codeql-queries
Overview
Per docs.github.com/code-security/codeql-cli:
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.
Per cql-docs 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 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:
| Mechanism | Example | When to use |
|---|
Inline // codeql[<rule-id>] | // codeql[js/sql-injection] - Reason: input pre-sanitized via library X | Single-line exception with documented rationale |
| SARIF post-processing filter | cat results.sarif | jq 'del(.runs[].results[] | select(.ruleId == "js/path-injection" and .locations[].physicalLocation.artifactLocation.uri | startswith("vendor/")))' | Bulk exclusion of vendored / generated code |
| GitHub Security tab dismissal | UI: "Dismiss alert" → False positive / Won't fix / Used in tests | Persistent, auditable, requires reviewer comment |
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
| Anti-pattern | Why it fails | Fix |
|---|
Skip --command for compiled languages | Database empty; analysis returns no findings silently | Always wrap the build (Step 2) |
Use security-extended without baseline | Flood of pre-existing findings overwhelms the team | Start with code-scanning; ratchet up |
| Inline comment without GitHub dismissal | No audit trail | Use Security-tab dismissal for persistent FPs (Step 4) |
| Run CodeQL on every PR for large codebase | Database creation is slow (10 - 30 min); PR cycle slow | Schedule full scan nightly; PR-only delta scanning via Code Scanning |
| Custom queries without test suite | Bugs in custom queries miss real findings | Use codeql test to validate against expected-results files |
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 - 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