alter command in batch.wdl

tasks/batch.wdl

@@ -15,9 +15,8 @@ task batch {
     String cluster_config
     String disk_size
 
-    String command = if defined(ref_flat) && !defined(reference) then "--annotate ${ref_flat}" \
-    elif !defined(ref_flat) && defined(reference) then "--reference ${reference}" \
-    else "--annotate ${ref_flat} --reference ${reference}"
+    String --annotate = if defined(ref_flat) then "--annotate ${ref_flat}" else ""
+    String --reference = if defined(reference) then "--reference ${reference}" else ""
 
     command <<<
         set -o pipefail
@@ -32,7 +31,7 @@ task batch {
         mkdir results
         cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --targets ${bed} --method ${method} \
-        ${command} \
+        ${--annotate} ${--reference} \
         --fasta hg38.fa --access ${access_bed} \
         --output-reference ~/${sample_id}.reference.cnn \
         --output-dir ./results/ \