Common Workflow Language
{{Short description|Standard for computational data-analysis workflows}}
{{Multiple issues|
{{Primary sources|date=August 2022}}
{{External links|date=October 2023}}
}}
{{Infobox technology standard
| title = Common Workflow Language
| long_name = The Common Workflow Language standards
| image = CWL-Logo-4k.png
| caption = CWL Logo
| status = Published
| year_started = {{Start date|2014|07|10|df=y}}
| first_published =
| version = [https://www.commonwl.org/v1.2/ 1.2]
| version_date = {{Start date|2020|08|07|df=y}}
| organization =
| committee =
| editors =
| authors =
| base_standards =
| related_standards = BioCompute Object
| abbreviation = CWL
| domain =
| license = Apache 2.0
| website = {{URL|commonwl.org}}
}}
The Common Workflow Language (CWL) is a standard for describing computational data-analysis workflows.{{Cite journal|last1=Peter|first1=Amstutz|last2=R.|first2=Crusoe, Michael|last3=Nebojša|first3=Tijanić|last4=Brad|first4=Chapman|last5=John|first5=Chilton|last6=Michael|first6=Heuer|last7=Andrey|first7=Kartashov|last8=Dan|first8=Leehr|last9=Hervé|first9=Ménager|date=2016-07-08|title=Common Workflow Language, v1.0|url=https://figshare.com/articles/Common_Workflow_Language_draft_3/3115156/2|journal=Figshare|language=en-US|doi=10.6084/m9.figshare.3115156.v2}} Development of CWL is focused particularly on serving the data-intensive sciences, such as bioinformatics,{{Cite journal|last=Leipzig|first=Jeremy|date=2017-05-01|title=A review of bioinformatic pipeline frameworks|url= |journal=Briefings in Bioinformatics|language=en|volume=18|issue=3|pages=530–536|doi=10.1093/bib/bbw020|pmid=27013646|issn=1467-5463|pmc=5429012}} 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.{{cite journal|last1=Perkel|first1=Jeffrey M.|title=Workflow systems turn raw data into scientific knowledge|journal=Nature|volume=573|issue=7772|year=2019|pages=149–150|issn=0028-0836|doi=10.1038/d41586-019-02619-z|pmid=31477884|bibcode=2019Natur.573..149P|s2cid=201713827|doi-access=free}}
The CWL originated from discussions in 2014 between [https://orcid.org/0000-0003-3566-7705 Peter Amstutz], [https://orcid.org/0000-0002-6794-0756 John Chilton], [https://orcid.org/0000-0001-8316-4067 Nebojša Tijanić], and [https://orcid.org/0000-0002-2961-9670 Michael R. Crusoe] (at that time their respective affiliations were: Galaxy, Arvados, Seven Bridges, and Michigan State University) at the Open Bioinformatics Foundation [https://www.open-bio.org/wiki/Codefest_2014 BOSC 2014] codefest.
CWL is supported by multiple analysis runners and platforms{{cite web |title=CWL Implementations |url=https://www.commonwl.org/#Implementations |website=Common Workflow Language (CWL) |access-date=10 October 2021 |language=en}} such as Apache Airflow (via [https://github.com/Barski-lab/cwl-airflow CWL-Airflow ]{{Cite journal|last1=Barski|first1=Artem|last2=Kartashov|first2=Andrey V.|last3=Kotliar|first3=Michael|date=2019-07-01|title=CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language|url= |journal=GigaScience|language=en|volume=8|issue=7|doi=10.1093/gigascience/giz084|pmid=31321430|pmc=6639121}}), [https://arvados.org/ Arvados], [http://rabix.io/ Rabix],{{cite book|last1=Kaushik |first1=Gaurav |last2=Ivković |first2=Sinisa |last3=Simonović |first3=Janko |last4=Tijanić |first4=Nebojša |last5=Davis-Dusenbery |first5=Brandi |last6=Kural |first6=Deniz |chapter=Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions |title=Pacific Symposium on Biocomputing 2017 |series=Proceedings of the Pacific Symposium |date=January 2017 |volume=22 |pages=154–165 |doi=10.1142/9789813207813_0016 |pmid=27896971|pmc=5166558 |isbn=978-981-320-780-6 }} [https://cromwell.readthedocs.io Cromwell workflow engine], [http://toil.ucsc-cgl.org/ Toil], [https://reana.readthedocs.io/ REANA - Reusable Analyses] and [https://github.com/IBMSpectrumComputing/cwlexec 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{{cite web |title=11.6. pegasus-cwl-converter — Pegasus WMS 5.0.1 documentation |url=https://pegasus.isi.edu/documentation/manpages/pegasus-cwl-converter.html |website=pegasus.isi.edu |access-date=10 October 2021}} and Galaxy.{{cite web |last1=Chilton |first1=John |last2=Soranzo |first2=Nicola |title=Implement a subset of the Common Workflow Language. by jmchilton · Pull Request #47 · common-workflow-language/galaxy |url=https://github.com/common-workflow-language/galaxy/pull/47 |website=GitHub |access-date=10 October 2021 |language=en}}
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, it publishes the CWL standards freely available via its [https://github.com/common-workflow-language/common-workflow-language GitHub repository] under a permissive Apache License 2.0.
References
External links
- [https://doi.org/10.6084/m9.figshare.3115156.v2 CWL v1.0 specification DOI]
- [https://www.commonwl.org/ CWL website]
- [https://github.com/common-workflow-language/common-workflow-language CWL GitHub Repository]
- [https://www.standict.eu/standards-repository/cwl-common-workflow-language-standards-v12 CWL entry in the EU Observatory for ICT Standardisation]