lohhla_hg38/tasks/lohhla.wdl

task lohhla {
    String sample_id
    File normBAM
    File normBAM_bai
    File tumorBAM
    File tumorBAM_bai
    File hlas
    File ascat
	
    String docker
    String cluster
    String disk_size

    command <<<
	
        set -o pipefail
        set -e
        
        now_path=`pwd`
        echo $now_path > $now_path/test.txt
        mkdir -p ./ana/${sample_id}/
        cp ${normBAM} ./ana/${sample_id}/
        cp ${normBAM_bai} ./ana/${sample_id}/
        cp ${tumorBAM} ./ana/${sample_id}/
        cp ${tumorBAM_bai} ./ana/${sample_id}/
        cp ${hlas} ./ana/
        cp ${ascat} ./ana/

        for line in `ls ./ana/${sample_id}|sed 's/.bam.*//'|sort|uniq`
        do
            new_name=`echo $line|sed 's/\./_/g'`
            mv ./ana/${sample_id}/$line.bam ./ana/${sample_id}/$new_name.bam
            mv ./ana/${sample_id}/$line.bam.bai ./ana/${sample_id}/$new_name.bam.bai
        done
        normBAM_file=`ls ./ana/${sample_id}/|grep bam|grep -v "TT"|grep -v "bai"|grep -v "_T_sorted"`

        Rscript /software/lohhla_hg38/LOHHLAscript_hg38.R --patientId ${sample_id} \
           --outputDir $now_path/ana/${sample_id}_output \
           --normalBAMfile  $now_path/ana/${sample_id}/$normBAM_file \
           --BAMDir $now_path/ana/${sample_id} \
           --hlaPath $now_path/ana/${sample_id}_winners.hlas \
           --HLAfastaLoc /software/lohhla_hg38/data/abc_complete.fasta \
           --CopyNumLoc $now_path/ana/${sample_id}_ascat.txt \
           --mappingStep TRUE --minCoverageFilter 10 --fishingStep TRUE --cleanUp FALSE \
           --gatkDir /software/picard-tools-1.122 \
           --novoDir /opt/conda/bin \
           --HLAexonLoc /software/lohhla_hg38/data/hla.dat

       tar -zcvf ./ana/${sample_id}_output.tgz ./ana/${sample_id}_output

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

    output {
        Array[File] lohhla_xls = glob("./ana/${sample_id}_output/*.xls")
        Array[File] lohhla_pdf = glob("./ana/${sample_id}_output/Figures/*.pdf")
        Array[File] lohhla_tgz = glob("./ana/*.tgz")
    }

}