test: gunzip

defaults

@@ -1,7 +1,7 @@
 {
   "benchmarking_dir": "oss://hcc1395/reference_genome/reference_datasets_v202103/",
   "fasta": "GRCh38.d1.vd1.fa",
-  "BENCHMARKdocker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/rtg-hap:latest",
+  "BENCHMARKdocker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/rtg-hap:latest", 
   "dbsnp_dir": "oss://hcc1395/reference_genome/GRCh38.d1.vd1/",
   "BEDTOOLSdocker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/bedtools:v2.27.1",
   "disk_size": "500",

tasks/rename_vcf.wdl

@@ -15,10 +15,14 @@ task rename_vcf {
 	String disk_size
 
 	command <<<
-		cp ${vcf_D5} ${vcf_D5_name}_${project}_LCL5.vcf
-		cp ${vcf_D6} ${vcf_D6_name}_${project}_LCL6.vcf
-		cp ${vcf_F7} ${vcf_F7_name}_${project}_LCL7.vcf
-		cp ${vcf_M8} ${vcf_M8_name}_${project}_LCL8.vcf
+		# cp ${vcf_D5} ${vcf_D5_name}_${project}_LCL5.vcf
+		# cp ${vcf_D6} ${vcf_D6_name}_${project}_LCL6.vcf
+		# cp ${vcf_F7} ${vcf_F7_name}_${project}_LCL7.vcf
+		# cp ${vcf_M8} ${vcf_M8_name}_${project}_LCL8.vcf
+    gunzip ${vcf_D5} ${vcf_D5_name}_${project}_LCL5.vcf
+		gunzip ${vcf_D6} ${vcf_D6_name}_${project}_LCL6.vcf
+		gunzip ${vcf_F7} ${vcf_F7_name}_${project}_LCL7.vcf
+		gunzip ${vcf_M8} ${vcf_M8_name}_${project}_LCL8.vcf
 	>>>
 
 	runtime {

workflow.wdl

@@ -65,7 +65,7 @@ workflow {{ project_name }} {
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
-			disk_size=disk_size			
+			disk_size=disk_size
 		}
 
 		call benchmark.benchmark as benchmark_D5_vcf {