battenberg/tasks/battenberg.wdl

task battenberg {
    String sample_id
    File tumor_bam
    String normal_id
    File normal_bam

    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
        samtools view -h ./${normal_id}.bam |sed 's/chr//g'|samtools view  -bS -o ./${normal_id}.sorted.deduped.nochr.bam
        samtools view -h ./${sample_id}.bam |sed 's/chr//g'|samtools view  -bS -o ./${sample_id}.sorted.deduped.nochr.bam
      
     
        samtools index  ./${normal_id}.sorted.deduped.nochr.bam
        samtools index  ./${sample_id}.sorted.deduped.nochr.bam
        cp /opt/battenberg_reference/battenberg_wgs.R ./
        Rscript ./battenberg_wgs.R -t ${sample_id} -n ${normal_id} --nb ./${normal_id}.sorted.deduped.nochr.bam --tb  ./${sample_id}.sorted.deduped.nochr.bam --cpu 4 --sex female -o ./
        mkdir ${sample_id}_chr_png
        cp ${sample_id}_subclones_chr*.png ./${sample_id}_chr_png/
        tar zcvf ./${sample_id}_chr_png.tgz ./${sample_id}_chr_png/

    >>>

    runtime {
        docker : docker
        cluster: cluster
        systemDisk: "cloud_ssd 100"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }

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

}