task delly { File tumor_bam File tumor_bam_idx File normal_bam File normal_bam_idx File ref_dir String fasta String sample_name String docker String disk_size String cluster_config command <<< set -o pipefail set -e echo -e "${sample_name}.tumor\ttumor\n${sample_name}.normal\tcontrol" > samples.tsv nt=$(nproc) export OMP_NUM_THREADS=$nt /opt/delly/src/delly call -g ${ref_dir}/${fasta} -o ${sample_name}.delly.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} /opt/delly/src/delly filter -f somatic -o ${sample_name}.delly.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.somatic.bcf >>> runtime { docker:docker cluster:cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File bcf = "${sample_name}.delly.somatic.filtered.bcf" File bcf_index = "${sample_name}.delly.somatic.filtered.bcf.csi" } }