cwltool
Common workflow language reference implementation
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires a container engine (Docker, Podman, Singularity, or Apptainer) to execute containerized workflow steps; node.js recommended for evaluating CWL expressions.
- 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).
License · maintenance · safety
permissive license (permissive) — Licensed under Apache Software License (permissive), allowing commercial and private use with minimal restrictions.
last release 2026-07-20 (25 days) · last repo commit 2026-08-14 · 376 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 294,687 downloads/mo, #7,944 on PyPI
Alternatives
Verify before relying
pip install cwltool
cwltool my_workflow.cwl my_inputs.yaml- 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.
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 on it.
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
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.
Requires a container engine (Docker, Podman, Singularity, or Apptainer) to execute containerized workflow steps; node.js recommended for evaluating CWL expressions.
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.yamlVerify 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
| License | permissive license permissive |
| Python support | Supports the current Python release <3.15,>=3.10 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 16 packagesrequestsruamel.yamlrdflibschema-saladprovmypy-extensionspsutilcoloredlogspydotargcompletepyparsingcwl-utilsspythonrich-argparsepygmentstyping-extensions |
| Maintenance | Actively maintained 25 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 294,687 / month, #7,944 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 5 - Production/StableEnvironment :: ConsoleIntended Audience :: DevelopersIntended Audience :: Healthcare IndustryIntended Audience :: Science/ResearchLicense :: OSI Approved :: Apache Software LicenseNatural Language :: EnglishOperating System :: MacOS :: MacOS XOperating System :: POSIXOperating System :: POSIX :: LinuxProgramming Language :: Python :: 3Programming Language :: Python :: 3.10Programming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.13Programming Language :: Python :: 3.14Topic :: Scientific/EngineeringTopic :: Scientific/Engineering :: AstronomyTopic :: Scientific/Engineering :: Atmospheric ScienceTopic :: Scientific/Engineering :: Bio-InformaticsTopic :: Scientific/Engineering :: Information AnalysisTopic :: Scientific/Engineering :: Medical Science Apps.Topic :: System :: Distributed ComputingTopic :: Utilities |
Evidence: cwltool-3.2.20260720092025-py3-none-any.whl
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See also cwl-upgrader · cwltest · cwl-utils · apache-airflow · vcstool · apache-airflow-providers-singularity · prefect-docker · metaflow-prebuilt · schema-salad · cwsandbox