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

        /opt/conda/envs/TREC/bin/samtools view -h ./${normal_id}.bam |sed 's/chr//g'|samtools view  -bS -o ./${normal_id}.sorted.deduped.nochr.bam
        /opt/conda/envs/TREC/bin/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
    >>>

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

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

}