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Common Workflow Language
Open standards project

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, medical imaging, astronomy, physics, and chemistry.

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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 platforms4 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.7 Several additional analysis environments are currently implementing support for CWL including Pegasus8 and Galaxy.9

Availability

The CWL Project10 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. doi:10.6084/m9.figshare.3115156.v2.{{cite journal}}: CS1 maint: multiple names: authors list (link) https://figshare.com/articles/Common_Workflow_Language_draft_3/3115156/2 ↩

  2. 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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429012 ↩

  3. Perkel, Jeffrey M. (2019). "Workflow systems turn raw data into scientific knowledge". Nature. 573 (7772): 149–150. Bibcode:2019Natur.573..149P. doi:10.1038/d41586-019-02619-z. ISSN 0028-0836. PMID 31477884. S2CID 201713827. https://doi.org/10.1038%2Fd41586-019-02619-z ↩

  4. "CWL Implementations". Common Workflow Language (CWL). Retrieved 10 October 2021. https://www.commonwl.org/#Implementations ↩

  5. 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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639121 ↩

  6. Kaushik, Gaurav; Ivković, Sinisa; Simonović, Janko; Tijanić, Nebojša; Davis-Dusenbery, Brandi; Kural, Deniz (January 2017). "Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions". Pacific Symposium on Biocomputing 2017. Proceedings of the Pacific Symposium. Vol. 22. pp. 154–165. doi:10.1142/9789813207813_0016. ISBN 978-981-320-780-6. PMC 5166558. PMID 27896971. 978-981-320-780-6 ↩

  7. 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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429012 ↩

  8. "11.6. pegasus-cwl-converter — Pegasus WMS 5.0.1 documentation". pegasus.isi.edu. Retrieved 10 October 2021. https://pegasus.isi.edu/documentation/manpages/pegasus-cwl-converter.html ↩

  9. Chilton, John; Soranzo, Nicola. "Implement a subset of the Common Workflow Language. by jmchilton · Pull Request #47 · common-workflow-language/galaxy". GitHub. Retrieved 10 October 2021. https://github.com/common-workflow-language/galaxy/pull/47 ↩

  10. 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 (2022). "Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language". Communications of the ACM. 65: 54–63. arXiv:2105.07028. doi:10.1145/3486897. S2CID 234742536. /wiki/ArXiv_(identifier) ↩