rename

inputs

@@ -5,7 +5,6 @@
   "{{ project_name }}.LCL8": "{{ LCL8 }}",
   "{{ project_name }}.disk_size": "500",
   "{{ project_name }}.LCL5": "{{ LCL5 }}",
-  "{{ project_name }}.rename": "{{ rename }}",
   "{{ project_name }}.project": "{{ project }}",
   "{{ project_name }}.SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
   "{{ project_name }}.BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
@@ -15,4 +14,4 @@
   "{{ project_name }}.LCL7": "{{ LCL7 }}",
   "{{ project_name }}.DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
   "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
-}
+}

tasks/merge_family.wdl

@@ -7,24 +7,19 @@
 	File LCL7_vcf_idx
 	File LCL8_vcf_gz
 	File LCL8_vcf_idx
-	File rename
 	String project
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL5_vcf_gz} -o LCL5.vcf.gz
 
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL6_vcf_gz} -o LCL6.vcf.gz
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfmerge --force-merge-all -o ${project}.family.vcf.gz ${LCL5_vcf_gz} ${LCL6_vcf_gz} ${LCL7_vcf_gz} ${LCL8_vcf_gz}
 
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL7_vcf_gz} -o LCL7.vcf.gz
-
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL8_vcf_gz} -o LCL8.vcf.gz
-
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfmerge --force-merge-all -o ${project}.family.vcf.gz LCL5.vcf.gz LCL6.vcf.gz LCL7.vcf.gz LCL8.vcf.gz
-
-		gunzip ${project}.family.vcf.gz 
+		zcat ${project}.family.vcf.gz | grep '##' > header
+		zcat ${project}.family.vcf.gz | grep -v '#' > body		
+		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5\tLCL6\tLCL7\tLCL8" > name
+		cat header name body > ${project}.family.vcf
 
 	>>>
 

workflow.wdl

@@ -22,7 +22,6 @@ workflow {{ project_name }} {
 	File sdf
 
 	File benchmarking_dir
-	File rename
 
 	String project
 
@@ -88,7 +87,6 @@ workflow {{ project_name }} {
 		LCL7_vcf_idx=LCL7benchmark.rtg_vcf_index,
 		LCL8_vcf_gz=LCL8benchmark.rtg_vcf,
 		LCL8_vcf_idx=LCL8benchmark.rtg_vcf,
-		rename=rename,
 		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=SMALLcluster_config,