fix(CNVkit): hrd input

tasks/CNVkit.wdl

@@ -1,14 +1,15 @@
 task CNVkit {
 
   String sample
+  File ref_dir
+  String fasta
+  File ref_flat
+  File regions
+  File hrd
   File tumor_bam
   File tumor_bam_index
   File? normal_bam
   File? normal_bam_index
-  File regions
-  File ref_dir
-  String fasta
-  File ref_flat
   String docker
   String cluster_config
   String disk_size

workflow.wdl

@@ -292,22 +292,6 @@ workflow {{ project_name }} {
     disk_size=disk_size
   }
   
-  call CNVkit.CNVkit as CNVkit {
-    input:
-    sample=sample_id,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    regions=regions,
-    ref_flat=ref_flat,
-    normal_bam=normal_BQSR.recaled_bam,
-    normal_bam_index=normal_BQSR.recaled_bam_index,
-    tumor_bam=tumor_BQSR.recaled_bam,
-    tumor_bam_index=tumor_BQSR.recaled_bam_index,
-    docker=cnvkit_docker,
-    cluster_config=cluster_config,
-    disk_size=disk_size
-  }
-  
   call MSIsensor.MSIsensor as MSIsensor {
     input:
     fasta=fasta,
@@ -346,4 +330,21 @@ workflow {{ project_name }} {
     cluster_config=cluster_config,
     disk_size=disk_size
   }
+
+  call CNVkit.CNVkit as CNVkit {
+    input:
+    sample=sample_id,
+    fasta=fasta,
+    ref_dir=ref_dir,
+    regions=regions,
+    ref_flat=ref_flat,
+    normal_bam=normal_BQSR.recaled_bam,
+    normal_bam_index=normal_BQSR.recaled_bam_index,
+    tumor_bam=tumor_BQSR.recaled_bam,
+    tumor_bam_index=tumor_BQSR.recaled_bam_index,
+    hrd=HRD.hrd,
+    docker=cnvkit_docker,
+    cluster_config=cluster_config,
+    disk_size=disk_size
+  }
 }