These links to the old Confluence wiki are broken and should be updated:
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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 more information on running Nextflow pipelines. |
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> **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. |
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- [ ] 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). |
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- [ ] I have reviewed the [Nextflow pipeline standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=Nextflow+pipeline+standardization). |
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- [ ] 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]. |
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- [ ] 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#GitHubStandards-Branchprotectionrule) before opening this pull request. |