wgs-caller/tasks/mapping.wdl

task mapping {
    
    String sample
    File fastq_1
    File fastq_2

    String SENTIEON_INSTALL_DIR
    String SENTIEON_LICENSE
    String group
    String pl
    File ref_dir
    String fasta
    
    String docker
    String cluster_config
    String disk_size

    command <<<
        set -o pipefail
        set -e	
        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
        nt=$(nproc)
        ${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
    >>>

    runtime {
        docker: docker
        cluster: cluster_config
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }
    output {
        File sorted_bam = "${sample}.sorted.bam"
        File sorted_bam_index = "${sample}.sorted.bam.bai"
    }
}