The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry.
CWL is developed by an informal, multi-vendor working group consisting of organizations and individuals aiming to enable scientists to share data analysis workflows. The CWL project is on Github and we follow the Open-Stand.org principles for collaborative open standards development
CWL builds on technologies such as JSON-LD for data modeling and Docker for portable runtime environments.
The CWL user guide (v1.0) provides a gentle introduction to learning how to write CWL command line tool and workflow descriptions.
For developers and advanced users, the current CWL specification (v1.0) provides authoritative documentation of the execution of CWL documents. Links older drafts: draft-1, draft-2, draft-3
Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
| Software | Description | CWL support | Platform support |
|---|---|---|---|
| cwltool | Reference implementation of CWL | Linux, OS X, local execution only | |
| Arvados | Distributed computing platform for data analysis on massive data sets. Using CWL on Arvados | AWS, GCP, Azure, Slurm | |
| Toil | Toil is a workflow engine entirely written in Python. | AWS, GCP, Azure, OpenStack, Grid Engine, Mesos | |
| Rabix Bunny | Reproducible Analyses for Bioinformatics | Java | |
| Apache Taverna | Domain-independent Workflow Management System | alpha | Java |
| Galaxy | Web-based platform for data intensive biomedical research. | alpha | Python |
| AWE | Workflow and resource management system for bioinformatics data analysis. | alpha | Go |
| Funnel | Use Google Genomics Pipeline API with CWL | alpha | GCP |
| Xenon | Run CWL workflows using Xenon | alpha | any Xenon backend: local, ssh, SLURM, Torque, Grid Engine |
| Repository | Description |
|---|---|
| Workflows repository | Git repository of user contributed tools and workflows. |
| Dockstore tool registry | An open platform for sharing Docker-based tools described with the Common Workflow Language used by the GA4GH. |
| Software | Description |
|---|---|
| cwltest | CWL testing framework, automated testing of tools and workflows written with CWL |
| cwl-upgrader | Upgrade CWL documents from draft-3 to v1.0 |
| argparse2tool | Generate CWL CommandLineTool wrappers (and/or Galaxy tool descriptions) from Python programs that use argparse. Also supports the click argument parser. |
| cwl2argparse | Generate Python argparse code from CWL CommandLineTool description. |
| pypi2cwl | Automatically run argparse2cwl on any package in PyPi |
| cwlavro | Java classes for loading CWL documents |
| acd2cwl | CWL generator for ACD (EMBOSS) files |
| CWLviewer | A web application to view and share Common Workflow Language workflows |
The recommended place to ask a question about all things CWL is on Biostars.
If you are interested in learning more or contributing ideas or code, come chat with us on Gitter, check out #CommonWL on Twitter, join the mailing list common-workflow-language on Google Groups or fork the repository and send a pull request!
Your CWL Community Engineer, Michael R. Crusoe, publishes a blog about his work with updates at http://mrc.commonwl.org.
The CWL Project is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, age, race, or religion. We do not tolerate harassment of participants in any form.
This code of conduct applies to all CWL Project spaces, including the Google Group, the Gitter chat room, the Google Hangouts chats, both online and off. Anyone who violates this code of conduct may be sanctioned or expelled from these spaces at the discretion of the leadership team.
For more details, see our Code of Conduct
- Curoverse
- Seven Bridges Genomics
- Galaxy Project
- Apache Taverna
- Institut Pasteur
- Wellcome Trust Sanger Institute
- University of California Santa Cruz
- Harvard Chan School of Public Health
- Cincinnati Children's Hospital Medical Center
- Broad Institute
- Wolfson Wohl Cancer Research Centre
- Netherlands eScience Center
- Texas Advanced Computing Center Life Science Computing Group
(Alphabetical)
- Peter Amstutz peter.amstutz@curoverse.com
- Robin Andeer robin.andeer@gmail.com
- Brad Chapman bchapman@hsph.harvard.edu
- John Chilton jmchilton@gmail.com
- Michael R. Crusoe michael.crusoe@gmail.com
- Roman Valls Guimerà brainstorm@nopcode.org
- Guillermo Carrasco Hernandez guille.ch.88@gmail.com
- Sinisa Ivkovic sinisa.ivkovic@sbgenomics.com
- Andrey Kartashov Andrey.Kartashov@cchmc.org
- John Kern kern3020@gmail.com
- Dan Leehr dan.leehr@duke.edu
- Hervé Ménager herve.menager@gmail.com
- Maxim Mikheev mikhmv@biodatomics.com
- Tim Pierce twp@unchi.org
- Josh Randall joshua.randall@sanger.ac.uk
- Janko Simonović janko.simonovic@sbgenomics.com
- Stian Soiland-Reyes soiland-reyes@cs.manchester.ac.uk
- Luka Stojanovic luka.stojanovic@sbgenomics.com
- Nebojša Tijanić nebojsa.tijanic@sbgenomics.com