output

tasks/benchmark.wdl

@@ -15,7 +15,10 @@ task benchmark {
 
 		nt=$(nproc)
 		mkdir -p /cromwell_root/tmp
+		cp -r ${ref_dir} /cromwell_root/tmp/
 		cp -r ${benchmarking_dir} /cromwell_root/tmp/
+
+		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 		
 		if [[ ${sample} =~ "gz" ]];then
 			gunzip ${vcf} -c > unzip.vcf
@@ -96,5 +99,6 @@ task benchmark {
 		File extended = "${sample}.extended.csv"
 		File metrics = "${sample}.metrics.json.gz"
 		File out_file = "filelist"
+		File filtered_vcf = "filtered_vcf"
 	}
 }