trec/tasks/trec.wdl

task trec {
    String sample_id
    File tumorBAM
    File tumorBAM_bai
    String TRA_cn
    String tumor_purity

    String docker
    String cluster
    String disk_size

    command <<<

        set -o pipefail
        set -e
        mkdir ./TREC_ana
        cp ${tumorBAM} ./TREC_ana/
        cp ${tumorBAM_bai} ./TREC_ana/
        cd ./TREC_ana
        cp /software/CBCGA_07604514_Padded_hg38.bed ./
        bam_name=`ls |grep bam|grep -v bai`
        echo $bam_name
        Rscript /software/TREC_script.Rscript --sample_id ${sample_id} \
           --wes_bed ./CBCGA_07604514_Padded_hg38.bed \
           --bam ./$bam_name \
           --tumor_purity ${tumor_purity} \
           --cn_TRA ${TRA_cn}
       
    >>>

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

    output {
        Array[File] trec_txt = glob("./TREC_ana/*.txt")
        Array[File] trec_pdf = glob("./TREC_ana/*.pdf")
    }

}