add annotate and faidx

defaults

 {
     "fasta": "GRCh38.d1.vd1.fa",
-    "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+    "faidx": "oss://pgx-reference-data/GRCh38.d1.vd1/",
     "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",

inputs

   "{{ project_name }}.tumor_bam": {{ tumor_bam | tojson }},
   "{{ 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 }}.faidx": "{{ faidx }}",
+  "{{ project_name }}.faidx": "{{ ref_flat }}",
   "{{ project_name }}.docker": "{{ docker }}",
   "{{ project_name }}.bed": "{{ bed }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",

tasks/access.wdl

 task access {
-	  File ref_dir
-	  String fasta
+	  File faidx
+	  File fasta
     String docker
     String cluster_config
     String disk_size
 
     command <<<
-        cnvkit.py access -s 5000 -o access-5kb-mappable.hg38.bed ${ref_dir}/${fasta}
+        cnvkit.py access -s 5000 -o access-5kb-mappable.hg38.bed ${fasta}
     >>>
 
     runtime {

tasks/batch.wdl

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

workflow.wdl

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