Standard for computational data-analysis workflows
Common Workflow Language CWL Logo
Abbreviation CWL Status Published Year started 10 July 2014 (2014-07-10 ) Latest version 1.2 (2020-08-07 ) Related standards BioCompute Object License Apache 2.0 Website commonwl
The Common Workflow Language (CWL ) is a standard for describing computational data-analysis workflows.[ 1] 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] 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.[ 2] Pegasus [ 7] Galaxy .[ 8]
Availability
The CWL Project[ 9] Software Freedom Conservancy , it publishes the CWL standards freely available via its GitHub repository under a permissive Apache License 2.0 .
References
^ 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 )^ 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 . ^ 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 . ^ "CWL Implementations" . Common Workflow Language (CWL) . Retrieved 10 October 2021 .^ 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 . ^ 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 . ^ "11.6. pegasus-cwl-converter — Pegasus WMS 5.0.1 documentation" . pegasus.isi.edu . Retrieved 10 October 2021 .^ 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 . ^ 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 .
External links
