To create or modify a code scanning workflow file (typically under .github/workflows/codeql-analysis.yml), you must have Write access to the repository.

Write permission allows you to commit the workflow file, which is required to run or configure code scanning using GitHub Actions.

When integrating CodeQL outside of GitHub Actions (e.g., in Jenkins, CircleCI):

Install the CLI : Needed to run CodeQL commands.

Analyze code : Perform the CodeQL analysis on your project with the CLI.

Upload scan results : Export the results in SARIF format and use GitHub’s API to upload them to your repo’s security tab.

You don’t need to write custom queries unless extending functionality. “Processing alerts” happens after GitHub receives the results.

The correct place to look is the SECURITY.md file. This file provides contributors and security researchers with instructions on how to responsibly report vulnerabilities. It may include contact methods, preferred communication channels (e.g., security team email), and disclosure guidelines.

This file is considered a GitHub best practice and, when present, activates a “Report a vulnerability” button in the repository’s Security tab.

If an alert is raised on a pull request dependency , best practice is to update the dependency to a secure version before merging the PR. This prevents the vulnerable version from entering the main codebase.

Merging or deploying the PR without fixing the issue exposes your production environment to known risks.

When dealing with a data flow issue in a code scanning alert, clicking on " Show paths " provides a detailed view of the data ' s journey through the code. This includes the source of the data, the path it takes, and where it ends up (the sink). This information is crucial for understanding how untrusted data might reach sensitive parts of your application and helps in identifying where to implement proper validation or sanitization.​

The GitHub Code Scanning API includes endpoints that allow you to:

List alerts for a repository (filtered by branch, state, or tool) — useful for monitoring security over time.

Get a single alert by its ID to inspect its metadata, status, and locations in the code.

However, GitHub does not support modifying the severity of alerts via API — severity is defined by the scanning tool (e.g., CodeQL). Likewise, alerts cannot be deleted via the API; they are resolved by fixing the code or dismissing them manually.

The Security tab in a GitHub repository provides a central location for viewing security-related information, especially when GitHub Advanced Security is enabled. The following can be accessed:

Number of alerts related to:

Code scanning

Secret scanning

Dependency (Dependabot) alerts

Summary and visibility into open, closed, and dismissed security issues.

It does not show 2FA options, access control settings, or configuration panels for GHAS itself. Those belong to account or organization-level settings.

Secret scanning is a feature provided by GitHub that scans the contents of your GitHub repositories for known types of secrets, such as API keys and tokens. It operates within the GitHub environment and does not scan external systems, services, or repositories outside of GitHub. Its primary function is to prevent the accidental exposure of sensitive information within your GitHub-hosted code.​

When a public repository contains credentials that match known secret formats, GitHub will automatically notify the service provider that issued the secret. This process is known as " secret scanning partner notification " . The provider may then revoke the secret or contact the user directly.

GitHub does not publicly display the alert and does not send internal repository notifications for public detections.

Dependabot alerts are generated as soon as GitHub detects a known vulnerability in one of your dependencies. GitHub does this by analyzing your repository’s dependency graph and matching it against vulnerabilities listed in the GitHub Advisory Database. Once a match is found, the system raises an alert automatically without waiting for a PR or manual action.

This allows organizations to proactively mitigate vulnerabilities as early as possible, based on real-time detection.