first commit

README.md

+# README.md
+
+> Author: Yaqing Liu
+>
+> Email: [yaqing.liu@outlook.com](mailto:yaqing.liu@outlook.com)
+> 
+> Last Updates: 09/04/2021
+
+#### Requirements
+
+- choppy
+- Ali-Cloud
+- Linux
+
+Annotated VCF files without index by ANNOVAR hg38 version.

defaults

+{
+    "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
+    "database": "oss://pgx-reference-data/annovar_hg38/",
+    "disk_size": "200",
+    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"
+}

inputs

+{
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.vcf": "{{ vcf }}",
+  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
+  "{{ project_name }}.database": "{{ database }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/annovar.wdl

+task annovar {
+	
+	File vcf
+	String annotated_vcf = basename(vcf,".vcf")
+	File database
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		/installations/annovar/table_annovar.pl ${vcf} ${database} -buildver hg38 -out ${annotated_vcf} -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+	>>>
+	
+	runtime {
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File avinput = "${annotated_vcf}.avinput"
+		File multianno_txt = "${annotated_vcf}.hg38_multianno.txt"
+		File multianno = "${annotated_vcf}.hg38_multianno.vcf"
+	}
+}

workflow.wdl

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