test

tasks/batch.wdl

@@ -15,8 +15,8 @@ task batch {
     String cluster_config
     String disk_size
 
-    String annotate_opt = if defined(ref_flat) then "--annotate ${ref_flat}" else ""
-    String reference_opt = if defined(reference) then "--reference ${reference}" else ""
+    String annotate_opt = if (ref_flat != "") then "--annotate ${ref_flat}" else ""
+    String reference_opt = if (reference != "") then "--reference ${reference}" else ""
 
     command <<<
         set -o pipefail