A pre-existing CodeQL workflow is disabled
If you see two workflows named CodeQL, one workflow may be a pre-existing CodeQL workflow file which has been disabled by default setup. Default setup overrides existing CodeQL setups by disabling any existing CodeQL workflows, and blocking any CodeQL analysis API uploads. This behavior stops you using GitHub Actions minutes to run workflows for CodeQL advanced setup when only the results from default setup will be used. For more information about switching between advanced and default setups, see "Troubleshooting your advanced setup for CodeQL."
Optionally, if you are certain you no longer need the pre-existing workflow file, you can delete the file from your repository. For more information, see "Deleting files in a repository."
In some cases, your repository may use multiple code scanning configurations. These configurations can generate duplicate alerts. Additionally, stale configurations that no longer run will display outdated alert statuses, and the stale alerts will stay open indefinitely. To avoid outdated alerts, you should remove stale code scanning configurations from a branch. For more information on multiple configurations and deleting stale configurations, see "About code scanning alerts" and "Managing code scanning alerts for your repository."
Enabling the default setup takes too long
If enabling your default setup is taking too long, try canceling the workflow run and restarting the setup. To restart your setup, navigate to the main page of your repository, then click Actions. Click the CodeQL workflow run that's in progress, then click Cancel workflow. Once appears beside the workflow run name, navigate back to the Code security and analysis settings and re-enable the default setup. If the default setup continues to stall, please contact GitHub Support or try enabling the advanced setup. For more information, see "Configuring code scanning for a repository."
Unclear what triggered a workflow run
If you don't know what triggered an analysis, look at the log for the last scan. For more information on viewing your last scan's log, see "Viewing code scanning logs."