docker

inputs

@@ -1,7 +1,7 @@
 {
   "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
-  "{{ project_name }}.BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
+  "{{ project_name }}.BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:v1.1",
   "{{ project_name }}.LCL8": "{{ LCL8 }}",
   "{{ project_name }}.disk_size": "500",
   "{{ project_name }}.LCL5": "{{ LCL5 }}",

tasks/benchmark.wdl

@@ -12,8 +12,7 @@ task benchmark {
 
 
 	command <<<
-		set -o pipefail
-		set -e
+
 		nt=$(nproc)
 		mkdir -p /cromwell_root/tmp
 		cp -r ${benchmarking_dir} /cromwell_root/tmp/
@@ -41,6 +40,7 @@ task benchmark {
 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL7" > LCL7_name
 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL8" > LCL8_name
 
+		ls > filelist
 
 		if [[ ${sample} =~ "LCL5" ]];then
 			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf filtered.vcf -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
@@ -73,8 +73,6 @@ task benchmark {
         else
         	echo "only for quartet samples"
         fi	
-
-        ls > filelist	
 	>>>
 
 	runtime {