codeql-queries

Overview

Per docs.github.com/code-security/codeql-cli (opens in new window):

CodeQL is GitHub's semantic-analysis SAST: build a database of the codebase (control flow, data flow, type info), run .ql queries against it, emit SARIF for GitHub Code Scanning. This database-then-query model catches cross-file taint flows (user input reaching a SQL sink unsanitized) that pattern matchers cannot express.

When to use

• The team uses GitHub-hosted repos (Code Scanning is GitHub-native).
• The codebase has cross-file taint flows that pattern-matchers miss (e.g., user input → service A → service B → SQL).
• A security audit requires CodeQL coverage (some compliance regimes prefer it).
• The team writes custom queries for org-specific patterns.

For multi-platform CI without GitHub, use semgrep-rules or sonarqube-rules.

Step 1 - Install

CodeQL CLI download from github.com/github/codeql-cli-binaries/releases (opens in new window). Per cql-docs (opens in new window) the CLI is bundled separately from the queries - install both:

# Download CodeQL CLI (per platform)
curl -L https://github.com/github/codeql-cli-binaries/releases/latest/download/codeql-linux64.zip -o codeql.zip
unzip codeql.zip
export PATH="$PATH:$PWD/codeql"

# Verify
codeql --version

Query packs (the .ql files) are pulled per-scan via --download flag or pre-installed via codeql pack download.

Step 2 - Create a database

# For interpreted languages (JS, Python, Ruby): no build needed
codeql database create my-db --language=javascript --source-root=.

# For compiled languages (Java, C#, Go): wrap the build
codeql database create my-db --language=java --command="./gradlew build" --source-root=.

codeql database create my-db --language=cpp --command="make all"

The --language flag accepts: cpp / csharp / go / java / javascript / python / ruby / swift / kotlin (verify support against cql-docs (opens in new window) for the current CodeQL release).

For JS/TS + Python, the --build-mode none extraction works without a build step. For Java/C#/C++, you MUST wrap the project's build via --command so CodeQL can observe compilation.

Step 3 - Analyze with query packs

codeql database analyze my-db \
  --format=sarif-latest \
  --output=results.sarif \
  codeql/javascript-queries

The full per-language pack list, the query suites (code-scanning, security-and-quality, security-extended), a custom .ql query example, and the GitHub Actions CI integration are in references/codeql-reference.md.

Step 4 - False-positive triage (MANDATORY)

Three layers:

Justification template (mandatory in code):

// codeql[js/sql-injection]
// Reason: parameter pre-validated via Joi schema (line 42); literal interpolation safe
// Reviewer: alice@example.com (2026-05-15)
// Expires: 2026-12-15
const result = await db.query(`SELECT * FROM users WHERE id = ${userId}`);

GitHub Security tab dismissals are persistent + auditable + show in the audit log; prefer them over inline comments for production suppressions.

Cadence: every quarter, review GitHub Security → "Dismissed alerts" filter; expired ones reopened for re-review.

Step 5 - Database performance

CodeQL databases can be GBs for large codebases. Performance flags:

codeql database create my-db --language=java \
  --command="./gradlew build" \
  --threads=8 \
  --ram=8192   # MB

For incremental scanning (changed-files-only), GitHub's hosted runner uses caching across runs. Self-hosted CI must implement caching manually (the codeql-action/init action handles it on GitHub).

Anti-patterns

Limitations

• Database creation is slow for large codebases (10 - 30 min on monorepos); incremental scanning helps but requires caching.
• Custom-query authoring has a steep learning curve; the CodeQL University courses help.
• Some languages have less depth than others (Go, Ruby, Swift are newer than JS/Java/C++).
• Self-hosted (non-GitHub) integration requires manual SARIF routing.
• License: CodeQL CLI is free for open-source repos; commercial use requires GitHub Advanced Security license.

References

• cql-docs (opens in new window) - CodeQL CLI getting started
• codeql.github.com/docs - official documentation root
• codeql.github.com/codeql-standard-libraries/ - per-language stdlibs
• github.com/github/codeql - query packs source
• learningqltest.github.io/learningql/ - CodeQL University training
• semgrep-rules, sonarqube-rules, language-native-sast - sister scanners