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Common Workflow Language
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========================
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The Common Workflow Language (CWL) is an informal, multi-vendor working group
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consisting of various organizations and individuals that have an interest in
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portability of data analysis workflows. Our goal is to create specifications
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that enable data scientists to describe analysis tools and workflows that are
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powerful, easy to use, portable, and support reproducibility.
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[![GitHub stars](https://img.shields.io/github/stars/common-workflow-language/common-workflow-language.svg)](https://github.com/common-workflow-language/common-workflow-language/stargazers) [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/common-workflow-language/common-workflow-language?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
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CWL builds on technologies such as [JSON-LD](http://json-ld.org)
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for data modeling and [Docker](http://docker.com) for portable runtime\
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environments.
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CWL is designed to express workflows for data-intensive science, such as
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Bioinformatics, Medical Imaging, Chemistry, Physics, and Astronomy.
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The Common Workflow Language (CWL) is a specification for describing analysis
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workflows and tools that are portable and scalable across a variety of software
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and hardware environments, from workstations to cluster, cloud, and high
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performance computing (HPC) environments. CWL is designed to meet the needs of
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data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy,
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Physics, and Chemistry.
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## CWL User Guide
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CWL is developed by an informal, multi-vendor working group consisting of
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organizations and individuals interested enabling scientists to share data
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analysis workflows. [The CWL project is on Github.](https://github.com/common-workflow-language/common-workflow-language)
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[User guide for the current stable specification (v1.0)](http://www.commonwl.org/v1.0/UserGuide.html),
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provides a gentle introduction to writing CWL command line tool and workflow descriptions.
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CWL builds on technologies such as [JSON-LD](http://json-ld.org)
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for data modeling and [Docker](http://docker.com) for portable runtime
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environments.
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## CWL Specification
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## User Guide
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The current stable specification is [v1.0](http://www.commonwl.org/v1.0/):
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The [CWL user guide (v1.0)](http://www.commonwl.org/v1.0/UserGuide.html) provides a
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gentle introduction to learning how to write CWL command line tool and workflow
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descriptions.
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http://www.commonwl.org/v1.0/
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## Specification
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Older drafts: [draft-1](https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-1), [draft-2](http://www.commonwl.org/draft-2/), [draft-3](http://www.commonwl.org/draft-3/)
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For developers and advanced users, the current
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[CWL specification (v1.0)](http://www.commonwl.org/v1.0/) provides
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authoritative documentation of the execution of CWL documents. Links older
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drafts:
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[draft-1](https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-1),
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[draft-2](http://www.commonwl.org/draft-2/),
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[draft-3](http://www.commonwl.org/draft-3/)
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### Citation
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Please cite https://dx.doi.org/10.6084/m9.figshare.3115156.v2
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## Implementations
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Some of the software supporting running Common Workflow Language tools or workflows:
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* [cwltool (reference implementation)](https://github.com/common-workflow-language/cwltool),
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[cwltool wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/cwltool-%28reference-implementation%29)
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* [Rabix](https://github.com/rabix/rabix),
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[Rabix wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/Rabix)
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* [Arvados](https://arvados.org),
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[Arvados wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/Arvados)
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* [Galaxy](https://github.com/common-workflow-language/Galaxy),
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[Galaxy wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/Galaxy)
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* [Parallel Recipes](https://github.com/yvdriess/precipes),
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[Parallel Recipes wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/Parallel-Recipes)
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* [Toil](https://github.com/BD2KGenomics/toil),
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[Toil wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/Toil)
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* [CancerCollaboratory](https://github.com/CancerCollaboratory),
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[CancerCollaboratory wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/CancerCollaboratory)
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* [Airflow (SciDAP)](https://github.com/SciDAP/scidap),
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[Airflow wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/SciDAP)
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* [cwl2script](https://github.com/common-workflow-language/cwl2script),
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[cwl2script page](https://github.com/common-workflow-language/common-workflow-language/wiki/cwl2script)
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* [Apache Taverna](http://taverna.incubator.apache.org/),
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[Apache Taverna wiki page](https://github.com/common-workflow-language/common-workflow-language/wiki/Taverna)
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We continuously run the CWL conformance tests on several implementations:
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https://ci.commonwl.org
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## Examples
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[Github repository of example tools and workflows.](https://github.com/common-workflow-language/workflows)
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## Support
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The best place to ask a question about all things CWL is on
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|Software|Description|CWL support|Platform support|Maturity|
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|--------|-----------|-----------|--------|--------|
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|[cwltool](https://github.com/common-workflow-language/cwltool)|Reference implementation of CWL|[![Build Status](https://ci.commonwl.org/job/cwltool-conformance/badge/icon)](http://ci.commonwl.org/job/cwltool-conformance/lastBuild/testReport/)|Linux, OS X, local execution only|Production|
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|[Arvados](https://arvados.org)|Distributed computing platform for data analysis on massive data sets. [Using CWL on Arvados](http://doc.arvados.org/user/cwl/cwl-runner.html)|[![Build Status](https://ci.commonwl.org/job/arvados-conformance/badge/icon)](http://ci.commonwl.org/job/arvados-conformance/lastBuild/testReport/)|AWS, GCP, Azure, Slurm|Production|
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|[Toil](https://github.com/BD2KGenomics/toil)|Toil is a workflow engine entirely written in Python.|[![Build Status](https://ci.commonwl.org/job/toil-conformance/badge/icon)](http://ci.commonwl.org/job/toil-conformance/lastBuild/testReport/)|AWS, GCP, Azure, OpenStack, Grid Engine, Mesos|Production|
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|[Apache Taverna](http://taverna.incubator.apache.org/)|Domain-independent Workflow Management System|[alpha](https://issues.apache.org/jira/browse/TAVERNA-900)|Java|Production|
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|[Galaxy](https://galaxyproject.org/)|Web-based platform for data intensive biomedical research.|[alpha](https://github.com/common-workflow-language/galaxy)|Python|Production|
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|[AWE](https://github.com/MG-RAST/AWE)|Workflow and resource management system for bioinformatics data analysis.|[alpha](https://github.com/wgerlach/AWE)|Go|Production|
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|[Funnel](https://github.com/bmeg/funnel)|Use Google Genomics Pipeline API with CWL|alpha|GCP|alpha|
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|[Rabix Bunny](https://github.com/rabix/bunny)|Reproducible Analyses for Bioinformatics|alpha|Java|alpha|
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## Repositories of CWL Tools and Workflows
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|Repository|Description|
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|----|-----------|
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|[Workflows repository](https://github.com/common-workflow-language/workflows)|Git repository of user contributed tools and workflows.|
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|[Dockstore tool registry](http://dockstore.org)|An open platform for sharing Docker-based tools described with the Common Workflow Language used by the GA4GH.|
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## Software for working with CWL
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|Software|Description|
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|--------|-----------|
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|[cwltest](https://github.com/common-workflow-language/cwltest)|CWL testing framework, automated testing of tools and workflows written with CWL|
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|[cwl-upgrader](https://github.com/common-workflow-language/cwl-upgrader)|Upgrade CWL documents from draft-3 to v1.0|
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|[argparse2cwl](https://github.com/common-workflow-language/gxargparse#argparse2cwl)|Generate CWL CommandLineTool wrapper from Python programs that use argparse. Also supports [click](http://click.pocoo.org/5/) argument parser.|
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|[cwl2argparse](https://github.com/common-workflow-language/cwl2argparse)|Generate Python argparse code from CWL CommandLineTool description.|
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|[pypi2cwl](https://github.com/common-workflow-language/pypi2cwl)|Automatically run argparse2cwl on any package in PyPi|
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|[cwlavro](https://github.com/common-workflow-language/cwlavro)|Java classes for loading CWL documents|
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## Support, Community and Contributing
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The recommended place to ask a question about all things CWL is on
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[Biostars](https://www.biostars.org/t/cwl/).
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[![Biostars
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CWL](https://www.biostars.org/static/biostar2.logo.png)](https://www.biostars.org/t/cwl/)
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</a>
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## Development and testing
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[The CWL project is on Github.](https://github.com/common-workflow-language/common-workflow-language)
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[![GitHub
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stars](https://img.shields.io/github/stars/common-workflow-language/common-workflow-language.svg)](https://github.com/common-workflow-language/common-workflow-language/stargazers)
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There is a Jenkins server maintained by Curoverse that runs tests for the
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reference implementation, builds and uploads packages, and builds and uploads
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Docker images:
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https://ci.curoverse.com/job/common-workflow-language/
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Current build status: [![Build Status](https://ci.curoverse.com/buildStatus/icon?job=common-workflow-language)](https://ci.curoverse.com/job/common-workflow-language/)
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## Community and Contributing
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[![Biostars CWL](https://www.biostars.org/static/biostar2.logo.png)](https://www.biostars.org/t/cwl/)
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If you are interested in learning more or contributing ideas or code,
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[come chat with us on Gitter](https://gitter.im/common-workflow-language/common-workflow-language),
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[fork the repository](https://github.com/common-workflow-language/common-workflow-language)
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and send a pull request!
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[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/common-workflow-language/common-workflow-language?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
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Your CWL Community Engineer, Michael R. Crusoe, publishes a blog about his work
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with updates at http://mrc.commonwl.org.
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