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🧪 Testing VEP Polaris

This project includes test scripts to verify that each tool behaves as expected. Tests are written in portable Bash and use only standard Unix utilities.

🔧 Requirements

  • Bash (4.x or higher)
  • Core Unix utilities: grep, gzip, head, mkdir, rm, echo, etc.
  • Optional: Node.js (for npm run test command more easily)

🚀 Run All Tests

If you've already installed the toolkit:

npm test

This runs the run-tests.sh script, which locates and executes all test scripts in test/.

Alternatively, run it manually:

chmod +x run-tests.sh # needs to be run initially
./run-tests.sh

This script will:

  • Find all test scripts in the test/ directory (with filenames like test-*.sh)
  • Run each one
  • Exit with an error if any test fails

🧪 Run an Individual Test

To run a single test directly:

bash test/test-plugin-inspect.sh

Useful when debugging or developing a specific tool.

🛠 Adding a New Test

To add a new test script:

  1. Name it test/test-<tool>.sh

  2. Make it executable:

    bash chmod +x test/test-yourtool.sh

  3. It will automatically be picked up by ./run-tests.sh

✅ Expected Output

If all tests pass, you'll see something like:

🔬 Running all VEP Polaris tests...
➡️  Running: test/test-plugin-inspect.sh
✔ PASS: Plain numeric chromosome format recognized
✔ PASS: chrN format recognized
✔ PASS: Warning for comment-only file shown

✅ All tests passed!

If a test fails, it will print a clear failure message and exit:

✘ FAIL: Expected output to contain: plain.tsv

🤖 Continuous Integration (Optional)

To include this in GitHub Actions or another CI tool, add a step to your workflow:

- name: Run VEP Polaris tests
  run: ./run-tests.sh

For more information about individual tools, see the documentation index.

vep-polaris <tool> --help