# Common Workflow Language

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{{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   = <!-- {{Start date|YYYY|MM|DD|df=y}} -->
| 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](/source/BioCompute_Object)
| abbreviation      = CWL
| domain            = 
| license           = [Apache 2.0](/source/Apache_License)
| website           = {{URL|commonwl.org}}
}}
The '''Common Workflow Language''' ('''CWL''') is a standard for describing computational data-analysis workflows.<ref>{{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}}</ref> Development of CWL is focused particularly on serving the data-intensive sciences, such as [bioinformatics](/source/bioinformatics),<ref name="Leipzig 2017">{{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}}</ref> [medical imaging](/source/medical_imaging), [astronomy](/source/astronomy), [physics](/source/physics), and [chemistry](/source/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.<ref name="Perkel2019">{{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}}</ref>

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](/source/Galaxy_(computational_biology)), Arvados, Seven Bridges, and [Michigan State University](/source/Michigan_State_University)) at the [Open Bioinformatics Foundation](/source/Open_Bioinformatics_Foundation) [https://www.open-bio.org/wiki/Codefest_2014 BOSC 2014] codefest.

CWL is supported by multiple analysis runners and platforms<ref>{{cite web |title=CWL Implementations |url=https://www.commonwl.org/#Implementations |website=Common Workflow Language (CWL) |access-date=10 October 2021 |language=en}}</ref> such as [Apache Airflow](/source/Apache_Airflow) (via [https://github.com/Barski-lab/cwl-airflow CWL-Airflow ]<ref>{{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}}</ref>), [https://arvados.org/ Arvados], [http://rabix.io/ Rabix],<ref>{{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 }}</ref> [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](/source/Platform_LSF), and was identified in 2017 as one of the future trends for bioinformatics pipeline development.<ref name="Leipzig 2017" /> Several additional analysis environments are currently implementing support for CWL including [Pegasus](/source/Pegasus_(workflow_management))<ref>{{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}}</ref> and [Galaxy](/source/Galaxy_(computational_biology)).<ref>{{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}}</ref>

== Availability ==
The CWL Project<ref>{{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 }}</ref> is a multi-stakeholder working group consisting of both organizations and individuals. A member project of [Software Freedom Conservancy](/source/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](/source/Apache_License).

== References ==
<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]

Category:Workflow languages
Category:Cloud standards
Category:Computer standards
Category:Data interchange standards

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Adapted from the Wikipedia article [Common Workflow Language](https://en.wikipedia.org/wiki/Common_Workflow_Language) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Common_Workflow_Language?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.