Configuring code scanning

You can configure how GitHub scans the code in your project for vulnerabilities and errors.

People with write permissions to a repository can configure code scanning for the repository.

Code scanning is available in public repositories, and in private repositories owned by organizations with an Advanced Security license. For more information, see "GitHub's products."

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About code scanning configuration

You can run code scanning within GitHub, using GitHub Actions, or from your continuous integration (CI) system, using the CodeQL runner. For more information about GitHub Actions, see "About GitHub Actions." For more information about the CodeQL runner, see "Running code scanning in your CI system."

This article is about running code scanning within GitHub.

Before you can configure code scanning for a repository, you must enable code scanning by adding a GitHub Actions workflow to the repository. For more information, see "Enabling code scanning for a repository."

Typically, you don't need to edit the default workflow for code scanning. However, if required, you can edit the workflow to customize some of the settings. For example, you can edit GitHub's CodeQL analysis workflow to specify the frequency of scans, the languages or directories to scan, and what CodeQL code scanning looks for in your code. You might also need to edit the CodeQL analysis workflow if you use a specific set of commands to compile your code.

CodeQL analysis is just one type of code scanning you can do in GitHub. GitHub Marketplace contains other code scanning workflows you can use. You can find a selection of these on the "Get started with code scanning" page, which you can access from the Security tab. The specific examples given in this article relate to the CodeQL analysis workflow file.

Editing a code scanning workflow

GitHub saves workflow files in the .github/workflows directory of your repository. You can find a workflow you have enabled by searching for its file name. For example, by default, the workflow file for CodeQL code scanning is called codeql-analysis.yml.

  1. In your repository, browse to the workflow file you want to edit.
  2. In the upper right corner of the file view, to open the workflow editor, click .
    Edit workflow file button
  3. After you have edited the file, click Start commit and complete the "Commit changes" form. You can choose to commit directly to the current branch, or create a new branch and start a pull request.
    Commit update to codeql.yml workflow

For more information about editing workflow files, see "Learn GitHub Actions."

Configuring frequency

You can configure the CodeQL analysis workflow to scan code on a schedule or when specific events occur in a repository.

Scanning code when someone pushes a change, and whenever a pull request is created, prevents developers from introducing new vulnerabilities and errors into the code. Scanning code on a schedule informs you about the latest vulnerabilities and errors that GitHub, security researchers, and the community discover, even when developers aren't actively maintaining the repository.

Scanning on push

By default, the CodeQL analysis workflow uses the on.push event to trigger a code scan on every push to the default branch of the repository and any protected branches. For code scanning to be triggered on a specified branch, the workflow must exist in that branch. For more information, see "Workflow syntax for GitHub Actions."

Scanning pull requests

The default CodeQL analysis workflow uses the pull_request event to trigger a code scan on the HEAD commit of a pull request against the default branch. If a pull request is from a private fork, the pull_request event will only be triggered if you've selected the "Run workflows from fork pull requests" option in the repository settings. For more information, see "Disabling or limiting GitHub Actions for a repository."

For more information about the pull_request event, see "Workflow syntax for GitHub Actions."

Scanning on a schedule

If you use the default CodeQL analysis workflow, the workflow will scan the code in your repository once a week, in addition to the scans triggered by events. To adjust this schedule, edit the cron value in the workflow. For more information, see "Workflow syntax for GitHub Actions."

Note: GitHub only runs scheduled jobs that are in workflows on the default branch. Changing the schedule in a workflow on any other branch has no effect until you merge the branch into the default branch.


The following example shows a CodeQL analysis workflow for a particular repository that has a default branch called main and one protected branch called protected.

    branches: [main, protected]
    branches: [main]
    - cron: '0 15 * * 0'

This workflow scans:

  • Every push to the default branch and the protected branch
  • Every pull request to the default branch
  • The default branch at 3 P.M. every Sunday

Specifying an operating system

If your code requires a specific operating system to compile, you can configure the operating system in your CodeQL analysis workflow. Edit the value of jobs.analyze.runs-on to specify the operating system for the machine that runs your code scanning actions.

If you choose to use a self-hosted runner for code scanning, you can specify an operating system by using an appropriate label as the second element in a two-element array, after self-hosted.

    name: Analyze
    runs-on: [self-hosted, ubuntu-latest]

For more information, see "About self-hosted runners" and "Adding self-hosted runners."

CodeQL code scanning supports the latest versions of Ubuntu, Windows, and macOS. Typical values for this setting are therefore: ubuntu-latest, windows-latest, and macos-latest. For more information, see "Workflow syntax for GitHub Actions."

If you use a self-hosted runner, you must ensure that Git is in the PATH variable.

Changing the languages that are analyzed

CodeQL code scanning automatically detects code written in the supported languages.

  • C/C++
  • C#
  • Go
  • Java
  • JavaScript/TypeScript
  • Python

The default CodeQL analysis workflow file contains a build matrix called language which lists the languages in your repository that are analyzed. CodeQL automatically populates this matrix when you add code scanning to a repository. Using the language matrix optimizes CodeQL to run each analysis in parallel. We recommend that all workflows adopt this configuration due to the performance benefits of parallelizing builds. For more information about build matrices, see "Managing complex workflows."

If your repository contains code in more than one of the supported languages, you can choose which languages you want to analyze. There are several reasons you might want to prevent a language being analyzed. For example, the project might have dependencies in a different language to the main body of your code, and you might prefer not to see alerts for those dependencies.

If your workflow uses the language matrix then CodeQL is hardcoded to analyze only the languages in the matrix. To change the languages you want to analyze, edit the value of the matrix variable. You can remove a language to prevent it being analyzed or you can add a language that was not present in the repository when code scanning was enabled. For example, if the repository initially only contained JavaScript when code scanning was enabled, and you later added Python code, you will need to add python to the matrix.

    name: Analyze
      fail-fast: false
        language: ['javascript', 'python']

If your workflow does not contain a matrix called language, then CodeQL is configured to run analysis sequentially. If you don't specify languages in the workflow, CodeQL automatically detects, and attempts to analyze, any supported languages in the repository. If you want to choose which languages to analyze, without using a matrix, you can use the languages parameter under the init action.

- uses: github/codeql-action/init@v1
    languages: cpp, csharp, python

Analyzing Python dependencies

For GitHub-hosted runners that use Linux only, the CodeQL analysis workflow will try to auto-install Python dependencies to give more results for the CodeQL analysis. You can control this behavior by specifying the setup-python-dependencies parameter for the action called by the "Initialize CodeQL" step. By default, this parameter is set to true:

  • If the repository contains code written in Python, the "Initialize CodeQL" step installs the necessary dependencies on the GitHub-hosted runner. If the auto-install succeeds, the action also sets the environment variable CODEQL_PYTHON to the Python executable file that includes the dependencies.

  • If the repository doesn't have any Python dependencies, or the dependencies are specified in an unexpected way, you'll get a warning and the action will continue with the remaining jobs. The action can run successfully even when there are problems interpreting dependencies, but the results may be incomplete.

Alternatively, you can install Python dependencies manually on any operating system. You will need to add setup-python-dependencies and set it to false, as well as set CODEQL_PYTHON to the Python executable that includes the dependencies, as shown in this workflow extract:


    runs-on: ubuntu-latest

    - name: Checkout repository
      uses: actions/checkout@v2
        fetch-depth: 2
    - name: Set up Python
      uses: actions/setup-python@v2
        python-version: '3.x'
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        if [ -f requirements.txt ]; 
        then pip install -r requirements.txt;
        # Set the `CODEQL-PYTHON` environment variable to the Python executable
        # that includes the dependencies
        echo "::set-env name=CODEQL_PYTHON::$(which python)"
    - run: git checkout HEAD^2
      if: $
    - name: Initialize CodeQL
      uses: github/codeql-action/init@v1
        languages: python
        # Override the default behavior so that the action doesn't attempt 
        # to auto-install Python dependencies
        setup-python-dependencies: false

Running additional queries

When you use CodeQL to scan code, the CodeQL analysis engine generates a database from the code and runs queries on it. For more information, see "About code scanning."

CodeQL analysis uses a default set of queries, but you can specify more queries to run, in addition to the default queries. The queries you want to run must belong to a QL pack and can be in your own repository or any public repository. For more information, see "About QL packs."

Queries must only depend on the standard libraries (that is, the libraries referenced by an import LANGUAGE statement in your query), or libraries in the same QL pack as the query. The standard libraries are located in the github/codeql repository. For more information, see "About CodeQL queries."

You can specify a single .ql file, a directory containing multiple .ql files, a .qls query suite definition file, or any combination. For more information about query suite definitions, see "Creating CodeQL query suites."

We don't recommend referencing query suites directly from the github/codeql repository, like github/codeql/cpp/ql/src@main. Such queries may not be compiled with the same version of CodeQL as used for your other queries, which could lead to errors during analysis.

To add one or more queries, add a with: queries: entry within the uses: github/codeql-action/init@v1 section of the workflow.

- uses: github/codeql-action/init@v1

You can also specify query suites in the value of queries. Query suites are collections of queries, usually grouped by purpose or language.

The following query suites are built into CodeQL code scanning and are available for use.

Query suiteDescription
security-extendedQueries of lower severity and precision than the default queries
security-and-qualityQueries from security-extended, plus maintainability and reliability queries

When you specify a query suite, the CodeQL analysis engine will run the queries contained within the suite for you, in addition to the default set of queries.

If you are also using a configuration file for custom settings, any additional queries specified in your workflow are used instead of any specified in the configuration file. If you want to run the combined set of additional queries specified here and in the configuration file, prefix the value of queries in the workflow with the + symbol. For more information, see "Using a custom configuration file."

In the following example, the + symbol ensures that the specified additional queries are used together with any queries specified in the referenced configuration file.

- uses: github/codeql-action/init@v1
    config-file: ./.github/codeql/codeql-config.yml
    queries: +security-and-quality,octo-org/python-qlpack/show_ifs.ql@main

Using a custom configuration file

As an alternative to specifying which queries to run in the workflow file, you can do this in a separate configuration file. You can also use a configuration file to disable the default queries and to specify which directories to scan during analysis.

In the workflow file, use the config-file parameter of the init action to specify the path to the configuration file you want to use. This example loads the configuration file ./.github/codeql/codeql-config.yml.

- uses: github/codeql-action/init@v1
    config-file: ./.github/codeql/codeql-config.yml

The configuration file can be located within the local repository, or in a public, remote repository. For remote repositories, you can use the owner/repository/file.yml@branch syntax. The settings in the file are written in YAML format.

Specifying additional queries

You specify additional queries in a queries array. Each element of the array contains a uses parameter with a value that identifies a single query file, a directory containing query files, or a query suite definition file.

  - uses: ./my-basic-queries/example-query.ql
  - uses: ./my-advanced-queries
  - uses: ./codeql-qlpacks/complex-python-qlpack/rootAndBar.qls

Optionally, you can give each array element a name, as shown in the example configuration files below.

For more information about additional queries, see "Running additional queries" above.

Disabling the default queries

If you only want to run custom queries, you can disable the default security queries by using disable-default-queries: true.

Specifying directories to scan

For the interpreted languages that CodeQL supports (Python and JavaScript/TypeScript), you can restrict code scanning to files in specific directories by adding a paths array to the configuration file. You can exclude the files in specific directories from scans by adding a paths-ignore array.

  - src 
  - node_modules
  - '**/*.test.js'


  • The paths and paths-ignore keywords, used in the context of the code scanning configuration file, should not be confused with the same keywords when used for on.<push|pull_request>.paths in a workflow. When they are used to modify on.<push|pull_request> in a workflow, they determine whether the actions will be run when someone modifies code in the specified directories. For more information, see "Workflow syntax for GitHub Actions."
  • ** characters can only be at the start or end of a line, or surrounded by slashes, and you can't mix ** and other characters. For example, foo/**, **/foo, and foo/**/bar are all allowed syntax, but **foo isn't. However you can use single stars along with other characters, as shown in the example. You'll need to quote anything that contains a * character.

For C/C++, C#, and Java, if you want to limit code scanning to specific directories in your project, you must specify appropriate build steps in the workflow. The commands you need to use to exclude a directory from the build will depend on your build system. For more information, see "Configuring the CodeQL workflow for compiled languages."

You can quickly analyze small portions of a monorepo when you modify code in specific directories. You'll need to both exclude directories in your build steps and use the paths-ignore and paths keywords for on.<push|pull_request> in your workflow.

Example configuration files

This configuration file adds the security-and-quality query suite to the list of queries run by CodeQL when scanning your code. For more information about the query suites available for use, see "Running additional queries."

name: "My CodeQL config"

  - uses: security-and-quality

The following configuration file disables the default queries and specifies a set of custom queries to run instead. It also configures CodeQL to scan files in the src directory (relative to the root), and to exclude the node_modules directory (also relative to the root), as well as any file whose name ends in .test.js.

name: "My CodeQL config"

disable-default-queries: true

  - name: Use an in-repository QL pack (run queries in the my-queries directory)
    uses: ./my-queries
  - name: Use an external JavaScript QL pack (run queries from an external repo)
    uses: octo-org/javascript-qlpack@main
  - name: Use an external query (run a single query from an external QL pack)
    uses: octo-org/python-qlpack/show_ifs.ql@main
  - name: Use a query suite file (run queries from a query suite in this repo)
    uses: ./codeql-qlpacks/complex-python-qlpack/rootAndBar.qls

  - node_modules
  - '**/*.test.js'
  - src 

Configuring code scanning for compiled languages

For the supported compiled languages, you can use the autobuild action in the CodeQL analysis workflow to build your code. This avoids you having to specify explicit build commands for C/C++, C#, and Java. CodeQL also runs a build for Go projects to set up the project. However, in contrast to the other compiled languages, all Go files in the repository are extracted, not just those that are built. Custom build commands are not supported for Go.

If the C/C++, C#, or Java code in your repository has a non-standard build process, autobuild may fail. You will need to remove the autobuild step from the workflow, and manually add build steps. For more information about how to configure CodeQL code scanning for compiled languages, see "Configuring the CodeQL workflow for compiled languages."

Accessing private repositories

If your workflow for code scanning accesses a private repository, other than the repository that contains the workflow, you'll need to configure Git to authenticate with a personal access token. Define the secret in the runner environment by using jobs.<job_id>.steps.env in your workflow before any CodeQL actions. For more information, see "Creating a personal access token for the command line" and "Creating and storing encrypted secrets."

For example, the following configuration has Git replace the full URLs to the github/foo, github/bar, and github/baz repositories on with URLs that include the personal access token that you store in the ACCESS_TOKEN environment variable.

- name: Configure access to private repositories
    TOKEN: ${{ secrets.ACCESS_TOKEN }}
  run: |
    git config --global url."https://${TOKEN}".insteadOf ""
    git config --global url."https://${TOKEN}".insteadOf ""
    git config --global url."https://${TOKEN}".insteadOf ""

Uploading code scanning data to GitHub

GitHub can display code analysis data generated externally by a third-party tool. You can upload code analysis data with the upload-sarif action. For more information, see "Uploading a SARIF file to GitHub."

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