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The most practical starting point is GitHub CodeQL. Turn on CodeQL default setup in the repository’s settings when GitHub’s automatic language, query, and event choices fit your project. Use advanced setup when you need to edit triggers, queries, or build behavior. Add dependency review to pull requests that change packages, then restrict workflow permissions and protect secrets.

This guide shows how to choose the right checks, enable them, scan workflow YAML itself, schedule recurring analysis, and avoid the permission and pull-request trust mistakes that can turn a security workflow into a new attack surface.

What security scanning in GitHub Actions should cover

“Security scanning” is not one check. A useful GitHub Actions design normally combines code analysis, dependency-change analysis, and secure workflow operation.

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Check What it examines Best use Main limitation or decision
CodeQL default setup Supported source languages and GitHub’s selected query suites Fastest way to start code scanning with little configuration GitHub chooses languages, queries, and scan events; confirm repository eligibility and coverage
CodeQL advanced setup Source code using a workflow you control Projects needing custom triggers, query packs, language lists, or build steps You must maintain the workflow and correctly configure compiled-language builds
CodeQL Actions queries GitHub Actions workflow files, including YAML Finding insecure workflow patterns in .github/workflows Workflow analysis is one layer; permissions, secrets, runners, and trust boundaries still need review
Dependency review Dependency additions, removals, and updates in a pull request Stopping a pull request from introducing a known vulnerable component It complements code scanning and focuses on the dependency changes in that pull request

The right combination depends on configuration effort, control, repository and plan eligibility, language and build coverage, when a scan runs, and whether you need to inspect source or dependency changes. GitHub describes CodeQL’s default and advanced paths in its repository security quickstart.

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Check eligibility before changing the repository

Code scanning access depends on repository type and plan. GitHub documents availability for public repositories and certain organization-owned repositories on paid plans with GitHub Code Security enabled. Private-repository eligibility can change with plan and product naming, so check the current GitHub Advanced Security documentation and the repository’s Security settings before promising that a feature will appear.

  • Open the repository on GitHub and select the Security tab.
  • Look for Code scanning, Set up, or a prompt to enable the required security product.
  • Confirm that the repository’s languages and build system are supported by the CodeQL path you intend to use.
  • Check whether organization policy prevents GitHub Actions, scheduled workflows, or security-event uploads.

If the Code scanning area is absent, do not work around the restriction by copying a workflow and assuming it will have the required permissions. Resolve the repository or organization entitlement first.

Enable CodeQL default setup for the quickest supported start

Default setup is appropriate when you want a working baseline and do not need to hand-author the workflow. GitHub determines the repository languages, query suites, and events that trigger analysis.

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  1. Open the repository and select Settings.
  2. In the security section, open Code security and analysis or the current equivalent security settings page.
  3. Find Code scanning and select Set up.
  4. Choose Default setup, review the detected languages and configuration summary, and enable it.
  5. Open the generated or associated workflow and verify that it runs for the branches and events your team actually uses.
  6. Create a small test pull request or push a harmless change, then inspect the resulting Actions run and the Code scanning alerts page.

Default setup reduces maintenance, but it also limits your control. If a language is detected incorrectly, a required build is not represented, or the team needs a different query suite or schedule, move to advanced setup rather than silently assuming the default is complete.

Use advanced setup when the workflow needs control

Advanced setup creates a workflow file that you can edit. It is the better fit when you need precise branch filters, scheduled scans, custom queries, explicit language selection, or a deliberate build for compiled code. GitHub’s current examples use the github/codeql-action family with @v4; action versions and setup guidance change, so verify the current workflow configuration documentation before copying a versioned example.

A minimal structure looks like this. Treat it as a starting pattern: replace the language matrix and build behavior with values that match your repository, and review every action reference before merging.

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name: CodeQL

on:
  push:
    branches: ["main"]
  pull_request:
    branches: ["main"]
  schedule:
    - cron: "30 1 * * 0"

permissions:
  contents: read

jobs:
  analyze:
    name: Analyze
    runs-on: ubuntu-latest
    permissions:
      contents: read
      actions: read
      packages: read
      security-events: write
    strategy:
      fail-fast: false
      matrix:
        language: ["javascript-typescript"]
    steps:
      - name: Check out source
        uses: actions/checkout@v4
      - name: Initialize CodeQL
        uses: github/codeql-action/init@v4
        with:
          languages: ${{ matrix.language }}
      - name: Build (when required)
        uses: github/codeql-action/autobuild@v4
      - name: Analyze
        uses: github/codeql-action/analyze@v4

The example grants the job permission to upload code-scanning results while keeping the workflow-level default to repository-content read access. Do not assume that the sample’s language, runner, build mode, or action versions fit your project.

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Choose languages and build behavior deliberately

For interpreted languages, CodeQL may be able to analyze without a separate build. Compiled languages can require a real build or a correctly configured autobuild step so that CodeQL sees the code produced by the project’s build system. A successful Actions run is not proof that the analysis covered every source file: inspect initialization and build logs for skipped languages, failed compilation, or unsupported configurations.

Customize queries only when the baseline is understood

Start with the standard query suite unless you have a clear reason to change it. Advanced setup can select query suites or additional query packs, but every customization creates maintenance work. Record why a query was added or excluded, and review changes when CodeQL or the repository’s languages evolve.

Run scans at the events that match your risk

Push scans

A push scan checks committed changes after they land on the selected branch. It provides a durable result even when a change was merged without an open pull request, but it is later feedback than a pull-request check.

Pull-request scans

Pull-request scans give developers feedback while a change is proposed. Filter them to the branches that protect production or other sensitive environments. A pull request from a fork has a different trust boundary from a branch in the same repository; do not expose write-capable tokens or secrets merely to make a scan pass.

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Scheduled scans

A schedule matters because a repository can become vulnerable without a new commit. New CodeQL logic, newly disclosed vulnerabilities, or changes in analysis dependencies can reveal an issue after active development stops. GitHub documents schedule and event configuration in its code-scanning workflow options. Choose a cadence your team can review, and account for scheduled-workflow behavior such as default-branch execution and any organization-level restrictions.

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For an actively maintained service, a practical baseline is pull-request and push coverage plus a scheduled scan. For a dormant repository, the scheduled run is especially valuable, but alerts still need an owner and a response process.

Add dependency review to pull requests

CodeQL analyzes source; dependency review focuses on package changes in a pull request. It can warn when an added, removed, or updated component is associated with vulnerability information. GitHub’s instructions are in Configuring the dependency review action.

  1. Open the dependency-review documentation and use its current workflow example rather than relying on an old action version copied from another repository.
  2. Place the workflow in .github/workflows and trigger it on pull_request for the branches where dependency changes require review.
  3. Give the job only the read permissions required to compare the pull request and publish its check result.
  4. Decide whether the check should warn or fail for vulnerability severity, license, or scope policies supported by the current action.
  5. Open a test pull request that changes a package manifest and confirm that the check reports the dependency diff, not merely the repository’s existing inventory.

Dependency review does not replace a full dependency inventory, lockfile hygiene, or CodeQL. It is a gate at the point where a pull request changes the supply chain.

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Scan GitHub Actions workflow files themselves

Workflow YAML is executable security configuration, not just project metadata. CodeQL includes built-in queries for GitHub Actions workflow files. See GitHub Actions queries for CodeQL analysis for the applicable query reference and repository conditions.

Workflow analysis can identify risky patterns, but it cannot make an unsafe trust model safe by itself. Review these files as code:

  • Who can trigger the workflow, including forked pull requests, issue activity, and reusable-workflow callers?
  • Does a job check out untrusted code before using a write-capable token or a secret?
  • Are shell commands interpolating pull-request titles, branch names, issue text, or other attacker-controlled values?
  • Are third-party actions pinned to a verified commit or otherwise controlled according to your organization’s policy?
  • Can a compromised runner reach production credentials, package registries, or deployment systems?

Set least-privilege token permissions

GitHub’s secure-use guidance recommends setting the default GITHUB_TOKEN permission for repository contents to read access. The exact wording is: “It’s good security practice to set the default permission for the GITHUB_TOKEN to read access only for repository contents.” Read the full Secure use reference for the current permission model and related risks.

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Set a restrictive workflow-level default, then grant a narrower job only what it needs. A CodeQL upload commonly needs security-events: write, while checkout generally needs contents: read. Some repositories also need read access to Actions or packages for their build. Do not grant write access globally because one step happens to need it.

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permissions:
  contents: read

jobs:
  scan:
    permissions:
      contents: read
      security-events: write

Review permissions after adding any action. A scanner that only reads source should not receive issue, pull-request, package, or deployment write access. If an organization sets a restrictive default, explicitly adding a permission may be necessary; if it sets a broader default, explicitly reducing permissions is safer.

Handle secrets and untrusted code safely

GitHub states that secrets are encrypted before they reach GitHub and are available to a workflow only when explicitly included. Its Secrets documentation recommends generating credentials with the minimum permissions required.

  • Do not pass production credentials to a pull-request job that checks out attacker-controlled code.
  • Prefer environment-specific, short-lived credentials and the smallest repository or cloud scope available.
  • Keep secrets out of command-line arguments and avoid printing environment variables.
  • Review reusable workflows and action inputs before forwarding a secret to them.
  • Separate untrusted analysis from deployment jobs so a compromised scanner cannot publish or alter production.

Redaction is not a guarantee. GitHub warns that “Because there are multiple ways a secret value can be transformed, this redaction is not guaranteed.” A secret that is encoded, split, transformed, or embedded in other output may not be recognized by log masking. Treat every workflow log as potentially visible to people who can read the run, and rotate a credential immediately if it appears in output.

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Pin and review action dependencies

Every action is executable code with the permissions of its job. Use trusted publishers, review release changes, and pin references to verified commits when your security policy requires immutable dependencies. Tags are easier to maintain but can move; commit pins reduce that supply-chain risk and require a process for intentional updates.

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Keep checkout, CodeQL, dependency-review, and any build or upload action under the same review standard as application dependencies. A scanner does not become trustworthy merely because its purpose is security.

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Verify results after enabling scanning

  1. Open the Actions tab and confirm that the scan starts on the intended push, pull request, and scheduled events.
  2. Inspect the job summary for detected languages, initialization status, build output, and upload status.
  3. Open the repository’s Security tab and review Code scanning alerts, including severity, affected file, and remediation guidance.
  4. For dependency review, inspect the pull-request check and verify that it describes the changed packages and associated vulnerability information.
  5. Confirm that required checks are actually required by branch protection if a finding must block merging.
  6. Record an owner and response deadline for alerts; an alert that nobody triages is only visibility, not risk reduction.

Troubleshoot the common failure modes

The setup option is missing

Recheck repository type, organization ownership, plan, and whether the relevant GitHub security product is enabled. Product names and eligibility change, so use the current Advanced Security availability documentation rather than an old screenshot.

The workflow runs but reports no languages

Inspect the checkout path and language matrix. Monorepos may need explicit language entries or separate jobs. Confirm that generated or vendored directories are not the only files being analyzed.

A compiled-language scan fails during build

Read the build log first. Install the project’s required toolchain, provide the same build inputs used in normal development, and choose an explicit build mode when autobuild cannot reproduce the project. Do not suppress the build error and treat the resulting partial analysis as complete.

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Pull-request scans expose a secret

Stop the run, revoke or rotate the exposed credential, remove it from logs and history where appropriate, and redesign the job so untrusted code never receives it. Also review token permissions and runner access.

Alerts do not block merging

Code scanning can report an alert without being a required status check. Configure branch protection or rulesets separately, and decide which severities or categories should block a merge. Make that policy explicit so developers are not surprised by a late enforcement change.

A practical rollout plan

  1. Enable CodeQL default setup and establish that the repository can run and upload results.
  2. Check language and build coverage; move to advanced setup if automatic choices are insufficient.
  3. Use push and pull-request events for active branches, then add a schedule for continued discovery.
  4. Add dependency review to pull requests that modify package manifests or lockfiles.
  5. Set workflow-level contents: read permissions and add only job-level permissions that a step demonstrably needs.
  6. Remove secrets from untrusted pull-request paths and separate scanning from deployment credentials.
  7. Review and pin action dependencies according to your organization’s policy.
  8. Make alert ownership, triage time, and merge-blocking rules part of the repository’s normal maintenance.

This layered approach gives you source analysis, dependency-change checks, and workflow-hardening practices without pretending that any single scan proves a repository is secure.

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