Currently the feature to manually trigger a pipeline is not supported with the GitHub Apps integration. This feature request is for the trigger pipelines feature to be supported.

If you would like to move from the GItHub OAuth integration to the GitHub Apps integration but are having trouble doing so, please feel free to provide additional feedback for our product team here: https://docs.google.com/forms/d/e/1FAIpQLSfnYhFLjmZ0OP8goemexAvgHDPJqgHyDF1QiIl2HdPktTKvlQ/viewform