fix(CNVkit): ref_flat

inputs

@@ -31,6 +31,7 @@
   "{{ project_name }}.annotsv_database": "{{ annotsv_database }}",
   "{{ project_name }}.gc": "{{ gc }}",
   "{{ project_name }}.baseline": "{{ baseline }}",
+  "{{ project_name }}.ref_flat": "{{ ref_flat }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"
 }

workflow.wdl

@@ -48,6 +48,7 @@ workflow {{ project_name }} {
   File annotsv_database
   File gc
   File baseline
+  File ref_flat
   
   File? regions
   Int? interval_padding