Codeql

CodeQL Static Analysis

When to Use CodeQL

Ideal scenarios:

• Deep interprocedural taint tracking across files and modules
• Complex data flow analysis requiring semantic understanding
• Security vulnerability detection in large codebases
• Finding vulnerabilities that span multiple function calls
• Variant analysis (finding similar bugs across codebase)
• GitHub Advanced Security integration
• Compliance-driven security scanning
• Custom query development for organization-specific patterns

Complements other tools:

• Use after Semgrep for deeper analysis of flagged areas
• Combine with SARIF Issue Reporter for detailed findings
• Pair with dependency scanners (OSV-Scanner) for supply chain
• Use alongside Gitleaks for secrets detection

Consider Semgrep instead when:

• Need quick pattern-based scans (minutes vs hours)
• Simple intra-file pattern matching sufficient
• Writing rules without learning QL language
• CI/CD needs fast feedback loops

When NOT to Use

Do NOT use this skill for:

• Quick pattern-based scans (use Semgrep)
• Secrets detection (use Gitleaks)
• Dependency vulnerability scanning (use OSV-Scanner, Depscan)
• IaC security analysis (use KICS)
• API endpoint discovery (use Noir)
• Binary analysis without source code
• Languages not supported by CodeQL

Supported Languages

| Language | Database | Maturity | |----------|----------|----------| | C/C++ | cpp | Stable | | C# | csharp | Stable | | Go | go | Stable | | Java/Kotlin | java | Stable | | JavaScript/TypeScript | javascript | Stable | | Python | python | Stable | | Ruby | ruby | Stable | | Swift | swift | Beta |

Installation

GitHub CLI (Recommended)

# Install CodeQL CLI via GitHub CLI
gh extension install github/gh-codeql

# Verify installation
gh codeql version

Direct Download

# Download latest release (Linux/macOS)
wget https://github.com/github/codeql-cli-binaries/releases/latest/download/codeql-linux64.zip
unzip codeql-linux64.zip
export PATH="$PWD/codeql:$PATH"

# Windows
# Download from: https://github.com/github/codeql-cli-binaries/releases

# Verify
codeql version

Clone Standard Queries

# Clone CodeQL queries repository
git clone --depth 1 https://github.com/github/codeql.git codeql-repo

# Set CODEQL_HOME
export CODEQL_HOME="$PWD/codeql-repo"

VS Code Extension

Install "CodeQL" extension from marketplace for query development and debugging.

Core Workflow

1. Create Database

# Auto-detect language
codeql database create  --source-root=

# Specify language explicitly
codeql database create my-db --language=python --source-root=./src

# Multiple languages
codeql database create my-db --language=javascript,python --source-root=.

# With build command (compiled languages)
codeql database create my-db --language=java --command="mvn clean compile" --source-root=.
codeql database create my-db --language=cpp --command="make" --source-root=.

# Overwrite existing database
codeql database create my-db --language=python --overwrite --source-root=.

2. Run Analysis

# Run default security queries
codeql database analyze  --format=sarif-latest --output=results.sarif

# Use specific query suite
codeql database analyze my-db codeql/python-queries:codeql-suites/python-security-extended.qls \
  --format=sarif-latest --output=results.sarif

# Run single query
codeql database analyze my-db path/to/query.ql --format=sarif-latest --output=results.sarif

# Multiple query packs
codeql database analyze my-db \
  codeql/javascript-queries \
  codeql/python-queries \
  --format=sarif-latest --output=results.sarif

3. Query Suites

| Suite | Description | |-------|-------------| | -security-extended.qls | Comprehensive security queries | | -security-and-quality.qls | Security + code quality | | -code-scanning.qls | GitHub code scanning default | | -lgtm-full.qls | All available queries |

# Python security extended
codeql database analyze my-db \
  codeql/python-queries:codeql-suites/python-security-extended.qls \
  --format=sarif-latest --output=python-results.sarif

# JavaScript security
codeql database analyze my-db \
  codeql/javascript-queries:codeql-suites/javascript-security-extended.qls \
  --format=sarif-latest --output=js-results.sarif

Output Formats

# SARIF (recommended for CI/CD)
codeql database analyze my-db --format=sarif-latest --output=results.sarif

# CSV
codeql database analyze my-db --format=csv --output=results.csv

# JSON
codeql database analyze my-db --format=json --output=results.json

# Text (human readable)
codeql database analyze my-db --format=text --output=results.txt

# SARIF with source snippets
codeql database analyze my-db --format=sarif-latest \
  --sarif-add-snippets --output=results.sarif

Writing Custom Queries

Basic Query Structure

/**
 * @name SQL injection vulnerability
 * @description User input flows to SQL query without sanitization
 * @kind path-problem
 * @problem.severity error
 * @security-severity 9.8
 * @precision high
 * @id py/sql-injection
 * @tags security
 *       external/cwe/cwe-089
 */

import python
import semmle.python.dataflow.new.DataFlow
import semmle.python.dataflow.new.TaintTracking
import semmle.python.Concepts
import DataFlow::PathGraph

class SqlInjectionConfig extends TaintTracking::Configuration {
  SqlInjectionConfig() { this = "SqlInjectionConfig" }

  override predicate isSource(DataFlow::Node source) {
    exists(RemoteFlowSource remote | source = remote)
  }

  override predicate isSink(DataFlow::Node sink) {
    exists(SqlExecution sql | sink = sql.getSql())
  }
}

from SqlInjectionConfig config, DataFlow::PathNode source, DataFlow::PathNode sink
where config.hasFlowPath(source, sink)
select sink.getNode(), source, sink,
  "SQL injection from $@ to $@.", source.getNode(), "user input", sink.getNode(), "SQL query"

Query Metadata

| Metadata | Description | |----------|-------------| | @name | Human-readable query name | | @description | Detailed description | | @kind | Query type: problem, path-problem, metric | | @problem.severity | error, warning, recommendation | | @security-severity | CVSS score (0.0-10.0) | | @precision | very-high, high, medium, low | | @id | Unique identifier (e.g., py/sql-injection) | | @tags | Categories: security, correctness, maintainability |

Data Flow vs Taint Tracking

| Feature | DataFlow | TaintTracking | |---------|----------|---------------| | Tracks | Exact values | Derived values | | Use case | Value equality | Security flows | | Example | "Is this exact password used?" | "Does user input reach SQL?" | | Sanitizers | Not applicable | Supported |

GitHub Actions Integration

Basic Workflow

name: CodeQL

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  schedule:
    - cron: '0 0 * * 0'  # Weekly

jobs:
  analyze:
    name: Analyze
    runs-on: ubuntu-latest
    permissions:
      actions: read
      contents: read
      security-events: write

    strategy:
      fail-fast: false
      matrix:
        language: ['javascript', 'python']

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Initialize CodeQL
        uses: github/codeql-action/init@v3
        with:
          languages: ${{ matrix.language }}
          queries: security-extended

      - name: Autobuild
        uses: github/codeql-action/autobuild@v3

      - name: Perform CodeQL Analysis
        uses: github/codeql-action/analyze@v3
        with:
          category: "/language:${{ matrix.language }}"

Custom Queries in CI

- name: Initialize CodeQL
  uses: github/codeql-action/init@v3
  with:
    languages: python
    queries: security-extended,./custom-queries
    config-file: ./.github/codeql/codeql-config.yml

CodeQL Config File

# .github/codeql/codeql-config.yml
name: "Custom CodeQL Config"

queries:
  - uses: security-extended
  - uses: security-and-quality
  - uses: ./custom-queries

paths-ignore:
  - '**/test/**'
  - '**/tests/**'
  - '**/vendor/**'
  - '**/node_modules/**'

query-filters:
  - exclude:
      id: py/redundant-comparison

CLI Quick Reference

| Command | Purpose | |---------|---------| | codeql database create | Create analysis database | | codeql database analyze | Run queries against database | | codeql database upgrade | Upgrade database schema | | codeql database bundle | Package database for sharing | | codeql query compile | Compile QL query | | codeql query run | Run query directly | | codeql pack download | Install query packs | | codeql pack ls | List installed packs | | codeql pack init | Create custom pack |

Common Use Cases

1. Full Security Audit

# Create database
codeql database create audit-db --language=python --source-root=./app

# Run comprehensive security analysis
codeql database analyze audit-db \
  codeql/python-queries:codeql-suites/python-security-extended.qls \
  --format=sarif-latest \
  --sarif-add-snippets \
  --output=security-audit.sarif

# View results
cat security-audit.sarif | jq '.runs[].results[] | {rule: .ruleId, message: .message.text, location: .locations[0].physicalLocation.artifactLocation.uri}'

2. Variant Analysis

# Run custom query to find similar patterns
codeql query run variant.ql --database=my-db --output=variants.bqrs
codeql bqrs decode variants.bqrs --format=csv --output=variants.csv

3. Multi-Language Analysis

# Create databases for each language
codeql database create js-db --language=javascript --source-root=./frontend
codeql database create py-db --language=python --source-root=./backend

# Analyze separately
codeql database analyze js-db codeql/javascript-queries \
  --format=sarif-latest --output=frontend.sarif

codeql database analyze py-db codeql/python-queries \
  --format=sarif-latest --output=backend.sarif

# Merge SARIF results
jq -s '.[0].runs += .[1].runs | .[0]' frontend.sarif backend.sarif > combined.sarif

Performance Optimization

# Increase memory for large codebases
codeql database analyze my-db --ram=8192 --threads=4 ...

# Use compilation cache
export CODEQL_COMPILATION_CACHE="$HOME/.codeql/cache"

# Incremental analysis (reuse database)
codeql database create my-db --overwrite=false ...

# Limit query timeout
codeql database analyze my-db --timeout=600 ...

Troubleshooting

Common Issues

# Database creation fails - check build command
codeql database create my-db --language=java --command="mvn -X compile" ...

# Query compilation errors
codeql query compile --warnings=show query.ql

# Missing dependencies
codeql pack download codeql/python-all

# Database version mismatch
codeql database upgrade my-db

# Debug query execution
codeql query run query.ql --database=my-db --output=debug.bqrs -- --dump-ra

Validation

# Validate SARIF output
codeql database analyze my-db --format=sarif-latest --output=results.sarif
jq '.runs[0].results | length' results.sarif

# Check query metadata
codeql query metadata query.ql

# Test query against expected results
codeql test run tests/

Limitations

• Build required: Compiled languages need successful build
• Analysis time: Deep analysis can take hours on large codebases
• Memory usage: Large databases require significant RAM (8GB+)
• Learning curve: QL language requires dedicated learning
• Language coverage: Not all languages equally supported
• False positives: Complex flows may produce FPs requiring tuning

Rationalizations to Reject

| Shortcut | Why It's Wrong | |----------|----------------| | "CodeQL found nothing, code is secure" | CodeQL queries cover known patterns; novel vulnerabilities need custom queries | | "Too slow for CI" | Use caching, incremental analysis, or run on schedule instead of every PR | | "QL is too hard" | Start with built-in queries; custom queries can wait | | "GitHub-only tool" | CLI works anywhere; GitHub integration is optional | | "Semgrep covers the same" | CodeQL excels at deep interprocedural analysis Semgrep can't do |

References

• Documentation:
• Query Reference:
• GitHub Repository:
• Query Suites:
• VS Code Extension:
• GitHub Actions:
• SARIF Spec:
• Learning Lab:
• Query Console:

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: igbuend
• Source: igbuend/grimbard
• License: MIT

Install and usage instructions live in the source repository linked above.