debug

tasks/deduped_Metrics.wdl

@@ -1,7 +1,7 @@
 task deduped_Metrics {
 
     File ref_dir
-    File bed
+    File? bed
 	String SENTIEON_INSTALL_DIR
 	String sample
 	String fasta

tasks/qualimap.wdl

@@ -1,14 +1,12 @@
 task qualimap {
 	File bam
 	File bai
-	File bed
+	File? bed
 	String bamname = basename(bam,".bam")
 	String docker
 	String cluster_config
 	String disk_size
 
-	File? bed
-
 	command <<<
 		set -o pipefail
 		set -e