This plugin is letting me do everything I wanted. https://wiki.jenkins-ci.org/display/JENKINS/GitHub+Integration+Plugin
The plugin lets me trigger pipelines based on pull request triggers from github without imposing any conventions on files that needs to be present in the source trees. I then able to simply provide my pipeline contents using the standard pipeline feature wherein a custom file from an SCM repo different from the one that contains the actual code to be built can be configured. -- You received this message because you are subscribed to the Google Groups "Jenkins Users" group. To unsubscribe from this group and stop receiving emails from it, send an email to jenkinsci-users+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/jenkinsci-users/20161101105804.GA13170%40aa. For more options, visit https://groups.google.com/d/optout.