task TNseq { String sample String SENTIEON_INSTALL_DIR String SENTIEON_LICENSE File tumor_recaled_bam File tumor_recaled_bam_index File tumor_recal_table File normal_recaled_bam File normal_recaled_bam_index File normal_recal_table String tumor_name String normal_name File ref_dir String fasta File germline_resource File germline_resource_tbi File? regions Int? interval_padding File? pon_vcf String docker String cluster_config String disk_size command <<< set -o pipefail set -e export SENTIEON_LICENSE=${SENTIEON_LICENSE} nt=$(nproc) if [ ${regions} ]; then INTERVAL="--interval ${regions} --interval_padding ${interval_padding}" else INTERVAL="" fi if [ ${pon_vcf} ]; then PON="--pon ${pon_vcf}" ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${pon_vcf} else PON="" fi ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \ -r ${ref_dir}/${fasta} $INTERVAL \ -i ${tumor_recaled_bam} -q ${tumor_recal_table} \ -i ${normal_recaled_bam} -q ${normal_recal_table} \ --algo TNhaplotyper2 \ --tumor_sample ${tumor_name} --normal_sample ${normal_name} \ --germline_vcf ${germline_resource} \ $PON \ ${sample}.TNseq.TN.tmp.vcf \ --algo OrientationBias --tumor_sample ${tumor_name} \ ${sample}.orientation \ --algo ContaminationModel \ --tumor_sample ${tumor_name} --normal_sample ${normal_name} \ --vcf ${germline_resource} \ --tumor_segments ${sample}.contamination.segments \ ${sample}.contamination ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r REFERENCE \ --algo TNfilter \ --tumor_sample ${tumor_name} --normal_sample ${normal_name} \ -v ${sample}.TNseq.TN.tmp.vcf \ --contamination ${sample}.contamination \ --tumor_segments ${sample}.contamination.segments \ --orientation_priors ${sample}.orientation \ ${sample}.TNseq.TN.vcf >>> runtime { docker: docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File TNseq_vcf = "${sample}.TNseq.TN.vcf" File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx" File contamination = "${sample}.contamination" File contamination_segments = "${sample}.contamination.segments" File orientation = "${sample}.orientation" } }