add --annotate and --faidx

defaults

     "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/cnvkit:0.9.7",
     "disk_size": "400",
     "cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
-    "bed": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed"
+    "bed": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",
+    "ref_flat": "oss://pgx-reference-data/GRCh38.d1.vd1/refFlat.txt"
 }

inputs

   "{{ project_name }}.tumor_bai": {{ tumor_bai | tojson }},
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
+  "{{ project_name }}.ref_dir": "{{ ref_flat }}",
   "{{ project_name }}.docker": "{{ docker }}",
   "{{ project_name }}.bed": "{{ bed }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",

tasks/batch.wdl

     File bed
     File ref_dir
     String fasta
+    File ref_flat
     File access_bed
     String docker
     String cluster_config
         
         mkdir results
         cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
-        --targets ${bed} \
+        --targets ${bed} --faidx --no-rebuild --annotate ${ref_flat} \
         --fasta ${ref_dir}/${fasta} --access ${access_bed} \
         --output-reference ${sample_id}.reference.cnn --output-dir /cromwell_root/tmp/cnvkit/results/ \
         --diagram --scatter

workflow.wdl

     File bed
 	File ref_dir
 	String fasta
+    File ref_flat
     String docker
     String cluster_config
     String disk_size
 
     call access.access as access {
         input: 
-        fasta=fasta,
-        ref_dir=ref_dir,
+        fasta = fasta,
+        ref_dir = ref_dir,
         docker = docker,
         cluster_config = cluster_config,
         disk_size = disk_size
     call batch.batch as batch {
         input: 
         sample_id = sample_id,
-        fasta=fasta,
-        ref_dir=ref_dir,
+        fasta = fasta,
+        ref_dir = ref_dir,
+        ref_flat = ref_flat,
         tumor_bam = tumor_bam,
         tumor_bai = tumor_bai,
         normal_bam = normal_bam,