alter command in batch.wdl

tasks/batch.wdl

@@ -15,8 +15,8 @@ task batch {
     String cluster_config
     String disk_size
 
-    String --annotate = if defined(ref_flat) then "--annotate ${ref_flat}" else ""
-    String --reference = if defined(reference) then "--reference ${reference}" else ""
+    String annotate_opt = if defined(ref_flat) then "--annotate ${ref_flat}" else ""
+    String reference_opt = if defined(reference) then "--reference ${reference}" else ""
 
     command <<<
         set -o pipefail
@@ -31,7 +31,7 @@ task batch {
         mkdir results
         cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --targets ${bed} --method ${method} \
-        ${--annotate} ${--reference} \
+        ${annotate_opt} ${reference_opt} \
         --fasta hg38.fa --access ${access_bed} \
         --output-reference ~/${sample_id}.reference.cnn \
         --output-dir ./results/ \