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Common Workflow Language

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Common Workflow Language
The Common Workflow Language standards
CWL Logo
AbbreviationCWL
StatusPublished
Year started10 July 2014 (2014-07-10)
Latest version1.1
8 June 2019 (2019-06-08)
Related standardsBioCompute Object
LicenseApache 2.0
Websitecommonwl.org

The Common Workflow Language (CWL) is a standard[1] for describing computational data-analysis workflows. Development of CWL is focused particularly on serving the data-intensive sciences, such as Bioinformatics,[2] Medical Imaging, Astronomy, Physics, and Chemistry. 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, Nebojsa Tijanic, 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 such as Apache Airflow (via CWL-Airflow [4]), Arvados, Rabix, Cromwell workflow engine, Toil, REANA - Reusable Analyses and CWLEXEC for IBM Spectrum LSF,[5] and was identified in 2017 as one of the future trends for bioinformatics pipeline development.[2] Several additional analysis environments are currently implementing support for CWL including Apache Taverna and Galaxy.[5]

Availability

CWL is developed by an informal, multi-vendor working group consisting of both organizations and individuals and is 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. doi:10.6084/m9.figshare.3115156.v2.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ a b Leipzig, Jeremy (2017-05-01). "A review of bioinformatic pipeline frameworks". Briefings in Bioinformatics. 18 (3): 530–536. doi:10.1093/bib/bbw020. ISSN 1467-5463. PMC 5429012. PMID 27013646.
  3. ^ Perkel, Jeffrey M. (2019). "Workflow systems turn raw data into scientific knowledge". Nature. 573 (7772): 149–150. doi:10.1038/d41586-019-02619-z. ISSN 0028-0836. PMID 31477884.
  4. ^ Barski, Artem; Kartashov, Andrey V.; Kotliar, Michael (2019-07-01). "CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language". GigaScience. 8 (7). doi:10.1093/gigascience/giz084. PMC 6639121. PMID 31321430.
  5. ^ a b https://www.commonwl.org/#Implementations

External links

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