Merge pull request #2 from gatk-workflows/dev

Updated doc links in the Readme

README.md

@@ -31,14 +31,14 @@ Indel discovery in human whole-genome sequencing data.
   - Successfully tested on v47
   - Does not work on versions < v23 due to output syntax
 
-### Important Note :
-- The provided JSON is meant to be a ready to use example JSON template of the workflow. It is the user’s responsibility to correctly set the reference and resource input variables using the [GATK Tool and Tutorial Documentations](https://software.broadinstitute.org/gatk/documentation/).
-- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://software.broadinstitute.org/gatk/download/bundle).
+### Important Notes :
+- The provided JSON is meant to be a ready to use example JSON template of the workflow. It is the user’s responsibility to correctly set the reference and resource input variables using the [GATK Tool and Tutorial Documentations](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591).
+- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://gatk.broadinstitute.org/hc/en-us/articles/360036212652).
 - Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
 - For help running workflows on the Google Cloud Platform or locally please
-view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://software.broadinstitute.org/gatk/documentation/article?id=12521).
-- The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : [GATK](https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team/) , [FireCloud](https://gatkforums.broadinstitute.org/firecloud/categories/ask-the-firecloud-team) or [Terra](https://broadinstitute.zendesk.com/hc/en-us/community/topics/360000500432-General-Discussion) , [WDL/Cromwell](https://gatkforums.broadinstitute.org/wdl/categories/ask-the-wdl-team).
-- Please visit the [User Guide](https://software.broadinstitute.org/gatk/documentation/) site for further documentation on our workflows and tools.
+view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://gatk.broadinstitute.org/hc/en-us/articles/360035530952).
+- The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : [GATK](https://gatk.broadinstitute.org/hc/en-us/community/topics) and  [Terra](https://broadinstitute.zendesk.com/hc/en-us/community/topics/360000500432-General-Discussion).
+- Please visit the [User Guide](https://gatk.broadinstitute.org/hc/en-us) site for further documentation on our workflows and tools.
 
 ### LICENSING :
 Copyright Broad Institute, 2019 | BSD-3