更新 'workflow.wdl'

workflow.wdl

     String docker_annotsv
     String docker_sequenza
 
-    call HRD.HRD as HRD{
-        input:
-            sample=sample_id,
-            fasta=ref_fasta,
-            ref_dir=ref_fasta_dir,
-            gc=gc,
-            normal_bam=normal_bam,
-            normal_bam_index=normal_bam_bai,
-            tumor_bam=tumor_bam,
-            tumor_bam_index=tumor_bam_bai,
-            docker=docker_sequenza,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-    }
+    #call HRD.HRD as HRD{
+    #    input:
+    #        sample=sample_id,
+    #        fasta=ref_fasta,
+    #        ref_dir=ref_fasta_dir,
+    #        gc=gc,
+    #        normal_bam=normal_bam,
+    #        normal_bam_index=normal_bam_bai,
+    #        tumor_bam=tumor_bam,
+    #        tumor_bam_index=tumor_bam_bai,
+    #        docker=docker_sequenza,
+    #        cluster_config=cluster_config,
+    #        disk_size=disk_size
+    #}
 
 
     call cnvkit.cnvkit as cnvkit{
             ref_dir=ref_fasta_cnvkit,
             fasta=ref_fasta,
             ref_flat=ref_flat,
-            hrd=HRD.hrd,
+            #hrd=HRD.hrd,
             tumor_bam=tumor_bam,
             tumor_bam_index=tumor_bam_bai,
             normal_bam=normal_bam,
             disk_size=disk_size
     }
 
-	call AnnotSV.AnnotSV as cnvkit_AnnotSV{
-		input:
-                sample=sample_id,
-                somatic_vcf=cnvkit.cnv_bed,
-                annotsv_database=annotsv_database,
-                docker=docker_annotsv,
-                cluster_config=cluster_config,
-                disk_size=disk_size
+	#call AnnotSV.AnnotSV as cnvkit_AnnotSV{
+	#	input:
+    #            sample=sample_id,
+    #            somatic_vcf=cnvkit.cnv_bed,
+    #           annotsv_database=annotsv_database,
+    #            docker=docker_annotsv,
+    #            cluster_config=cluster_config,
+    #            disk_size=disk_size
 		
-}
+#}
 
 
 }