Open-source tools for Common Workflow Language
Your workflow is more than its execution.¶
Turn CWL workflows into documentation, citations, research objects, and software supply-chain insights.
Transpiler-Mate connects your workflow description and software metadata to a growing family of independent plugins. Describe your software once. Put that description to work across your research and development lifecycle.
Get started Explore the plugins
Built around CWL · Independent Python packages · Open source
One description. Many useful artifacts.¶
The runtime loads your CWL and discovers installed plugins. Each plugin turns the shared context into a specific output, so you can install only what your project needs. Meet the foundations.
What can you do with Transpiler-Mate?¶
Start with an outcome. Find the tools that help you get there.
Make workflows understandable¶
Generate Markdown documentation, PlantUML diagrams, and interactive workflow explorers. Give collaborators a way to inspect steps, dependencies, and inputs.
Make research software reusable¶
Export discovery metadata, generate citations, and package workflows as RO-Crates. Connect your software to research publication tools and services.
Inspect your software supply chain¶
Inventory workflow containers and generate local CycloneDX SBOMs with Trivy. Record image identities and coverage gaps for downstream assessment.
Prepare workflows for integration¶
Generate input templates, CLI scaffolding, and MCP tool definitions. Validate inputs with schemas and policies before execution.
Get started¶
Install the runtime and a plugin in the same Python 3.10+ environment. For example, start with documentation generation:
python -m pip install transpiler-mate-runtime cwl2markdown
transpiler-mate --help
transpiler-mate cwl2markdown --help
Installed plugins become subcommands of transpiler-mate. The plugin's help lists the options for your workflow and output location.
- Choose a CWL workflow. Start with a workflow you want to document, inspect, or share.
- Add the metadata your plugin needs. Use the online metadata generator and the Software Application metadata reference.
- Generate your artifacts. Follow the cwl2markdown guide for documentation, or choose another plugin above.
Already using several plugins? Run them together with a batch execution plan and reuse the same resolved CWL context.
Built to use. Open to extend.¶
Build a plugin¶
Bring your own output format or integration. Shared API contracts and a project template help you develop and distribute plugins independently.
Get involved¶
Help improve the tools with bug reports, workflow examples, documentation, or code. Open an issue or pull request in the relevant repository and follow its contribution guide.