cwltool

What it is and what it does

cwltool is the official reference implementation of the Common Workflow Language (CWL) standard, a specification for describing computational workflows in a portable, platform-agnostic way. It provides a command-line tool and Python library for parsing, validating, and executing CWL workflow definitions, allowing you to define complex scientific pipelines once and run them on different systems—from local machines to cloud platforms and high-performance computing clusters.

The tool integrates with container engines (Docker, Podman, Singularity, Apptainer, or udocker) to isolate and execute individual workflow steps, manages data flow between tasks, and handles resource allocation. It depends on schema-salad for CWL schema validation, rdflib for semantic data handling, prov for provenance tracking, and several utility libraries for logging, argument parsing, and visualization. The package is actively developed by the CWL project (a Software Freedom Conservancy member) and supports Python 3.10 through 3.14.

Use it for:

• Execute bioinformatics pipelines (genomics, proteomics) defined in CWL across different HPC clusters or cloud providers without modification.
• Validate CWL workflow files for correctness before deployment in production environments.
• Integrate scientific workflows into larger systems by using cwltool as a Python library to programmatically run and monitor CWL tasks.
• Port existing workflows between institutional computing environments (local, cloud, or shared HPC) by leveraging CWL's platform-agnostic design.
• Combine multiple containerized tools into reproducible multi-step workflows with explicit data dependencies and resource requirements.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

cwltool is the reference implementation of the Common Workflow Language standard, enabling you to write, validate, and execute portable scientific workflows defined in CWL format across different computing environments.

Yes. cwltool is the canonical reference implementation of an open standard, actively maintained, permissively licensed, and widely used in scientific computing. Install it if you need to execute portable workflows, validate CWL definitions, or integrate CWL workflows into Python applications. The main prerequisite is having a container engine available; without one, containerized workflow steps cannot run.

Install

cwltool on PyPI

pip install cwltool

uv add cwltool

poetry add cwltool

Installing cwltool

Before you install

Low install friction with a pure Python wheel distribution. The package is actively maintained (last commit 2026-08-14, release 25 days ago) and supports current Python versions (3.10–3.14). It has 16 runtime dependencies, all widely available, with no known vulnerabilities.

License in practice

Licensed under Apache Software License (permissive), allowing commercial and private use with minimal restrictions.

Quickstart

pip install cwltool

cwltool my_workflow.cwl my_inputs.yaml

Requires a container engine (Docker, Podman, Singularity, or Apptainer) to execute containerized workflow steps; node.js recommended for evaluating CWL expressions.

Verify before relying

• Performance characteristics when executing large-scale workflows or handling thousands of tasks.
• Specific memory and CPU overhead for workflow orchestration and validation.
• Compatibility details with all supported container engines and their versions.

Package facts

Evidence: cwltool-3.2.20260720092025-py3-none-any.whl

Tags

More Scientific/Engineering packages