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uclahs-cds / pipeline-call-NonCanonicalPeptide

Nextflow pipeline to call non-canonical peptides as custom databases for proteogenomic analysis
https://automatic-adventure-o4l96o9.pages.github.io/
GNU General Public License v2.0
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Autofix broken Confluence links #94

Closed nwiltsie closed 9 months ago

nwiltsie commented 1 year ago

This PR replaces links to the old Confluence wiki in all plain-text files in this repository. I manually created a table of replacement links and used a regex to find and replace them - it's very possible something was mangled in that process, so whoever reviews this should confirm each of the replacement links.

Old Link Replacement Link
https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=GitHub+Standards#GitHubStandards-Branchprotectionrule https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190380/GitHub+Standards#GitHubStandards-Branchprotectionrule
https://confluence.mednet.ucla.edu/display/BOUTROSLAB/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
https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Guidelines https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3187646/Code+Review+Guidelines

Closes #93