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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:


  • Copyright © 2019-2020, Ignacio Eguinoa, VIB, Universiteit Gent, and 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 install

This should install cwl2galaxy on your PATH.

Alternatively you can run python3 galaxy2cwl/ directly.


A simple workflow to use as example can be found in

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

  • The Galaxy .ga format is in examples/
  • 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


Contributions welcome! Raise pull requests, issues etc on

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

Project details

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