Add annovar parameter

defaults

@@ -25,5 +25,6 @@
   "haplotyper": false,
   "tnseq": false,
   "tnscope": false,
-  "varscan": false
+  "varscan": false,
+  "annovar": false
 }

inputs

@@ -28,5 +28,6 @@
   "{{ project_name }}.haplotyper": {{ haplotyper | tojson }},
   "{{ project_name }}.tnseq": {{ tnseq | tojson }},
   "{{ project_name }}.tnscope": {{ tnscope | tojson }},
-  "{{ project_name }}.varscan": {{ varscan | tojson }}
+  "{{ project_name }}.varscan": {{ varscan | tojson }},
+  "{{ project_name }}.annovar": {{ annovar | tojson }}
 }

tasks/annovar.wdl

@@ -1,4 +1,4 @@
-task annovar {
+task ANNOVAR {
 
   File vcf
   String annotated_vcf = basename(vcf,".vcf")

workflow.wdl

@@ -9,7 +9,7 @@ import "./tasks/TNscope.wdl" as TNscope
 import "./tasks/somatic.wdl" as somatic
 import "./tasks/processSomatic.wdl" as processSomatic
 import "./tasks/somaticFilter.wdl" as somaticFilter
-import "./tasks/annovar.wdl" as annovar
+import "./tasks/ANNOVAR.wdl" as ANNOVAR
 
 
 workflow {{ project_name }} {
@@ -50,6 +50,8 @@ workflow {{ project_name }} {
   Boolean tnscope
   Boolean varscan
 
+  Boolean annovar
+
   if (tumor_fastq_1!= "") {
     call mapping.mapping as tumor_mapping {
       input: 
@@ -248,14 +250,16 @@ workflow {{ project_name }} {
       disk_size=disk_size
     }
 
-    call annovar.annovar as TNseq_annovar {
-      input:
-      vcf=TNseq.TNseq_vcf,
-      hg=hg,
-      database=database,
-      docker=annovar_docker,
-      cluster_config=cluster_config,
-      disk_size=disk_size
+    if (annovar) {
+      call ANNOVAR.ANNOVAR as TNseq_annovar {
+        input:
+        vcf=TNseq.TNseq_vcf,
+        hg=hg,
+        database=database,
+        docker=annovar_docker,
+        cluster_config=cluster_config,
+        disk_size=disk_size
+      }
     }
   }
 
@@ -285,14 +289,16 @@ workflow {{ project_name }} {
       disk_size=disk_size
     }
     
-    call annovar.annovar as TNscope_annovar {
-      input:
-      vcf=TNscope.TNscope_vcf,
-      hg=hg,
-      database=database,
-      docker=annovar_docker,
-      cluster_config=cluster_config,
-      disk_size=disk_size
+    if (annovar) {
+      call ANNOVAR.ANNOVAR as TNscope_annovar {
+        input:
+        vcf=TNscope.TNscope_vcf,
+        hg=hg,
+        database=database,
+        docker=annovar_docker,
+        cluster_config=cluster_config,
+        disk_size=disk_size
+      }
     }
   }
 
@@ -336,14 +342,16 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    call annovar.annovar as VarScan_annovar {
-      input:
-      vcf=somaticFilter.varscan_somatic_filter,
-      hg=hg,
-      database=database,
-      docker=annovar_docker,
-      cluster_config=cluster_config,
-      disk_size=disk_size
+    if (annovar) {
+      call ANNOVAR.ANNOVAR as VarScan_annovar {
+        input:
+        vcf=somaticFilter.varscan_somatic_filter,
+        hg=hg,
+        database=database,
+        docker=annovar_docker,
+        cluster_config=cluster_config,
+        disk_size=disk_size
+      }
     }
   }
 }