更新 'workflow.wdl'

workflow.wdl

@@ -24,7 +24,7 @@ workflow {{ project_name }} {
     String docker_annotsv
     String docker_sequenza
     if (defined(inputBams)) {
-	    call cnvkit_multi.cnvkit_multi as cnvkit{
+	    call cnvkit_multi.cnvkit_multi as cnvkit_multi{
             input:
                 sample_id=sample_id,
                 ref_dir=ref_fasta_cnvkit,
@@ -40,6 +40,18 @@ workflow {{ project_name }} {
                 cluster_config=cluster_config,
                 disk_size=disk_size
        }
+       
+       	call AnnotSV.AnnotSV as cnvkit_AnnotSV{
+		input:
+               sample=sample_id,
+               somatic_vcf=cnvkit_multi.cnv_bed,
+               annotsv_database=annotsv_database,
+               docker=docker_annotsv,
+               cluster_config=cluster_config,
+               disk_size=disk_size
+		
+   		}
+   
     } 
     if (!defined(inputBams)) {
         call cnvkit.cnvkit as cnvkit{
@@ -58,10 +70,8 @@ workflow {{ project_name }} {
                 cluster_config=cluster_config,
                 disk_size=disk_size
         }
-    }
-
 
-	call AnnotSV.AnnotSV as cnvkit_AnnotSV{
+        call AnnotSV.AnnotSV as cnvkit_AnnotSV{
 		input:
                sample=sample_id,
                somatic_vcf=cnvkit.cnv_bed,
@@ -70,7 +80,11 @@ workflow {{ project_name }} {
                cluster_config=cluster_config,
                disk_size=disk_size
 		
-   }
+      }
+    }
+
+
+
 
 
 }