name

tasks/benchmark.wdl

@@ -2,7 +2,7 @@ task benchmark {
 	File vcf
 	File benchmarking_dir
 	File ref_dir
-	String sample = basename(vcf,"raw.vcf.gz")
+	String sample = basename(vcf,".raw.vcf.gz")
 	String fasta
 	String docker
 	String cluster_config
@@ -18,7 +18,6 @@ task benchmark {
 
 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 
-
 		gunzip ${vcf} -c > unzip.vcf
  
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip unzip.vcf -c > ${sample}.rtg.vcf.gz
@@ -35,6 +34,8 @@ task benchmark {
         else
         	echo "only for quartet samples"
         fi		
+
+        ls reference_datasets_v202103/ > files.txt
 	>>>
 
 	runtime {
@@ -57,5 +58,6 @@ task benchmark {
 		File summary = "${sample}.summary.csv"
 		File extended = "${sample}.extended.csv"
 		File metrics = "${sample}.metrics.json.gz"
+		File file_list="files.txt"
 	}
 }