From ebb6ddee5d4b7acc6b6f20708e60e0f60870e60c Mon Sep 17 00:00:00 2001 From: bshifaw Date: Wed, 23 May 2018 07:52:07 -0400 Subject: [PATCH] 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 --- mutect2.exome.inputs.json | 2 +- mutect2.wdl | 2 +- mutect2_nio.wdl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/mutect2.exome.inputs.json b/mutect2.exome.inputs.json index 60ed4e2..84341c3 100644 --- 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 index 1fa9c68..af28ebb 100644 --- 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 index 2e848c0..f98141d 100644 --- 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