battenberg_samtools/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 -@ 16 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam
        samtools view -h -@ 16 -o ${sample_id}.sorted.deduped.sam ./${sample_id}.bam

        #sed -i 's/chr//g' ${normal_id}.sorted.deduped.sam
        #sed -i 's/chr//g' ${sample_id}.sorted.deduped.sam

        samtools sort -@ 16 -o ${normal_id}.sorted.deduped.nochr.bam ${normal_id}.sorted.deduped.sam
        samtools sort -@ 16 -o ${sample_id}.sorted.deduped.nochr.bam ${sample_id}.sorted.deduped.sam
   


    >>>

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

    output {
        File tumor_bam_data = "${normal_id}.sorted.deduped.nochr.bam"
        File normal_bam_data = "${sample_id}.sorted.deduped.nochr.bam"
    }

}