Common Workflow Language Explained

Common Workflow Language
Long Name:The Common Workflow Language standards
Status:Published
Version:1.2
Related Standards:BioCompute Object
Abbreviation:CWL
License:Apache 2.0

The Common Workflow Language (CWL) is a standard for describing computational data-analysis workflows.[1] Development of CWL is focused particularly on serving the data-intensive sciences, such as bioinformatics,[2] medical imaging, astronomy, physics, and chemistry.

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.[3]

The CWL originated from discussions in 2014 between Peter Amstutz, John Chilton, Nebojša Tijanić, and Michael R. Crusoe (at that time their respective affiliations were: Galaxy, Arvados, Seven Bridges, and Michigan State University) at the Open Bioinformatics Foundation BOSC 2014 codefest.

CWL is supported by multiple analysis runners and platforms[4] such as Apache Airflow (via CWL-Airflow [5]), Arvados, Rabix,[6] Cromwell workflow engine, Toil, REANA - Reusable Analyses and CWLEXEC for IBM Spectrum LSF, 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[7] and Galaxy.[8]

Availability

The CWL Project[9] is a multi-stakeholder working group consisting of both organizations and individuals. A member project of Software Freedom Conservancy, it publishes the CWL standards freely available via its GitHub repository under a permissive Apache License 2.0.

References

  1. Peter. Amstutz. R.. Crusoe, Michael. Nebojša. Tijanić. Brad. Chapman. John. Chilton. Michael. Heuer. Andrey. Kartashov. Dan. Leehr. Hervé. Ménager. 2016-07-08. Common Workflow Language, v1.0. Figshare. en-US. 10.6084/m9.figshare.3115156.v2.
  2. Leipzig. Jeremy. 2017-05-01. A review of bioinformatic pipeline frameworks. Briefings in Bioinformatics. en. 18. 3. 530–536. 10.1093/bib/bbw020. 27013646. 1467-5463. 5429012.
  3. Perkel. Jeffrey M.. Workflow systems turn raw data into scientific knowledge. Nature. 573. 7772. 2019. 149–150. 0028-0836. 10.1038/d41586-019-02619-z. 31477884. 2019Natur.573..149P. 201713827. free.
  4. Web site: CWL Implementations . Common Workflow Language (CWL) . 10 October 2021 . en.
  5. Barski. Artem. Kartashov. Andrey V.. Kotliar. Michael. 2019-07-01. CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language. GigaScience. en. 8. 7. 10.1093/gigascience/giz084. 31321430. 6639121.
  6. Book: Kaushik . Gaurav . Ivković . Sinisa . Simonović . Janko . Tijanić . Nebojša . Davis-Dusenbery . Brandi . Kural . Deniz . Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions . Pacific Symposium on Biocomputing 2017 . Proceedings of the Pacific Symposium . January 2017 . 22 . 154–165 . 10.1142/9789813207813_0016 . 27896971. 5166558 . 978-981-320-780-6 .
  7. Web site: 11.6. pegasus-cwl-converter — Pegasus WMS 5.0.1 documentation . pegasus.isi.edu . 10 October 2021.
  8. Web site: Chilton . John . Soranzo . Nicola . Implement a subset of the Common Workflow Language. by jmchilton · Pull Request #47 · common-workflow-language/galaxy . GitHub . 10 October 2021 . en.
  9. Crusoe . Michael R. . Abeln . Sanne . Iosup . Alexandru . Amstutz . Peter . Chilton . John . Tijanić . Nebojša . Ménager . Hervé . Soiland-Reyes . Stian . Gavrilović . Bogdan . Goble . Carole . The CWL Community . Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language . Communications of the ACM . 2105.07028 . 2022 . 65 . 54–63 . 10.1145/3486897. 234742536 .

External links

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Common Workflow Language".

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