battenberg/tasks/battenberg.wdl

task battenberg {
    String tumor_id
    File tumor_bam
    String normal_id
    File normal_bam

    String docker
    String cluster
    String disk_size

    command <<<

        set -o pipefail
        set -e
        samtools view -h ${normal_bam} |sed 's/chr//g'|samtools view  -bS > ./${normal_id}.sorted.deduped.nochr.bam
        samtools view -h ${tumor_bam} |sed 's/chr//g'|samtools view  -bS > ./${tumor_id}.sorted.deduped.nochr.bam
        samtools index  ./${normal_id}.sorted.deduped.nochr.bam
        samtools index  ./${tumor_id}.sorted.deduped.nochr.bam
        cp /opt/battenberg_reference/battenberg_wgs.R ./
        Rscript ./battenberg_wgs.R -t ${tumor_id} -n ${normal_id} --nb ${normal_id}.sorted.deduped.nochr.bam --tb  ${tumor_id}.sorted.deduped.nochr.bam --cpu 10 --sex female -o ./
         
    >>>

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

    output {
        File subclones = "${tumor_id}_subclones.txt"
        File rho = "${tumor_id}_rho_and_psi.txt"
        File average_png = "${tumor_id}_BattenbergProfile_average.png"
        File subclones_png = "${tumor_id}_subclones.png"
        File distance_png = "${tumor_id}_distance.png"
        File tumor_png = "${tumor_id}.tumour.png"
        File germline_png = "${tumor_id}.germline.png"
        File coverage_png = "${tumor_id}_coverage.png"
        File alleleratio_png = "${tumor_id}_alleleratio.png"
        
    }

}