Update

defaults

@@ -1,6 +1,6 @@
 {
   "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2019.10",
-  "database": "oss://pgx-reference-data/annovar_hg38/",
+  "annovar_database": "oss://pgx-reference-data/annovar/",
   "hg": "hg38",
   "disk_size": "200",
   "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"

inputs

@@ -2,7 +2,7 @@
   "{{ project_name }}.vcf": "{{ vcf }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
   "{{ project_name }}.hg": "{{ hg }}",
-  "{{ project_name }}.database": "{{ database }}",
+  "{{ project_name }}.annovar_database": "{{ annovar_database }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"
 }

tasks/annovar.wdl

@@ -1,9 +1,9 @@
 task annovar {
 
   File vcf
-  String annotated_vcf = basename(vcf,".vcf")
+  String basename = basename(vcf,".vcf")
   String hg
-  File database
+  File annovar_database
   String docker
   String cluster_config
   String disk_size
@@ -13,7 +13,14 @@ task annovar {
     set -o pipefail
     set -e
     nt=$(nproc)
-    /installations/annovar/table_annovar.pl ${vcf} ${database} -buildver ${hg} -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
+
+    if [ ${hg} == "hg38" ]; then
+    /installations/annovar/table_annovar.pl ${vcf} ${annovar_database} -buildver ${hg} -out ${basename} -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
+    fi
+
+    if [ ${hg} == "hg19" ]; then
+    /installations/annovar/table_annovar.pl ${vcf} ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,snp138,cosmic78,intervar_20170202,popfreq_all_20150413,clinvar_20190305 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+    fi
   >>>
   
   runtime {
@@ -24,8 +31,8 @@ task annovar {
   }
 
   output {
-    File avinput = "${annotated_vcf}.avinput"
-    File multianno_txt = "${annotated_vcf}.${hg}_multianno.txt"
-    File multianno = "${annotated_vcf}.${hg}_multianno.vcf"
+    File avinput = "${basename}.avinput"
+    File multianno_txt = "${basename}.${hg}_multianno.txt"
+    File multianno_vcf = "${basename}.${hg}_multianno.vcf"
   }
 }

workflow.wdl

@@ -1,21 +1,21 @@
 import "./tasks/annovar.wdl" as annovar
 
 workflow {{ project_name }} {
-	
-	File vcf
+  
+  File vcf
   String hg
-	File database
-	String annovar_docker
-	String disk_size
-	String cluster_config
+  File annovar_database
+  String annovar_docker
+  String disk_size
+  String cluster_config
 
-	call annovar.annovar as annovar {
-		input: 
-		vcf=vcf,
+  call annovar.annovar as annovar {
+    input: 
+    vcf=vcf,
     hg=hg,
-		database=database,
-		docker=annovar_docker,
-		cluster_config=cluster_config,
-		disk_size=disk_size
-	}
+    annovar_database=annovar_database,
+    docker=annovar_docker,
+    cluster_config=cluster_config,
+    disk_size=disk_size
+  }
 }