update

defaults

@@ -1,7 +1,7 @@
 {
   "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
   "fasta": "GRCh38.d1.vd1.fa",
-  "picard_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/picard:2.20.2",
+  "picard_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/picard:2.25.4",
   "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
   "disk_size": "200",
   "SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",

tasks/bed_to_interval_list.wdl

@@ -11,7 +11,7 @@ task bed_to_interval_list {
 	command <<<
 		set -o pipefail
 		set -e 
-       java -jar /usr/bin/picard/picard.jar BedToIntervalList \
+       java -jar /usr/picard/picard.jar BedToIntervalList \
        I=${bed} \
        O=${interval_list_name}.txt \
        SD=${reference_bed_dict}

tasks/reference_dict.wdl

@@ -10,8 +10,8 @@ task reference_dict {
 	command <<<
 		set -o pipefail
 		set -e 
-        java -jar /usr/bin/picard/picard.jar CreateSequenceDictionary \ 
-        R=${ref_dir}/${fasta}\ 
+        java -jar /usr/picard/picard.jar CreateSequenceDictionary \ 
+        R=${ref_dir}/${fasta} \ 
         O=reference_bed_dict.txt
 	>>>