# Codeql

> CodeQL setup — GitHub Actions scanning, CLI queries, alert triage

- Skill: `mouadja02/codeql` (Agent Skill, multi-file: 7 files)
- Install (CLI): `npx skillmds@latest add mouadja02/codeql`
- Raw SKILL.md: https://api.skillmd.com/api/skills/mouadja02/codeql/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: mouadja02 (https://skillmd.com/u/mouadja02)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/mouadja02/codeql

---


# CodeQL Code Scanning

This skill provides procedural guidance for configuring and running CodeQL code scanning — both through GitHub Actions workflows and the standalone CodeQL CLI.

## When to Use This Skill

Use this skill when the request involves:

- Creating or customizing a `codeql.yml` GitHub Actions workflow
- Choosing between default setup and advanced setup for code scanning
- Configuring CodeQL language matrix, build modes, or query suites
- Running CodeQL CLI locally (`codeql database create`, `database analyze`, `github upload-results`)
- Understanding or interpreting SARIF output from CodeQL
- Troubleshooting CodeQL analysis failures (build modes, compiled languages, runner requirements)
- Setting up CodeQL for monorepos with per-component scanning
- Configuring dependency caching, custom query packs, or model packs

## Supported Languages

CodeQL supports the following language identifiers:

| Language | Identifier | Alternatives |
|---|---|---|
| C/C++ | `c-cpp` | `c`, `cpp` |
| C# | `csharp` | — |
| Go | `go` | — |
| Java/Kotlin | `java-kotlin` | `java`, `kotlin` |
| JavaScript/TypeScript | `javascript-typescript` | `javascript`, `typescript` |
| Python | `python` | — |
| Ruby | `ruby` | — |
| Rust | `rust` | — |
| Swift | `swift` | — |
| GitHub Actions | `actions` | — |

> Alternative identifiers are equivalent to the standard identifier (e.g., `javascript` does not exclude TypeScript analysis).

## Core Workflow — GitHub Actions

### Step 1: Choose Setup Type

- **Default setup** — Enable from repository Settings → Advanced Security → CodeQL analysis. Best for getting started quickly. Uses `none` build mode for most languages.
- **Advanced setup** — Create a `.github/workflows/codeql.yml` file for full control over triggers, build modes, query suites, and matrix strategies.

To switch from default to advanced: disable default setup first, then commit the workflow file.

### Step 2: Configure Workflow Triggers

Define when scanning runs:

```yaml
on:
  push:
    branches: [main, protected]
  pull_request:
    branches: [main]
  schedule:
    - cron: '30 6 * * 1'  # Weekly Monday 6:30 UTC
```

- `push` — scans on every push to specified branches; results appear in Security tab
- `pull_request` — scans PR merge commits; results appear as PR check annotations
- `schedule` — periodic scans of the default branch (cron must exist on default branch)
- `merge_group` — add if repository uses merge queues

To skip scans for documentation-only PRs:

```yaml
on:
  pull_request:
    paths-ignore:
      - '**/*.md'
      - '**/*.txt'
```

> `paths-ignore` controls whether the workflow runs, not which files are analyzed.

### Step 3: Configure Permissions

Set least-privilege permissions:

```yaml
permissions:
  security-events: write   # Required to upload SARIF results
  contents: read            # Required to checkout code
  actions: read             # Required for private repos using codeql-action
```

### Step 4: Configure Language Matrix

Use a matrix strategy to analyze each language in parallel:

```yaml
jobs:
  analyze:
    name: Analyze (${{ matrix.language }})
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        include:
          - language: javascript-typescript
            build-mode: none
          - language: python
            build-mode: none
```

For compiled languages, set the appropriate `build-mode`:
- `none` — no build required (supported for C/C++, C#, Java, Rust)
- `autobuild` — automatic build detection
- `manual` — custom build commands (advanced setup only)

> For detailed per-language autobuild behavior and runner requirements, search `references/compiled-languages.md`.

### Step 5: Configure CodeQL Init and Analysis

```yaml
steps:
  - name: Checkout repository
    uses: actions/checkout@v4

  - name: Initialize CodeQL
    uses: github/codeql-action/init@v4
    with:
      languages: ${{ matrix.language }}
      build-mode: ${{ matrix.build-mode }}
      queries: security-extended
      dependency-caching: true

  - name: Perform CodeQL Analysis
    uses: github/codeql-action/analyze@v4
    with:
      category: "/language:${{ matrix.language }}"
```

**Query suite options:**
- `security-extended` — default security queries plus additional coverage
- `security-and-quality` — security plus code quality queries
- Custom query packs via `packs:` input (e.g., `codeql/javascript-queries:AlertSuppression.ql`)

**Dependency caching:** Set `dependency-caching: true` on the `init` action to cache restored dependencies across runs.

**Analysis category:** Use `category` to distinguish SARIF results in monorepos (e.g., per-language, per-component).

### Step 6: Monorepo Configuration

For monorepos with multiple components, use the `category` parameter to separate SARIF results:

```yaml
category: "/language:${{ matrix.language }}/component:frontend"
```

To restrict analysis to specific directories, use a CodeQL configuration file (`.github/codeql/codeql-config.yml`):

```yaml
paths:
  - apps/
  - services/
paths-ignore:
  - node_modules/
  - '**/test/**'
```

Reference it in the workflow:

```yaml
- uses: github/codeql-action/init@v4
  with:
    config-file: .github/codeql/codeql-config.yml
```

### Step 7: Manual Build Steps (Compiled Languages)

If `autobuild` fails or custom build commands are needed:

```yaml
- language: c-cpp
  build-mode: manual
```

Then add explicit build steps between `init` and `analyze`:

```yaml
- if: matrix.build-mode == 'manual'
  name: Build
  run: |
    make bootstrap
    make release
```

## Core Workflow — CodeQL CLI

### Step 1: Install the CodeQL CLI

Download the CodeQL bundle (includes CLI + precompiled queries):

```bash
# Download from https://github.com/github/codeql-action/releases
# Extract and add to PATH
export PATH="$HOME/codeql:$PATH"

# Verify installation
codeql resolve packs
codeql resolve languages
```

> Always use the CodeQL bundle, not a standalone CLI download. The bundle ensures query compatibility and provides precompiled queries for better performance.

### Step 2: Create a CodeQL Database

```bash
# Single language
codeql database create codeql-db \
  --language=javascript-typescript \
  --source-root=src

# Multiple languages (cluster mode)
codeql database create codeql-dbs \
  --db-cluster \
  --language=java,python \
  --command=./build.sh \
  --source-root=src
```

For compiled languages, provide the build command via `--command`.

### Step 3: Analyze the Database

```bash
codeql database analyze codeql-db \
  javascript-code-scanning.qls \
  --format=sarif-latest \
  --sarif-category=javascript \
  --output=results.sarif
```

Common query suites: `<language>-code-scanning.qls`, `<language>-security-extended.qls`, `<language>-security-and-quality.qls`.

### Step 4: Upload Results to GitHub

```bash
codeql github upload-results \
  --repository=owner/repo \
  --ref=refs/heads/main \
  --commit=<commit-sha> \
  --sarif=results.sarif
```

Requires `GITHUB_TOKEN` environment variable with `security-events: write` permission.

### CLI Server Mode

To avoid repeated JVM initialization when running multiple commands:

```bash
codeql execute cli-server
```

> For detailed CLI command reference, search `references/cli-commands.md`.

## Alert Management

### Severity Levels

Alerts have two severity dimensions:
- **Standard severity:** `Error`, `Warning`, `Note`
- **Security severity:** `Critical`, `High`, `Medium`, `Low` (derived from CVSS scores; takes display precedence)

### Copilot Autofix

GitHub Copilot Autofix generates fix suggestions for CodeQL alerts in pull requests automatically — no Copilot subscription required. Review suggestions carefully before committing.

### Alert Triage in PRs

- Alerts appear as check annotations on changed lines
- Check fails by default for `error`/`critical`/`high` severity alerts
- Configure merge protection rulesets to customize the threshold
- Dismiss false positives with a documented reason for audit trail

> For detailed alert management guidance, search `references/alert-management.md`.

## Custom Queries and Packs

### Using Custom Query Packs

```yaml
- uses: github/codeql-action/init@v4
  with:
    packs: |
      my-org/my-security-queries@1.0.0
      codeql/javascript-queries:AlertSuppression.ql
```

### Creating Custom Query Packs

Use the CodeQL CLI to create and publish packs:

```bash
# Initialize a new pack
codeql pack init my-org/my-queries

# Install dependencies
codeql pack install

# Publish to GitHub Container Registry
codeql pack publish
```

### CodeQL Configuration File

For advanced query and path configuration, create `.github/codeql/codeql-config.yml`:

```yaml
paths:
  - apps/
  - services/
paths-ignore:
  - '**/test/**'
  - node_modules/
queries:
  - uses: security-extended
packs:
  javascript-typescript:
    - my-org/my-custom-queries
```

## Code Scanning Logs

### Summary Metrics

Workflow logs include key metrics:
- **Lines of code in codebase** — baseline before extraction
- **Lines extracted** — including external libraries and auto-generated files
- **Extraction errors/warnings** — files that failed or produced warnings during extraction

### Debug Logging

To enable detailed diagnostics:
- **GitHub Actions:** re-run the workflow with "Enable debug logging" checked
- **CodeQL CLI:** use `--verbosity=progress++` and `--logdir=codeql-logs`

## Troubleshooting

### Common Issues

| Problem | Solution |
|---|---|
| Workflow not triggering | Verify `on:` triggers match event; check `paths`/`branches` filters; ensure workflow exists on target branch |
| `Resource not accessible` error | Add `security-events: write` and `contents: read` permissions |
| Autobuild failure | Switch to `build-mode: manual` and add explicit build commands |
| No source code seen | Verify `--source-root`, build command, and language identifier |
| C# compiler failure | Check for `/p:EmitCompilerGeneratedFiles=true` conflicts with `.sqlproj` or legacy projects |
| Fewer lines scanned than expected | Switch from `none` to `autobuild`/`manual`; verify build compiles all source |
| Kotlin in no-build mode | Disable and re-enable default setup to switch to `autobuild` |
| Cache miss every run | Verify `dependency-caching: true` on `init` action |
| Out of disk/memory | Use larger runners; reduce analysis scope via `paths` config; use `build-mode: none` |
| SARIF upload fails | Ensure token has `security-events: write`; check 10 MB file size limit |
| SARIF results exceed limits | Split across multiple uploads with different `--sarif-category`; reduce query scope |
| Two CodeQL workflows | Disable default setup if using advanced setup, or remove old workflow file |
| Slow analysis | Enable dependency caching; use `--threads=0`; reduce query suite scope |

> For comprehensive troubleshooting with detailed solutions, search `references/troubleshooting.md`.

### Hardware Requirements (Self-Hosted Runners)

| Codebase Size | RAM | CPU |
|---|---|---|
| Small (<100K LOC) | 8 GB+ | 2 cores |
| Medium (100K–1M LOC) | 16 GB+ | 4–8 cores |
| Large (>1M LOC) | 64 GB+ | 8 cores |

All sizes: SSD with ≥14 GB free disk space.

### Action Versioning

Pin CodeQL actions to a specific major version:

```yaml
uses: github/codeql-action/init@v4      # Recommended
uses: github/codeql-action/autobuild@v4
uses: github/codeql-action/analyze@v4
```

For maximum security, pin to a full commit SHA instead of a version tag.

## Reference Files

For detailed documentation, load the following reference files as needed:

- `references/workflow-configuration.md` — Full workflow trigger, runner, and configuration options
  - Search patterns: `trigger`, `schedule`, `paths-ignore`, `db-location`, `model packs`, `alert severity`, `merge protection`, `concurrency`, `config file`
- `references/cli-commands.md` — Complete CodeQL CLI command reference
  - Search patterns: `database create`, `database analyze`, `upload-results`, `resolve packs`, `cli-server`, `installation`, `CI integration`
- `references/sarif-output.md` — SARIF v2.1.0 object model, upload limits, and third-party support
  - Search patterns: `sarifLog`, `result`, `location`, `region`, `codeFlow`, `fingerprint`, `suppression`, `upload limits`, `third-party`, `precision`, `security-severity`
- `references/compiled-languages.md` — Build modes and autobuild behavior per language
  - Search patterns: `C/C++`, `C#`, `Java`, `Go`, `Rust`, `Swift`, `autobuild`, `build-mode`, `hardware`, `dependency caching`
- `references/troubleshooting.md` — Comprehensive error diagnosis and resolution
  - Search patterns: `no source code`, `out of disk`, `out of memory`, `403`, `C# compiler`, `analysis too long`, `fewer lines`, `Kotlin`, `extraction errors`, `debug logging`, `SARIF upload`, `SARIF limits`
- `references/alert-management.md` — Alert severity, triage, Copilot Autofix, and dismissal
  - Search patterns: `severity`, `security severity`, `CVSS`, `Copilot Autofix`, `dismiss`, `triage`, `PR alerts`, `data flow`, `merge protection`, `REST API`