first commit

README.md

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+clean NVG data

inputs

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+{
+  "{{ project_name }}.disk_size": "50",
+  "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01",
+  "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.xlarge img-ubuntu-vpc",
+  "{{ project_name }}.gzvcf": "{{ gzvcf }}",
+  "{{ project_name }}.sample": "{{ sample }}"
+}

tasks/index.wdl

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+task index {
+	File snv_gzvcf
+	File indel_gzvcf
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		mv ${snv_gzvcf} ./${sample}.snv.vcf.gz
+		mv ${indel_gzvcf} ./${sample.indel.vcf.gz}
+		rtg index -f vcf ${sample}.snv.vcf.gz
+		rtg index -f vcf ${sample}.indel.vcf.gz
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File snv_gzvcf_index = "${sample}.snv.vcf.gz.tbi"
+		File indel_gzvcf_index = "${sample}.indel.vcf.gz.tbi"
+	}
+}

tasks/merge.wdl

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+task merge {
+	File snv_gzvcf
+	File indel_gzvcf
+	File snv_gzvcf_index
+	File indel_gzvcf_index
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		bcftools concat -a ${snv_gzvcf} ${indel_gzvcf} > ${sample}.vcf
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File vcf = "${sample}.vcf"
+	}
+}

workflow.wdl

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+import "./tasks/index.wdl" as index
+import "./tasks/merge.wdl" as merge
+
+workflow {{ project_name }} {
+	File snv_gzvcf
+	File indel_gzvcf
+	String sample
+	String cluster_config
+	String disk_size
+
+	call index.index as index {
+		input:
+		snv_gzvcf=snv_gzvcf,
+		indel_gzvcf=indel_gzvcf,
+		sample=sample,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+
+	call merge.merge as merge {
+		input:
+		snv_gzvcf=snv_gzvcf,
+		indel_gzvcf=indel_gzvcf,
+		snv_gzvcf_index=index.snv_gzvcf_index,
+		indel_gzvcf_index=index.indel_gzvcf_index,
+		sample=sample,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+
+}