Dev (#30)


* updated docker to 4.1.4.1, updated mutect.wdl to 4.1.4.1 gatk release

GATK 4.1.4.0 Dev (#27)

* README.md

* Update to gatk4.1

* Updated forum links in Readme

* changed ref file VM path to google bucket path

* updated import link to git tag url

* updated to GATK4.1.1.0

* minor edits

* changed import to dev for pon

* updated filter bias variable

* updated filter bias variable

* updated output variable names, removed artifact_mode from normal-normal

* changed index to idx

* removed artifact_modes

* updated import to next release: 2.4.0

* specified gatk version in readme

* Added Funcotator note to readme

* Update to gatk4.1.2.0

* updated input variable for mutect2

* correctin to input vairalbe

* correction to output variable

* corrected variable name and simplified json

* renamed input json, removed optional variables from json, updated regular mutect2 wdl with wdl version 1, updated mutect_pon wdl with wdl version 1

* removed nio wdl

* minor update

* removed comments in json because later version of cromwell throws error, replaced oncotator in json variables with funcotator

* corrections to import url for pon wdl

* mutect2 WDL and pon WDL had inconsistent input names

* mutect2 WDL and pon WDL had inconsistent input names

* added standard_runtime to pon

* add runtime structs

* add runtime structs for mergevcf

* Update mutect2_pon.wdl

minor spacing edit

* cleaned up input variables

* Update README.md

Replaced firecloud link with terra

* updated docker to 4.1.4.0, updated import url to latest release

update output variable (#22)

Dev (#18)

* specified gatk version in readme

Dev (#16)

* README.md

* Update to gatk4.1

* Updated forum links in Readme

* changed ref file VM path to google bucket path

* updated import link to git tag url

Wdlupdate (#9)

* Update to gatk4.0.8.1 release

* added link to 'How to run workflow' document

Wdlupdate (#8)

* updated wdl to gatk4.0.5.0 release
* realignment_index_bundle variable to json

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

Wdlupdate (#1)

* updated wdl/json to gatk4.0.1.1 release, add info for Readme

First version of complete M2 workflow