first commit

inputs

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+{
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.disk_size": "50",
+  "{{ project_name }}.dbsnp_1000G_phase1": "1000G_phase1.snps.high_confidence.hg38.vcf.gz",
+  "{{ project_name }}.dbsnp_hapmap": "hapmap_3.3.hg38.vcf.gz",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.dbsnp_Mill": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
+  "{{ project_name }}.vcf_index": "{{ vcf_index }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+  "{{ project_name }}.dbsnp_1000G_omni": "1000G_omni2.5.hg38.vcf.gz",
+  "{{ project_name }}.vcf": "{{ vcf }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",
+  "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
+}

tasks/VQSR.wdl

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+task VQSR {
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	File vcf
+	File vcf_index
+	File ref_dir
+	String dbsnp
+	String dbsnp_Mill
+	String dbsnp_1000G_omni
+	String dbsnp_hapmap
+	String dbsnp_1000G_phase1
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+
+		resource_text="--resource ${dbsnp_1000G_phase1} \
+              --resource_param 1000G,known=false,training=true,truth=false,prior=10.0 "
+		resource_text="$resource_text --resource ${dbsnp_1000G_omni} \
+              --resource_param omni,known=false,training=true,truth=true,prior=12.0 "
+		resource_text="$resource_text --resource ${dbsnp} \
+              --resource_param dbsnp,known=true,training=false,truth=false,prior=2.0 "
+		resource_text="$resource_text --resource ${dbsnp_hapmap} \
+              --resource_param hapmap,known=false,training=true,truth=true,prior=15.0"
+
+        annotation_array="DP QD FS SOR MQ MQRankSum ReadPosRankSum"
+        for annotation in $annotation_array; do
+		  annotate_text="$annotate_text --annotation $annotation"
+		done
+
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo VarCal -v ${vcf} $resource_text $annotate_text --var_type SNP --plot_file ${sample}.vqsrSNP.hc.plotfile --tranches_file ${sample}.vqsrSNP.hc.tranches ${sample}.vqsrSNP.hc.recal
+  		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo ApplyVarCal -v ${vcf} --var_type SNP --tranches_file ${sample}.vqsrSNP.hc.tranches --sensitivity 99.0 --recal ${sample}.vqsrSNP.hc.recal ${sample}.vqsrSNP.hc.recaled.vcf.gz
+  		${SENTIEON_INSTALL_DIR}/bin/sentieon plot vqsr -o ${sample}.vqsrSNP.pdf ${sample}.vqsrSNP.hc.plotfile
+
+  		resource_text="$resource_text --resource ${dbsnp_Mill} \
+              --resource_param Mills,known=false,training=true,truth=true,prior=12.0 "
+		resource_text="$resource_text --resource ${dbsnp} \
+              --resource_param dbsnp,known=true,training=false,truth=false,prior=2.0 "
+
+        annotation_array="QD DP FS SOR MQ ReadPosRankSum"
+		annotate_text=""
+		for annotation in $annotation_array; do
+  		  annotate_text="$annotate_text --annotation $annotation"
+		done
+
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo VarCal -v ${vcf} $resource_text $annotate_text --var_type INDEL --plot_file ${sample}.vqsrINDEL.hc.plotfile --max_gaussians 4 --tranches_file ${sample}.vqsrINDEL.hc.tranches ${sample}.vqsrINDEL.hc.recal
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo ApplyVarCal -v ${sample}.vqsrSNP.hc.recaled.vcf.gz --var_type INDEL --recal ${sample}.vqsrINDEL.hc.recal --tranches_file ${sample}.vqsrINDEL.hc.tranches --sensitivity 99.0 ${sample}.vqsrSNPINDEL.hc.recaled.vcf.gz
+		${SENTIEON_INSTALL_DIR}/bin/sentieon plot vqsr -o ${sample}.vqsrINDEL.VQSR.pdf ${sample}.vqsrINDEL.hc.plotfile
+
+	>>>
+	
+	runtime {
+		dockerTag:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+	File filtered_vcf = "${sample}.vqsrSNPINDEL.hc.recaled.vcf.gz"
+	}
+}
+
+

workflow.wdl

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+import "./tasks/VQSR.wdl" as VQSR
+
+workflow {{ project_name }} {
+
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	File vcf
+	File vcf_index
+	File ref_dir
+	String dbsnp
+	String dbsnp_Mill
+	String dbsnp_1000G_omni
+	String dbsnp_hapmap
+	String dbsnp_1000G_phase1
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	call VQSR.VQSR as VQSR {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		vcf=vcf,
+		vcf_index=vcf_index,
+		ref_dir=ref_dir,
+		dbsnp=dbsnp,
+		dbsnp_Mill=dbsnp_Mill,
+		dbsnp_1000G_omni=dbsnp_1000G_omni,
+		dbsnp_hapmap=dbsnp_hapmap,
+		dbsnp_1000G_phase1=dbsnp_1000G_phase1,
+		sample=sample,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+
+	}
+