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Convert a Galaxy workflow to abstract Common Workflow Language (CWL)

Project description

Convert Galaxy workflow files to (abstract) CWL

This is a standalone tool that creates CWL-abstract descriptions of Galaxy workflow runs or Galaxy workflow files (static files).

  • Usage:
galaxy2cwl INPUT_GALAXY_WORKFLOW(.ga/.yaml) > OUTPUT_WORKFLOW.cwl

License

  • Copyright © 2019-2020, Ignacio Eguinoa, VIB, Universiteit Gent, and workflowhub.eu contributors

Distributed under a BSD 3-Clause license.

Installing from source

Easiest is to use pip:

pip3 install .

or, assuming all dependencies are installed:

python setup.py install

This should install cwl2galaxy on your PATH.

Alternatively you can run python3 galaxy2cwl/get_cwl_interface.py directly.

Examples

A simple workflow to use as example can be found in https://usegalaxy.eu/u/igegu/w/simple-workflow

This workflow is available in different formats in the examples/ directory of the source repository.

  • The Galaxy .ga format is in examples/simple_workflow_galaxy.ga
  • The format2 version yaml wrapped in json can be found in examples/simple_workflow_format2_yaml_wrapped.json
  • The format2 pure yaml in examples/simple_workflow_format2.yaml
  • The resulting CWL-interface can be found in examples/simple_workflow_cwl-interface.cwl

Packaging with RO-Crate

The objects created with this project are aimed to be part of workflow based RO-Crate packages for registering in WorkflowHub.

WorkflowHub is a project under development that aims at, among other things, serve as a repository for workflows standardizing the metadata description.

As such it provides the possibility of registering workflows in a diverse set of formats and packaging them in a RO-Crate package.

All examples included in this project are readily available in https://dev.workflowhub.eu/

Contribute

Contributions welcome! Raise pull requests, issues etc on https://github.com/workflowhub-eu/galaxy2cwl/.

Submitted patches are assumed to be licensed under the same BSD 3-Clause license.

Project details


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