first commit

inputs

+{
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
+  "{{ project_name }}.database": "oss://pgx-reference-data/annovar/",
+  "{{ project_name }}.vcf_file": "{{ vcf }}"
+}
+

tasks/annovar.wdl

+task annovar {
+
+	File vcf_file
+	File database
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		nt=$(nproc)
+		/installations/annovar/table_annovar.pl ${vcf_file} ${database} -buildver hg19 -out ${sample} -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20190305,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File avinput = "${sample}.avinput"
+		File multianno_txt = "${sample}.hg19_multianno.txt"
+		File multianno_vcf = "${sample}.hg19_multianno.vcf"
+
+	}
+}
+

workflow.wdl

+import "./tasks/annovar.wdl" as annovar
+
+workflow {{ project_name }} { 
+	File vcf_file
+	File database
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+	
+	call annovar.annovar as annovar {
+		input: 
+		vcf_file=vcf_file,
+		database=database,
+		sample=sample,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+
+}