task in_out { File vcf File vcf_idx File confidence_bed String sample_name String docker String cluster_config String disk_size command <<< rtg vcffilter -i ${vcf} -o ${sample_name}.insideBed.vcf.gz --include-bed=${confidence_bed} rtg vcffilter -i ${vcf} -o ${sample_name}.outsideBed.vcf.gz --exclude-bed=${confidence_bed} >>> runtime { docker:docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File in_vcf = "${sample_name}.insideBed.vcf.gz" File in_vcf_idx = "${sample_name}.insideBed.vcf.gz.tbi" File out_vcf = "${sample_name}.outsideBed.vcf.gz" File out_vcf_idx = "${sample_name}.outsideBed.vcf.gz.tbi" } }