Format 2

This package defines a high-level Galaxy workflow description termed “Format 2”. The current schema version is v19_09 and the schema can be found here. This version of workflow format can be consumed by Galaxy since version 19.09.

The Format 2 workflow description is still somewhat experimental and may yet change in small potentially backward incompatible ways until the format is exported by Galaxy by default.

The traditional Galaxy workflow description (files ending in .ga extension, sometimes called native workflows in this project) was not designed to be concise and is neither readily human readable or human writable. Galaxy workflow Format 2 is being designed to address these limitations, while also moving Galaxy’s workflow description language toward standards such as the Common Workflow Language.

gxformat2

This Python project can be installed from PyPI using pip.

$ pip install gxformat2

Checkout the project tests or how it used in projects such as Planemo and Galaxy to see how to use the gxformat2 library. Reference documentation for the modules can be found as part of the project’s documentation.

This project also includes various scripts for working with Galaxy workflows. Checkout their help for more information.

$ gxwf-lint --help
$ gxwf-viz --help
$ gxwf-abstract-export --help
$ gxwf-to-native --help
$ gxwf-to-format2 --help

Development

Setup a development environment with uv:

$ uv sync --group test --group lint --group mypy

Run tests:

$ uv run --group test pytest tests/ -x -q

Run linting:

$ uv run --group lint ruff check
$ uv run --group lint flake8
$ uv run --group lint black --check --diff .

Run type checking:

$ uv run --group mypy mypy gxformat2

This library and associated scripts are licensed under the MIT License.