Update: hg19 and hg38 is optional

README.md

@@ -1,15 +1,24 @@
-# README.md
+### ANNOVAR
+This APP developed for the annotation of VCF files.
 
-> Author: Yaqing Liu
->
-> Email: [yaqing.liu@outlook.com](mailto:yaqing.liu@outlook.com)
-> 
-> Last Updates: 09/04/2021
+The version can be set by changing the parameter `hg`. Note that the path to the database is also need to be modified.
+### Getting Started
 
-#### Requirements
+We recommend using choppy system and Aliyun OSS service. The command will look like this:
 
-- choppy
-- Ali-Cloud
-- Linux
+```
+# Activate the choppy environment
+$ open-choppy-env
 
-Annotated VCF files without index by ANNOVAR hg38 version.
+# Install the APP
+$ choppy install YaqingLiu/annovar [-f]
+
+# List the parameters
+$ choppy samples YaqingLiu/annovar-latest [--no-default]
+
+# Submit you task with the `samples.csv file` and `project name`
+$ choppy batch YaqingLiu/annovar-latest samples.csv -p Project [-l project:Label]
+
+# Query the status of all tasks in the project
+$ choppy query -L project:Label | grep "status"
+```

defaults

@@ -1,6 +1,7 @@
 {
-    "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"
+  "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
+  "database": "oss://pgx-reference-data/annovar_hg38/",
+  "hg": "hg38",
+  "disk_size": "200",
+  "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"
 }

inputs

@@ -1,6 +1,7 @@
 {
   "{{ project_name }}.vcf": "{{ vcf }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
+  "{{ project_name }}.hg": "{{ hg }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"

tasks/annovar.wdl

@@ -1,30 +1,31 @@
 task annovar {
-	
-	File vcf
-	String annotated_vcf = basename(vcf,".vcf")
-	File database
-	String docker
-	String cluster_config
-	String disk_size
+  
+  File vcf
+  String annotated_vcf = basename(vcf,".vcf")
+  String hg
+  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 $nt
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    /installations/annovar/table_annovar.pl ${vcf} ${database} -buildver ${hg} -hgvs -out ${annotated_vcf} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation 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 = "${annotated_vcf}.hg38_multianno.vcf"
-	}
+  output {
+    File avinput = "${annotated_vcf}.avinput"
+    File multianno_txt = "${annotated_vcf}.multianno.txt"
+    File multianno = "${annotated_vcf}.multianno.vcf"
+  }
 }

workflow.wdl

@@ -3,6 +3,7 @@ import "./tasks/annovar.wdl" as annovar
 workflow {{ project_name }} {
 	
 	File vcf
+  String hg
 	File database
 	String annovar_docker
 	String disk_size
@@ -11,6 +12,7 @@ workflow {{ project_name }} {
 	call annovar.annovar as annovar {
 		input: 
 		vcf=vcf,
+    hg=hg,
 		database=database,
 		docker=annovar_docker,
 		cluster_config=cluster_config,