test: gunzip

tasks/rename_vcf.wdl

@@ -19,10 +19,14 @@ task rename_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
+    cp ${vcf_D5} vcf_D5.vcf.gz
+    cp ${vcf_D6} vcf_D6.vcf.gz
+    cp ${vcf_F7} vcf_F7.vcf.gz
+    cp ${vcf_M8} vcf_M8.vcf.gz
+    gunzip vcf_D5.vcf.gz > ${vcf_D5_name}_${project}_LCL5.vcf
+		gunzip vcf_D6.vcf.gz > ${vcf_D6_name}_${project}_LCL6.vcf
+		gunzip vcf_F7.vcf.gz > ${vcf_F7_name}_${project}_LCL7.vcf
+		gunzip vcf_M8.vcf.gz > ${vcf_M8_name}_${project}_LCL8.vcf
 	>>>
 
 	runtime {