delete joint variant calling

inputs

@@ -7,7 +7,6 @@
   "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
   "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
-  "{{ project_name }}.quartet_sample": "{{ quartet_sample }}",
   "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
   "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",
   "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"

tasks/gVCF_calling.wdl

@@ -0,0 +1,36 @@
+task gVCF_calling {
+	
+	File bam
+	File bai
+	File ref_dir
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	String sample
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${bam} -q ${sample}_RECAL_DATA_TABLE --algo Haplotyper --emit_mode gvcf \ ${sample}_VARIANT_GVCF
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File consensus_bed = "${sample}.27consensus.bed"
+		File filtered_bed = "${sample}.filtered.bed"
+	}
+}
+
+
+
+

tasks/joint_variant_calling.wdl

@@ -0,0 +1,31 @@
+task joint_variant_calling {
+	
+	File merged_bed
+	String sample
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+		
+		sentieon driver -r REFERENCE --algo GVCFtyper -v s1_VARIANT_GVCF \ -v s2_VARIANT_GVCF -v s3_VARIANT_GVCF VARIANT_VCF
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File consensus_bed = "${sample}.27consensus.bed"
+		File filtered_bed = "${sample}.filtered.bed"
+	}
+}
+
+
+
+

workflow.wdl

@@ -5,7 +5,6 @@ import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
 import "./tasks/Realigner.wdl" as Realigner
 import "./tasks/BQSR.wdl" as BQSR
 import "./tasks/Haplotyper.wdl" as Haplotyper
-import "./tasks/GVCFtyper.wdl" as GVCFtyper
 
 
 
@@ -15,7 +14,6 @@ workflow {{ project_name }} {
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
 
 	String SENTIEON_INSTALL_DIR
-	String quartet_sample
 	String docker
 	
 	String fasta
@@ -123,16 +121,4 @@ workflow {{ project_name }} {
 			cluster_config=cluster_config
 		}
 	}
-	call GVCFtyper.GVCFtyper as GVCFtyper {
-		input:
-		ref_dir=ref_dir,
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		fasta=fasta,
-		vcf=Haplotyper.vcf,
-		vcf_idx=Haplotyper.vcf_idx,
-		quartet_sample=quartet_sample,
-		docker=docker,
-		cluster_config=cluster_config,
-		disk_size=disk_size
-	}
 }