aa

inputs

@@ -1,13 +1,16 @@
 {
   "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript/benchmark_calls_v3.0/",
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
-  "{{ project_name }}.gvcf": "{{ gvcf }}",
+  "{{ project_name }}.gvcf": "{{ gvcf_list.split(";") | tojson }}",
+  "{{ project_name }}.gvcf_idx": "{{ gvcf_idx_list.split(";") | tojson }}",
   "{{ project_name }}.disk_size": "500",
   "{{ 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",
+  "{{ project_name }}.SENTIEONdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
   "{{ project_name }}.MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "{{ 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/qualimap.wdl

@@ -10,7 +10,7 @@ task qualimap {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G 
+		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=60G 
 		tar -zcvf ${bamname}_qualimap.zip ${bamname}
 	>>>
 

tasks/quartet_mendelian.wdl

@@ -8,7 +8,7 @@ task quartet_mendelian {
 	command <<<
 		for i in ${sep=" " project_mendelian_summary}
 		do
-		  cat $i |  sed -n '2,2p' >> mendelian.summary
+		  cat $i |  sed -n '2,3p' >> mendelian.summary
 		done
 		sed '1i\Family\tReproducibility_D5_D6\tMendelian_Concordance_Quartet' mendelian.summary > ${project}.mendelian.txt
 

workflow.wdl

@@ -1,4 +1,5 @@
 import "./tasks/split_gvcf_files.wdl" as split_gvcf_files
+import "./tasks/GVCFtyper.wdl" as GVCFtyper
 import "./tasks/benchmark.wdl" as benchmark
 import "./tasks/mendelian.wdl" as mendelian
 import "./tasks/merge_mendelian.wdl" as merge_mendelian
@@ -9,11 +10,15 @@ import "./tasks/merge_family.wdl" as merge_family
 
 workflow {{ project_name }} {
 
-	File gvcf
+	Array[File] gvcf
+	Array[File] gvcf_idx
 
 	String BENCHMARKdocker
 	String MENDELIANdocker
 	String DIYdocker
+	String SENTIEON_INSTALL_DIR
+	String SENTIEONdocker
+
 
 	String fasta
 	File ref_dir
@@ -26,6 +31,18 @@ workflow {{ project_name }} {
 	String BIGcluster_config
 	String SMALLcluster_config
 
+	call GVCFtyper.GVCFtyper as GVCFtyper {
+		input:
+		ref_dir=ref_dir,
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		vcf=gvcf,
+		vcf_idx=gvcf_idx,
+		project=project,
+		docker=SENTIEONdocker,
+		cluster_config=BIGcluster_config,
+		disk_size=disk_size
+	}
 
 	call split_gvcf_files.split_gvcf_files as split_gvcf_files {
 		input: