task BQSR { File ref_dir File dbsnp_dir File dbmills_dir String sample String SENTIEON_INSTALL_DIR String SENTIEON_LICENSE String fasta String dbsnp String db_mills File deduped_bam File deduped_bam_index 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 QualCal \ -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \ ${sample}_recal_data.table >>> runtime { docker: docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File recal_table = "${sample}_recal_data.table" } }