task Realigner { File ref_dir File dbmills_dir String SENTIEON_INSTALL_DIR String SENTIEON_LICENSE String sample String fasta File deduped_bam File deduped_bam_index String db_mills 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/sentieon driver -t $nt \ -r ${ref_dir}/${fasta} \ -i ${deduped_bam} \ --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam >>> runtime { docker: docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File realigned_bam = "${sample}.sorted.deduped.realigned.bam" File realigned_bam_index = "${sample}.sorted.deduped.realigned.bam.bai" } }