Resolve broken Confluence links (#118)

.github/PULL_REQUEST_TEMPLATE.md

@@ -20,14 +20,13 @@
 # Checklist
 <!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
 
-- [ ] I have read the [code review guidelines](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Best+Practice+on+GitHub+-+Check+List).
+- [ ] I have read the [code review guidelines](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3187646/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189956/Code+Review+Best+Practice+on+GitHub+-+Check+List).
 
-- [ ] I have reviewed the [Nextflow pipeline standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=Nextflow+pipeline+standardization).
+- [ ] I have reviewed the [Nextflow pipeline standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3193890/Nextflow+pipeline+standardization).
 
-- [ ] The name of the branch is meaningful and well formatted following the [standards](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Best+Practice+on+GitHub+-+Check+List), using \[AD_username (or 5 letters of AD if AD is too long)]-\[brief_description_of_branch].
+- [ ] The name of the branch is meaningful and well formatted following the [standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189956/Code+Review+Best+Practice+on+GitHub+-+Check+List), using \[AD_username (or 5 letters of AD if AD is too long)]-\[brief_description_of_branch].
 
-- [ ] I have set up or verified the branch protection rule following the [github standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=GitHub+Standards#GitHubStanda
-rds-Branchprotectionrule) before opening this pull request.
+- [ ] I have set up or verified the branch protection rule following the [github standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190380/GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request.
 
 - [ ] I have added my name to the contributors listings in the ``manifest`` block in the `nextflow.config` as part of this pull request, am listed
 already, or do not wish to be listed. (*This acknowledgement is optional.*)

README.md

@@ -19,7 +19,7 @@ This pipeline is developed using Nextflow, docker and can run either on a single
 
 ## How to Run:
 
-Below is a summary of how to run the pipeline.  See [here](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=How+to+run+a+nextflow+pipeline) for full instructions.
+Below is a summary of how to run the pipeline.  See [here](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3197004/How+to+run+a+nextflow+pipeline) for full instructions.
 
 Pipelines should be run **WITH A SINGLE SAMPLE AT A TIME**. Otherwise resource allocation and Nextflow errors could cause the pipeline to fail.
 
@@ -61,7 +61,7 @@ In the above command, the partition type can be changed based on the size of the
 
 \* Manta SV calling wouldn't work on an F2 node due to incompatible resources. In order to test the pipeline for tasks not relevant to Manta, please set `algorithm = ['delly']` in the sample specific [config](config/template.config) file.
 
-> **Note**: Because this pipeline uses an image stored in the GitHub Container Registry, you must follow the steps listed in the [Docker Introduction](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+Introduction#DockerIntroduction-GitHubContainerRegistryGitHubContainerRegistry|Setup) on Confluence to set up a PAT for your GitHub account and log into the registry on the cluster before running this pipeline.
+> **Note**: Because this pipeline uses an image stored in the GitHub Container Registry, you must follow the steps listed in the [Docker Introduction](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190419/Docker+Introduction#DockerIntroduction-HowtosetupPATandlogintotheregistryHowtosetupPATandlogintotheregistry) on Confluence to set up a PAT for your GitHub account and log into the registry on the cluster before running this pipeline.
 
 ## Flow Diagram: