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

Author: bshifaw

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",

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

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