Update 'tasks/bed_to_interval_list.wdl'

tasks/bed_to_interval_list.wdl

@@ -2,6 +2,8 @@ task bed_to_interval_list {
 
 	File reference_bed_dict
     File bed
+    File ref_dir
+	File fasta
 	String interval_list_name
 	String docker
 	String cluster_config
@@ -11,10 +13,14 @@ task bed_to_interval_list {
 	command <<<
 		set -o pipefail
 		set -e 
+       mkdir -p /cromwell_root/tmp
+       cp ${ref_dir}/${fasta} /cromwell_root/tmp/
+       cp ${reference_bed_dict} /cromwell_root/tmp/          
+                  
        java -jar /usr/picard/picard.jar BedToIntervalList \
        I=${bed} \
        O=${interval_list_name}.txt \
-       SD=${reference_bed_dict}
+       SD=/cromwell_root/tmp/${reference_bed_dict}
 	>>>
 
 	runtime {