The Common Workflow Language (CWL) is a standard for describing computational data-analysis workflows. Development of CWL is focused particularly on serving the data-intensive sciences, such as

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

medical imaging Medical imaging is the technique and process of imaging the interior of a body for clinical analysis and medical intervention, as well as visual representation of the function of some organs or tissues (physiology). Medical imaging seeks to revea ...

astronomy Astronomy is a natural science that studies celestial objects and the phenomena that occur in the cosmos. It uses mathematics, physics, and chemistry in order to explain their origin and their overall evolution. Objects of interest includ ...

physics Physics is the scientific study of matter, its Elementary particle, fundamental constituents, its motion and behavior through space and time, and the related entities of energy and force. "Physical science is that department of knowledge whi ...

, and

chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a physical science within the natural sciences that studies the chemical elements that make up matter and chemical compound, compounds made of atoms, molecules a ...

Standard

A key goal of the CWL is to allow the creation of a workflow that is portable and thus may be run reproducibly in different computational environments. The CWL originated from discussions in 2014 betwee
Peter AmstutzJohn ChiltonNebojša Tijanić
an
Michael R. Crusoe
(at that time their respective affiliations were:

Galaxy A galaxy is a Physical system, system of stars, stellar remnants, interstellar medium, interstellar gas, cosmic dust, dust, and dark matter bound together by gravity. The word is derived from the Ancient Greek, Greek ' (), literally 'milky', ...

, Arvados, Seven Bridges, and

Michigan State University Michigan State University (Michigan State or MSU) is a public university, public Land-grant university, land-grant research university in East Lansing, Michigan, United States. It was founded in 1855 as the Agricultural College of the State o ...

) at the

Open Bioinformatics Foundation The Open Bioinformatics Foundation is a non-profit, volunteer-run organization focused on supporting open source programming in bioinformatics. The mission of the foundation is to support the development of open source toolkits for bioinformatics, ...

br>BOSC 2014
codefest. CWL is supported by multiple analysis runners and platforms such as Apache Airflow (vi
CWL-Airflow

ArvadosRabixCromwell workflow engineToilREANA - Reusable Analyses
and
CWLEXEC
for

IBM Spectrum LSF IBM Spectrum LSF (LSF, originally Platform Load Sharing Facility) is a workload management platform, job scheduler, for distributed high performance computing (HPC) by IBM. Details It can be used to execute batch jobs on networked Unix and Window ...

, and was identified in 2017 as one of the future trends for bioinformatics pipeline development. Several additional analysis environments are currently implementing support for CWL including

Pegasus Pegasus (; ) is a winged horse in Greek mythology, usually depicted as a white stallion. He was sired by Poseidon, in his role as horse-god, and foaled by the Gorgon Medusa. Pegasus was the brother of Chrysaor, both born from Medusa's blood w ...

and

Availability

The CWL Project{{cite journal , last1=Crusoe , first1=Michael R. , last2=Abeln , first2=Sanne , last3=Iosup , first3=Alexandru , last4=Amstutz , first4=Peter , last5=Chilton , first5=John , last6=Tijanić , first6=Nebojša , last7=Ménager , first7=Hervé , last8=Soiland-Reyes , first8=Stian , last9=Gavrilović , first9=Bogdan , last10=Goble , first10=Carole , last11=The CWL Community , title=Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language , journal=Communications of the ACM , arxiv=2105.07028 , year=2022 , volume=65 , pages=54–63 , doi=10.1145/3486897, s2cid=234742536 is a multi-stakeholder working group consisting of both organizations and individuals. A member project of

Software Freedom Conservancy Software Freedom Conservancy, Inc. (also known as "Conservancy") is an organization that provides a Nonprofit organization, non-profit home, infrastructure support, and legal support for free software, free and open source software projects. The ...

, it publishes the CWL standards freely available via it
GitHub repository
under a permissive Apache License 2.0.

References

External links

CWL v1.0 specification DOI

CWL website

CWL GitHub Repository

CWL entry in the EU Observatory for ICT Standardisation
Workflow languages Cloud standards Computer standards Data interchange standards