.bai
        cp ${tumor_bam_bai} ./${sample_id}.bam.bai
      
        cp /opt/battenberg_reference/a.R ./
        Rscript a.R
        echo ${sample_id}
        echo ${sample_id} > ${sample_id}_test.txt
        cp data.csv ${sample_id}.csv

    >>>

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

    output {
        File subclones = "${sample_id}.csv"
        File s_test = "${sample_id}_test.txt"
    }

}