更新 'workflow.wdl'

workflow.wdl

@@ -1,4 +1,6 @@
 import "./tasks/stralka.wdl" as stralka
+import "./tasks/bcftools_concat.wdl" as bcftools_concat
+import "/tasks/annovar.wdl" as annovar
 
 workflow {{ project_name }} {
     File tumour_bam
@@ -10,11 +12,14 @@ workflow {{ project_name }} {
     String sample_id
     File? manta_indel_vcf
     File? manta_indel_vcf_index
+    File annovar_database
     
     # excute env
     String docker_stralka
     String cluster_config
     String disk_size
+    String docker_bcftools
+    String docker_annovar
 
     call stralka.strelka_calling as stralka{
         input:
@@ -30,4 +35,28 @@ workflow {{ project_name }} {
             disk_size=disk_size
     }
 
+    call bcftools_concat.bcftools as bcftools{
+        input:
+            ref_dir=ref_dir,
+            fasta=ref_fasta,
+            vcf_indels=stralka.indel_vcf,
+            vcf_snvs=stralka.snv_vcf,
+            sample_id=sample_id,
+            docker=docker_bcftools,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+
+    }
+
+    call annovar.ANNOVAR as ANNOVAR{
+        input:
+              vcf=bcftools.concat_vcf,
+              annovar_database=annovar_database,
+              docker=docker_annovar,
+              cluster_config=cluster_config,
+              disk_size=disk_size
+    }
+
+
+
 }