virtool-workflow

Virtool Workflow

A framework for developing bioinformatic workflows in Python.

from virtool_workflow import step


@step
def step_function():
    ...


@step
def step_function_2():
    ...

Contributing

Commits

We require specific commit formatting. Any commit that does not follow the guidelines will be squashed at our discretion.

Read our commit and release documentation for more information.

Tests

Run tests with:

# Bring up Redis and the test container.
docker compose up -d

# Run tests in the test container.
docker compose exec test poetry run pytest

Run specific tests like:

docker compose exec test poetry run pytest tests/test_status.py