rename vcf gz

inputs

@@ -1,5 +1,6 @@
 {
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.VCFrename.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.sister.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "{{ project_name }}.mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "{{ project_name }}.disk_size": "150",

tasks/VCFrename.wdl

@@ -0,0 +1,40 @@
+task VCFrename {
+	File mother_vcf_gz
+	File father_vcf_gz
+	File twins_vcf_gz
+	File mother_vcf_idx
+	File father_vcf_idx
+	File twins_vcf_idx
+	String mother_name
+	String father_name
+	String family_name
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		echo "MOTHER ${mother_name}" > mother_rename.txt
+		rtg vcfannotate -i ${mother_vcf_gz} -o ${mother_name}.rename.vcf.gz --relabel=mother_rename.txt
+
+		echo "FATHER ${father_name}" > father_rename.txt
+		rtg vcfannotate -i ${father_vcf_gz} -o ${father_name}.rename.vcf.gz --relabel=father_rename.txt
+
+		echo "CHILD ${family_name}" > child_rename.txt
+		rtg vcfannotate -i ${twins_vcf_gz} -o ${family_name}.twins.rename.vcf.gz --relabel=child_rename.txt
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File rename_mother_vcf_gz = "${mother_name}.rename.vcf.gz"
+		File rename_father_vcf_gz = "${father_name}.rename.vcf.gz"
+		File rename_twins_vcf_gz = "${family_name}.twins.rename.vcf.gz"
+		File rename_mother_vcf_idx = "${mother_name}.rename.vcf.gz.tbi"
+		File rename_father_vcf_idx = "${father_name}.rename.vcf.gz.tbi"
+		File rename_twins_vcf_idx = "${family_name}.twins.rename.vcf.gz.tbi"
+	}
+}

tasks/merge.wdl

@@ -1,21 +1,21 @@
 task merge {
-	Array[File] mother_vcf_gz
-	Array[File] mother_vcf_idx
-	Array[File] father_vcf_gz
-	Array[File] father_vcf_idx
-	Array[File] twins_vcf_gz
-	Array[File] twins_vcf_idx
+	Array[File] rename_mother_vcf_gz
+	Array[File] rename_mother_vcf_idx
+	Array[File] rename_father_vcf_gz
+	Array[File] rename_father_vcf_idx
+	Array[File] rename_twins_vcf_gz
+	Array[File] rename_twins_vcf_idx
 	String mapper_caller
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-		rtg vcfmerge --force-merge-all --no-gzip -o LCL8.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " mother_vcf_gz}
+		rtg vcfmerge --force-merge-all --no-gzip -o LCL8.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " rename_mother_vcf_gz}
 
-		rtg vcfmerge --force-merge-all --no-gzip -o LCL7.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " father_vcf_gz}
+		rtg vcfmerge --force-merge-all --no-gzip -o LCL7.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " rename_father_vcf_gz}
 
-		rtg vcfmerge --force-merge-all --no-gzip -o Twins.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " twins_vcf_gz}
+		rtg vcfmerge --force-merge-all --no-gzip -o Twins.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " rename_twins_vcf_gz}
 	>>>
 
 	runtime {

workflow.wdl

@@ -2,6 +2,7 @@ import "./tasks/variantsNorm.wdl" as variantsNorm
 import "./tasks/sister.wdl" as sister
 import "./tasks/mendelian.wdl" as mendelian
 import "./tasks/zipIndex.wdl" as zipIndex
+import "./tasks/VCFrename.wdl" as VCFrename
 import "./tasks/merge.wdl" as merge
  
 workflow {{ project_name }} {
@@ -82,16 +83,30 @@ workflow {{ project_name }} {
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
+		call VCFrename.VCFrename as VCFrename{
+			input:
+			mother_vcf_gz=zipIndex.mother_vcf_gz,
+			father_vcf_gz=zipIndex.father_vcf_gz,
+			twins_vcf_gz=zipIndex.twins_vcf_gz,
+			mother_vcf_idx=zipIndex.mother_vcf_idx,
+			father_vcf_idx=zipIndex.father_vcf_idx,
+			twins_vcf_idx=zipIndex.twins_vcf_idx,
+			mother_name=sample[7],
+			father_name=sample[6],
+			family_name=sample[8],
+			cluster_config=cluster_config,
+			disk_size=disk_size
+		}
 	}
 
 	call merge.merge as merge {
 		input:
-		mother_vcf_gz=zipIndex.mother_vcf_gz,
-		mother_vcf_idx=zipIndex.mother_vcf_idx,
-		father_vcf_gz=zipIndex.father_vcf_gz,
-		father_vcf_idx=zipIndex.father_vcf_idx,
-		twins_vcf_gz=zipIndex.twins_vcf_gz,
-		twins_vcf_idx=zipIndex.twins_vcf_idx,
+		rename_mother_vcf_gz=VCFrename.rename_mother_vcf_gz,
+		rename_mother_vcf_idx=VCFrename.rename_mother_vcf_idx,
+		rename_father_vcf_gz=VCFrename.rename_father_vcf_gz,
+		rename_father_vcf_idx=VCFrename.rename_father_vcf_idx,
+		rename_twins_vcf_gz=VCFrename.rename_twins_vcf_gz,
+		rename_twins_vcf_idx=VCFrename.rename_twins_vcf_idx,
 		mapper_caller=mapper_caller,
 		cluster_config=cluster_config,
 		disk_size=disk_size