Update: ANNOVAR

defaults

@@ -10,7 +10,7 @@
   "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
   "hg": "hg38",
-  "database": "oss://pgx-reference-data/annovar_hg38/",
+  "annovar_database": "oss://pgx-reference-data/annovar/",
   "germline_resource": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
   "germline_resource_tbi": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
   "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Padded.bed",

inputs

@@ -20,7 +20,7 @@
   "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.interval_padding": "{{ interval_padding }}",
   "{{ project_name }}.hg": "{{ hg }}",
-  "{{ project_name }}.database": "{{ database }}",
+  "{{ project_name }}.annovar_database": "{{ annovar_database }}",
   "{{ project_name }}.tnseq_pon": "{{ tnseq_pon }}",
   "{{ project_name }}.tnscope_pon": "{{ tnscope_pon }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",

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

@@ -35,7 +35,7 @@ workflow {{ project_name }} {
   File germline_resource
   File germline_resource_tbi
   String hg
-  File database
+  File annovar_database
   
   File? regions
   Int? interval_padding
@@ -255,7 +255,7 @@ workflow {{ project_name }} {
         input:
         vcf=TNseq.TNseq_vcf,
         hg=hg,
-        database=database,
+        annovar_database=annovar_database,
         docker=annovar_docker,
         cluster_config=cluster_config,
         disk_size=disk_size
@@ -294,7 +294,7 @@ workflow {{ project_name }} {
         input:
         vcf=TNscope.TNscope_vcf,
         hg=hg,
-        database=database,
+        annovar_database=annovar_database,
         docker=annovar_docker,
         cluster_config=cluster_config,
         disk_size=disk_size
@@ -347,7 +347,7 @@ workflow {{ project_name }} {
         input:
         vcf=somaticFilter.varscan_somatic_filter,
         hg=hg,
-        database=database,
+        annovar_database=annovar_database,
         docker=annovar_docker,
         cluster_config=cluster_config,
         disk_size=disk_size