Unable to validate code scanning workflow: error: getWorkflow() failed

When I run my build it includes this step:

# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v3
with:
languages: ${{ matrix.language }}
source-root: source/my-app
queries: security-extended

I'm getting this warning:

> Initialize CodeQL
> Unable to validate code scanning workflow: error: getWorkflow() failed: Error: Expected to find a code scanning workflow file at /home/runner/work/My-Repo-Name/My-Repo-Name/.github/workflows/ci-build.yml, but no such file existed. This can happen if the currently running workflow checks out a branch that doesn't contain the corresponding workflow file.

But the repo isn't being checked out to the root of the directory, as explained in `source-root`. Is there any way of telling CodeQL to look in the subdirectory to find the workflow?