I believe that the branch is defaulted to the branch that is set via the UI or by the repos REST API.

In your workflow I would think that you will need to call a REST api to change the branch of the repo, Then you would execute the notebook. For example, this may be a situation where you create a release branch and want to dynamically change the code that is executing. You may need to make a pull request as well but not certain.

Let me know if this helps. I can provide more detail.