Update: varscan somatic annovar

tasks/somaticFilter.wdl

@@ -40,8 +40,8 @@ task somaticFilter {
   }
 
   output {
-		File varscan_snp_somatic_filter = "${sample}.VarScan.TN.Somatic.filter.vcf"
-    File varscan_snp_germline_filter = "${sample}.VarScan.TN.Germline.filter.vcf"
-		File varscan_snp_loh_filter = "${sample}.VarScan.TN.LOH.filter.vcf"
+		File varscan_somatic_filter = "${sample}.VarScan.TN.Somatic.filter.vcf"
+    File varscan_germline_filter = "${sample}.VarScan.TN.Germline.filter.vcf"
+		File varscan_loh_filter = "${sample}.VarScan.TN.LOH.filter.vcf"
   }
 }

workflow.wdl

@@ -371,40 +371,11 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
 
-    call annovar.annovar as snp_somatic_annovar {
+    call annovar.annovar as VarScan_annovar {
       input: 
       sample=sample_id,
-      vcf=somaticFilter.varscan_snp_somatic_filter,
-      database=database,
-      docker=annovar_docker,
-      cluster_config=cluster_config,
-      disk_size=disk_size
-    }
-    
-    call annovar.annovar as snp_loh_annovar {
-      input: 
-      sample=sample_id,
-      vcf=somaticFilter.varscan_snp_loh_filter,
-      database=database,
-      docker=annovar_docker,
-      cluster_config=cluster_config,
-      disk_size=disk_size
-    }
-    
-    call annovar.annovar as indel_somatic_annovar {
-      input: 
-      sample=sample_id,
-      vcf=somaticFilter.varscan_indel_somatic_filter,
-      database=database,
-      docker=annovar_docker,
-      cluster_config=cluster_config,
-      disk_size=disk_size
-    }
-    
-    call annovar.annovar as indel_loh_annovar {
-      input: 
-      sample=sample_id,
-      vcf=somaticFilter.varscan_indel_loh_filter,
+      vcf=somaticFilter.varscan_somatic_filter,
+      hg=hg,
       database=database,
       docker=annovar_docker,
       cluster_config=cluster_config,