更新 'workflow.wdl'

workflow.wdl

@@ -9,7 +9,7 @@ workflow {{ project_name }} {
     String ref_fasta
     File ref_flat
     File bed_file
-    String center_at
+    String method
     File gc
     File tumor_bam
     File tumor_bam_bai
@@ -22,20 +22,20 @@ workflow {{ project_name }} {
     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{
@@ -45,7 +45,8 @@ workflow {{ project_name }} {
             fasta=ref_fasta,
             ref_flat=ref_flat,
             center_at=center_at,
-            #hrd=HRD.hrd,
+            hrd=HRD.hrd,
+            method=method,
             bed_file=bed_file,
             tumor_bam=tumor_bam,
             tumor_bam_index=tumor_bam_bai,