By default, Aikido will scan the default branch in your repository for dependency and code issues. The default branch is usually main/master.
If you update the default branch, Aikido will pick up this change during it's nightly sync, so no changes are needed on Aikido's end.
In some cases, it might be interesting to scan another branch instead of the default branch. This could be the case if you are developing on another branch for an extended period of time. You can overwrite the branch being scanned on the repository detail page in Aikido by clicking the branch button at the top.
A modal will appear that will allow you to change the branch being scanned every night.