Update: Add ANOVVAR

tasks/annovar.wdl

@@ -0,0 +1,31 @@
+task annovar {
+
+  String sample
+  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

@@ -1,5 +1,6 @@
 import "./tasks/TNseq.wdl" as TNseq
 import "./tasks/TNscope.wdl" as TNscope
+import "./tasks/annovar.wdl" as annovar
 
 workflow {{ project_name }} {
     
@@ -69,6 +70,16 @@ workflow {{ project_name }} {
             cluster_config=cluster_config,
             disk_size=disk_size
         }
+
+        call annovar.annovar as TNseq_annovar {
+        input:
+            sample=sample_id,
+            vcf=TNseq.TNseq_vcf,
+            database=database,
+            docker=annovar_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
     }
 
     if (tnscope) {
@@ -96,5 +107,15 @@ workflow {{ project_name }} {
             cluster_config=cluster_config,
             disk_size=disk_size
         }
+
+        call annovar.annovar as TNscope_annovar {
+            input:
+            sample=sample_id,
+            vcf=TNscope.TNscope_vcf,
+            database=database,
+            docker=annovar_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
     }
 }