Wdlupdate (#7)

* updated wdl/json to gatk4.0.1.1 release * Update mutect2.exome.inputs.json * Update mutect2.exome.inputs.json minor edits * add info for Readme * Update wdl to gatk4.0.1.2 Release * Update docker to gatk4.0.1.2 * added mutect2_pon.wdl, added Parameter descriptions to readme * Update mutect2_pon.inputs.json * Update mutect2.exome.inputs.json * updated mutect2.wdl to gatk4.0.2.0 * additional description for * Update to gatk4.0.4.0 , Addtion of NIO supported mutect2 version * updated oncotator docker default image
gatk-workflows · May 23, 2018 · ebb6dde · ebb6dde
1 parent 1c458a9
commit ebb6dde
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/mutect2.exome.inputs.json b/mutect2.exome.inputs.json
@@ -1,6 +1,6 @@
 {
   "##_COMMENT1": "Runtime",
-  "Mutect2.oncotator_docker": "broadinstitute/oncotator:1.9.6.1",
+  "##Mutect2.oncotator_docker": "(optional) String?",
   "Mutect2.gatk_docker": "broadinstitute/gatk:4.0.4.0",
 
   "##_COMMENT2": "Workflow options",

diff --git a/mutect2.wdl b/mutect2.wdl
@@ -112,7 +112,7 @@ workflow Mutect2 {
     String gatk_docker
     String basic_bash_docker = "ubuntu:16.04"
     String? oncotator_docker
-    String oncotator_docker_or_default = select_first([oncotator_docker, "broadinstitute/oncotator:1.9.8.0"])
+    String oncotator_docker_or_default = select_first([oncotator_docker, "broadinstitute/oncotator:1.9.9.0"])
     Boolean? filter_oncotator_maf
     Boolean filter_oncotator_maf_or_default = select_first([filter_oncotator_maf, true])
     String? oncotator_extra_args

diff --git a/mutect2_nio.wdl b/mutect2_nio.wdl
@@ -112,7 +112,7 @@ workflow Mutect2 {
     String gatk_docker
     String basic_bash_docker = "ubuntu:16.04"
     String? oncotator_docker
-    String oncotator_docker_or_default = select_first([oncotator_docker, "broadinstitute/oncotator:1.9.8.0"])
+    String oncotator_docker_or_default = select_first([oncotator_docker, "broadinstitute/oncotator:1.9.9.0"])
     Boolean? filter_oncotator_maf
     Boolean filter_oncotator_maf_or_default = select_first([filter_oncotator_maf, true])
     String? oncotator_extra_args