output

tasks/benchmark.wdl

@@ -6,6 +6,7 @@ task benchmark {
 	File ref_dir
 	File fasta
 	String sample = basename(vcf,".vcf.gz")
+	String file_type = basename(vcf)
 	String docker
 	String cluster_config
 	String disk_size
@@ -20,7 +21,7 @@ task benchmark {
 
 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 		
-		if [[ ${sample} =~ "gz" ]];then
+		if [[ ${file_type} =~ "gz" ]];then
 			gunzip ${vcf} -c > unzip.vcf
 		else
 			cp ${vcf} unzip.vcf