rtg bgzip stout

inputs

@@ -7,6 +7,7 @@
   "{{ project_name }}.zipIndex.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
   "{{ project_name }}.LCL6variantsNorm.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
+  "{{ project_name }}.mapper_caller": "{{ mapper_caller }}",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
   "{{ project_name }}.LCL7variantsNorm.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
   "{{ project_name }}.LCL5variantsNorm.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",

tasks/merge.wdl

@@ -5,16 +5,17 @@ task merge {
 	Array[File] father_vcf_idx
 	Array[File] twins_vcf_gz
 	Array[File] twins_vcf_idx
+	String mapper_caller
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-		rtg vcfmerge --force-merge-all --no-gzip -o LCL8.sister.consistent.merged.vcf ${sep=" " mother_vcf_gz}
+		rtg vcfmerge --force-merge-all --no-gzip -o LCL8.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " mother_vcf_gz}
 
-		rtg vcfmerge --force-merge-all --no-gzip -o LCL7.sister.consistent.merged.vcf ${sep=" " father_vcf_gz}
+		rtg vcfmerge --force-merge-all --no-gzip -o LCL7.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " father_vcf_gz}
 
-		rtg vcfmerge --force-merge-all --no-gzip -o Twins.sister.consistent.vcf ${sep=" " twins_vcf_gz}
+		rtg vcfmerge --force-merge-all --no-gzip -o Twins.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " twins_vcf_gz}
 	>>>
 
 	runtime {

tasks/zipIndex.wdl

@@ -2,19 +2,20 @@ task zipIndex {
 	File mother_vcf
 	File father_vcf
 	File twins_vcf
+	String family_name
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-		rtg bgzip ${mother_vcf} 
-		rtg index -f vcf ${mother_vcf}.gz
+		rtg bgzip ${mother_vcf} -c > ${family_name}.LCL8.vcf.gz
+		rtg index -f vcf ${family_name}.LCL8.vcf.gz
 
-		rtg bgzip ${father_vcf} 
-		rtg index -f vcf ${father_vcf}.gz
+		rtg bgzip ${father_vcf} -c > ${family_name}.LCL7.vcf.gz
+		rtg index -f vcf ${family_name}.LCL7.vcf.gz
 
-		rtg bgzip ${twins_vcf} 
-		rtg index -f vcf ${twins_vcf}.gz
+		rtg bgzip ${twins_vcf} -c > ${family_name}.twins.vcf.gz
+		rtg index -f vcf ${family_name}.twins.vcf.gz
 
 	>>>
 
@@ -25,11 +26,11 @@ task zipIndex {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File mother_vcf_gz = "${mother_vcf}.gz"
-		File father_vcf_gz = "${father_vcf}.gz"
-		File twins_vcf_gz = "${twins_vcf}.gz"
-		File mother_vcf_idx = "${mother_vcf}.gz.tbi"
-		File father_vcf_idx = "${father_vcf}.gz.tbi"
-		File twins_vcf_idx = "${twins_vcf}.gz.tbi"
+		File mother_vcf_gz = "${family_name}.LCL8.vcf.gz"
+		File father_vcf_gz = "${family_name}.LCL7.vcf.gz"
+		File twins_vcf_gz = "${family_name}.twins.vcf.gz"
+		File mother_vcf_idx = "${family_name}.LCL8.vcf.gz.tbi"
+		File father_vcf_idx = "${family_name}.LCL7.vcf.gz.tbi"
+		File twins_vcf_idx = "${family_name}.twins.vcf.gz.tbi"
 	}
 }

workflow.wdl

@@ -11,6 +11,7 @@ workflow {{ project_name }} {
 	String fasta
 	String cluster_config
 	String disk_size
+	String mapper_caller
 
 	scatter (sample in inputSamples){
 		call variantsNorm.variantsNorm as LCL5variantsNorm{
@@ -77,6 +78,7 @@ workflow {{ project_name }} {
 			mother_vcf=mendelian.mother_vcf,
 			father_vcf=mendelian.father_vcf,
 			twins_vcf=mendelian.twins_vcf,
+			family_name=sample[8],
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
@@ -90,6 +92,7 @@ workflow {{ project_name }} {
 		father_vcf_idx=zipIndex.father_vcf_idx,
 		twins_vcf_gz=zipIndex.twins_vcf_gz,
 		twins_vcf_idx=zipIndex.twins_vcf_idx,
+		mapper_caller=mapper_caller,
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}