cwl_runner

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

https://github.com/common-workflow-language/common-workflow-language

Keywords

common-workflow-language commonwl containers cwl science sciworkflows workflow workflows

Keywords from Contributors

bioinformatics gcp workflow-engine arvados bigdata cluster genomics hack cwl-workflow

Last synced: 4 months ago · JSON representation ·

Repository

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Basic Info

Host: GitHub
Owner: common-workflow-language
License: apache-2.0
Language: Common Workflow Language
Default Branch: main
Homepage: https://www.commonwl.org
Size: 3.63 MB

Statistics

Stars: 1,469
Watchers: 105
Forks: 196
Open Issues: 242
Releases: 6

Topics

common-workflow-language commonwl containers cwl science sciworkflows workflow workflows

Created over 11 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Code of conduct Citation

Common Workflow Language

Main website: https://www.commonwl.org

GitHub repository for www.commonwl.org: https://www.github.com/common-workflow-language/cwl-website

CWL v1.0.x: https://github.com/common-workflow-language/common-workflow-language (this repository)

CWL v1.1.x: https://github.com/common-workflow-language/cwl-v1.1/

CWL v1.2.x: https://github.com/common-workflow-language/cwl-v1.2/

Support

The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a\ variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry.

CWL is developed by a multi-vendor working group consisting of organizations and individuals aiming to enable scientists to share data analysis workflows. The CWL project is maintained on Github and we follow the Open-Stand.org principles for collaborative open standards development. Legally, CWL is a member project of Software Freedom Conservancy and is formally managed by the elected CWL leadership team, however every-day project decisions are made by the CWL community which is open for participation by anyone.

CWL builds on technologies such as JSON-LD for data modeling and Docker for portable runtime environments.

User Guide

The CWL user guide provides a gentle introduction to learning how to write CWL command line tool and workflow descriptions.

CWL is a 15 minute introduction to the CWL project in Japanese.

CWL Recommended Practices

CWL is a 15 minute introduction to the CWL project in Japanese.

A series of video lessons about CWL is available in Russian as part of the (Computation Management) free online course.

Citation

To reference the CWL project in a scholary work, please use the following citation:

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Neboja Tijani, Herv Mnager, Stian Soiland-Reyes, Bogdan Gavrilovi, Carole Goble, and The CWL Community. (2022): Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. Commun. ACM 65, 6 (June 2022), 5463. https://doi.org/10.1145/3486897

To cite version 1.0 of the CWL standards specifically, please use the following citation inclusive of the DOI.

Peter Amstutz, Michael R. Crusoe, Neboja Tijani (editors), Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Herv Mnager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes, Luka Stojanovic (2016): Common Workflow Language, v1.0. Specification, Common Workflow Language working group. https://w3id.org/cwl/v1.0/ doi:10.6084/m9.figshare.3115156.v2

A collection of existing references to CWL can be found at https://zotero.org/groups/cwl

Code of Conduct

The CWL Project is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, age, race, or religion. We do not tolerate harassment of participants in any form. This code of conduct applies to all CWL Project spaces, including the Google Group, the Gitter chat room, the Google Hangouts chats, both online and off. Anyone who violates this code of conduct may be sanctioned or expelled from these spaces at the discretion of the leadership team.

For more details, see our Code of Conduct.

For the following content: - Support, Community and Contributing - CWL Implementations - Repositories of CWL Tools and Workflows - Software for working with CWL - Editors and viewers - Utilities - Converters and code generators - Code libraries - Projects the CWL community is participating in - Participating Organizations - Individual Contributors - CWL Advisors - CWL Leadership team

Please see https://www.commonwl.org

Owner

Name: Common Workflow Language
Login: common-workflow-language
Kind: organization

Website: https://www.commonwl.org
Twitter: commonwl
Repositories: 34
Profile: https://github.com/common-workflow-language

Citation (CITATION.cff)

# Are you editing this file?
# Synchronize any changes made with
# README.md
# and
# https://github.com/common-workflow-language/user_guide/blob/main/CITATION.md

cff-version: "1.1.0"
message: |
  To reference the CWL project in scholarly work, please cite the following work.
  To reference a particular version of the CWL standards, please see the entries
  under "references"
title: "Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language"
identifiers: 
  - type: doi
    value: 10.1145/3486897
abstract: "A widely used standard for portable multilingual data analysis pipelines would enable considerable benefits to scholarly publication reuse, research/industry collaboration, regulatory cost control, and to the environment. Published research that used multiple computer languages for their analysis pipelines would include a complete and reusable description of that analysis that is runnable on a diverse set of computing environments. Researchers would be able to easier collaborate and reuse these pipelines, adding or exchanging components regardless of programming language used; collaborations with and within the industry would be easier; approval of new medical interventions that rely on such pipelines would be faster. Time will be saved and environmental impact would also be reduced, as these descriptions contain enough information for advanced optimization without user intervention. Workflows are widely used in data analysis pipelines, enabling innovation and decision-making for the modern society. In many domains the analysis components are numerous and written in multiple different computer languages by third parties. However, lacking a standard for reusable and portable multilingual workflows, then reusing published multilingual workflows, collaborating on open problems, and optimizing their execution would be severely hampered. Moreover, only a standard for multilingual data analysis pipelines that was widely used would enable considerable benefits to research-industry collaboration, regulatory cost control, and to preserving the environment. Prior to the start of the CWL project, there was no standard for describing multilingual analysis pipelines in a portable and reusable manner. Even today / currently, although there exist hundreds of single-vendor and other single-source systems that run workflows, none is a general, community-driven, and consensus-built standard."
authors: 
  - given-names: "Michael R."
    family-names: Crusoe
    affiliation: "VU Amsterdam, Department of Computer Science; Software Freedom Conservancy, Common Workflow Language project"
    orcid: "https://orcid.org/0000-0002-2961-9670"
  - given-names: Sanne
    family-names: Abeln
    affiliation: "VU Amsterdam, Department of Computer Science"
    orcid: "https://orcid.org/0000-0002-2779-7174"
  - given-names: Alexandru
    family-names: Iosup
    affiliation: "VU Amsterdam, Department of Computer Science"
    orcid: "https://orcid.org/0000-0001-8030-9398"
  - given-names: Peter
    family-names: Amstutz
    affiliation: "Curii Corporation"
    orcid: "https://orcid.org/0000-0003-3566-7705"
  - given-names: John
    family-names: Chilton
    affiliation: "Pennsylvania State University, Department of Biochemistry and Molecular Biology; Galaxy Project"
    orcid: "https://orcid.org/0000-0002-6794-0756"
  - given-names: "Nebojša"
    family-names: "Tijanić"
    affiliation: Totient
    orcid: "https://orcid.org/0000-0001-8316-4067"
  - given-names: "Hervé"
    family-names: "Ménager"
    affiliation: "Institut Pasteur"
    orcid: "https://orcid.org/0000-0002-7552-1009"
  - given-names: Stian
    family-names: "Soiland-Reyes"
    affiliation: "The University of Manchester, Department of Computer Science; Informatics Institute, University of Amsterdam"
    orcid: "https://orcid.org/0000-0001-9842-9718"
  - given-names: Carole
    family-names: Goble
    affiliation: "The University of Manchester, Department of Computer Science"
    orcid: "https://orcid.org/0000-0003-1219-2137"
  - name: "The CWL Community"
    website: "https://www.commonwl.org"
references:
  - type: standard
    title: "Common Workflow Language, v1.0"
    doi: 10.6084/m9.figshare.3115156.v2
    date-published: 2016-07-08
    license: Apache-2.0
    url: "https://w3id.org/cwl/v1.0/"
    repository-code: "https://github.com/common-workflow-language/common-workflow-language/"
    authors:
     - given-names: Peter
       family-names: Amstutz
       orcid: "https://orcid.org/0000-0003-3566-7705"
       affiliation: "Arvados Project, Veritas Genetics"
     - given-names: "Michael R."
       family-names: Crusoe
       orcid: "https://orcid.org/0000-0002-2961-9670"
     - given-names: Nebojša
       family-names: Tijanić
       orcid: "https://orcid.org/0000-0001-8316-4067"
       affiliation: "Seven Bridges Genomics, Inc."
  - type: standard
    title: "Common Workflow Language, v1.1"
    date-published: 2019-06-06
    license: Apache-2.0
    url: "https://w3id.org/cwl/v1.1/"
    repository-code: "https://github.com/common-workflow-language/cwl-v1.1/"
    authors:
     - given-names: Peter
       family-names: Amstutz
       affiliation: "Curii Corporation / Arvados"
       orcid: "https://orcid.org/0000-0003-3566-7705"
     - given-names: "Michael R."
       family-names: Crusoe
       orcid: "https://orcid.org/0000-0002-2961-9670"
  - type: standard
    title: "Common Workflow Language, v1.2"
    date-published: 2020-08-07
    license: Apache-2.0
    url: "https://w3id.org/cwl/v1.2/"
    repository-code: "https://github.com/common-workflow-language/cwl-v1.2/"
    authors:
     - given-names: Peter
       family-names: Amstutz
       affiliation: "Curii Corporation / Arvados"
       orcid: "https://orcid.org/0000-0003-3566-7705"
     - given-names: "Michael R."
       family-names: Crusoe
       orcid: "https://orcid.org/0000-0002-2961-9670"
     - given-names: Kaushik
       family-names: Ghose
       orcid: "https://orcid.org/0000-0003-2933-1260"
       affiliation: "Seven Bridges Genomics, Inc."

GitHub Events

Total

Watch event: 16
Issue comment event: 1
Push event: 1
Gollum event: 5

Last Year

Watch event: 16
Issue comment event: 1
Push event: 1
Gollum event: 5

Committers

Last synced: 8 months ago

All Time

Total Commits: 1,515
Total Committers: 74
Avg Commits per committer: 20.473
Development Distribution Score (DDS): 0.549

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Peter Amstutz	p**z@c**m	684
Michael R. Crusoe	m**e@g**m	382
Manvendra Singh	m**0@g**m	60
Peter Amstutz	p**z@v**m	51
Stian Soiland-Reyes	s**n@a**g	31
John Chilton	j**n@g**m	27
Luka Stojanovic	l**c@s**m	26
Peter Amstutz	t**n@i**g	23
Tomoya Tanjo	t**o@g**m	17
Nebojsa Tijanic	n**c@s**m	17
Hervé Ménager	h**r@g**m	16
kapilkd13	k**3@g**m	16
Anton Khodak	a**k@u**t	15
Hiromu OCHIAI	o**0@g**m	11
Manabu ISHII	m**b@g**m	9
Pau Ruiz i Safont	p**t@e**k	8
ThomasHickman	T**2@g**m	7
Guillermo Carrasco	g**8@g**m	7
Dan Leehr	d**r@d**u	7
Josh Holland	j**6@s**k	6
Gijs Molenaar	g**s@p**l	5
Andrey Kartashov	p**r@p**t	5
Nebojsa Tijanic	n****c	4
Michael Kotliar	m**r@g**m	4
bogdang989	b**c@s**m	4
Denis Yuen	d**n@o**a	3
James Porter	p**j@g**m	3
Ward Vandewege	c****e	3
Wolfgang Gerlach	w****h	3
boysha	b**a@s**l	3
and 44 more...

Committer Domains (Top 20 + Academic)

sbgenomics.com: 5 broadinstitute.org: 4 curoverse.com: 2 sanger.ac.uk: 2 veritasgenetics.com: 1 apache.org: 1 interreality.org: 1 ukr.net: 1 ebi.ac.uk: 1 duke.edu: 1 pythonic.nl: 1 porter.st: 1 oicr.on.ca: 1 50mail.com: 1 ci.curoverse.com: 1 epcc.ed.ac.uk: 1 jic.ac.uk: 1 illumina.com: 1 systemsbiology.org: 1 biologie.kappa.ro: 1 ohsu.edu: 1 student.unimelb.edu.au: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time

Total issues: 92
Total pull requests: 23
Average time to close issues: over 2 years
Average time to close pull requests: 10 months
Total issue authors: 33
Total pull request authors: 10
Average comments per issue: 4.82
Average comments per pull request: 0.83
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 3
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: 25 days
Issue authors: 2
Pull request authors: 1
Average comments per issue: 0.33
Average comments per pull request: 0.5
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

mr-c (34)
tom-tan (10)
ghost (9)
bogdang989 (5)
tetron (4)
manabuishii (3)
whlavina (1)
nyue (1)
hmenager (1)
jmfernandez (1)
swzCuroverse (1)
illusional (1)
kinow (1)
tonyyzy (1)
stevekm (1)

Pull Request Authors

tom-tan (9)
mr-c (7)
rupertnash (1)
lgtm-com[bot] (1)
DimitriPapadopoulos (1)
kinow (1)
ThomasHickman (1)
GlassOfWhiskey (1)
Smyja (1)
tetron (1)

Top Labels

Issue Labels

proposal (6) Unimplemented-Idea (5) conformance test (3) help wanted (3) spec change (3) conditionals (3) make running scripts easier (2) bug (1) simplify syntax (1) needs-response (1) enhancement (1)

Pull Request Labels

Packages

Total packages: 5
Total downloads:
- pypi 4,348 last-month
Total docker downloads: 38

Total dependent packages: 2
(may contain duplicates)
Total dependent repositories: 39
(may contain duplicates)
Total versions: 7
Total maintainers: 4

pypi.org: cwlref-runner

Common workflow language reference implementation

Homepage: http://www.commonwl.org
Documentation: https://cwlref-runner.readthedocs.io/
License: Apache 2.0
Latest release: 1.0
published over 9 years ago

Versions: 1
Dependent Packages: 2
Dependent Repositories: 36
Downloads: 1,623 Last month
Docker Downloads: 38

Rankings

Dependent repos count: 2.4%

Dependent packages count: 3.2%

Average: 4.1%

Docker downloads count: 4.3%

Downloads: 6.4%

Maintainers (2)

mvdbeek mcrusoe

Last synced: 5 months ago

proxy.golang.org: github.com/common-workflow-language/common-workflow-language

Documentation: https://pkg.go.dev/github.com/common-workflow-language/common-workflow-language#section-documentation
License: apache-2.0
Latest release: v1.0.2
published over 6 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 5 months ago

pypi.org: cwl_runner

Common workflow language reference implementation

Homepage: https://github.com/common-workflow-language/common-workflow-language
Documentation: https://cwl_runner.readthedocs.io/
License: Apache 2.0
Latest release: 1.0
published over 10 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 2,714 Last month

Rankings

Stargazers count: 1.8%

Forks count: 3.7%

Dependent packages count: 10.0%

Average: 10.4%

Downloads: 14.8%

Dependent repos count: 21.7%

Maintainers (3)

arvados mcrusoe tetron

Last synced: 5 months ago

pypi.org: cwltool_service

Common workflow language runner service

Homepage: https://github.com/common-workflow-language/common-workflow-language
Documentation: https://cwltool_service.readthedocs.io/
License: Apache 2.0
Latest release: 1.0.1
published over 10 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 2
Downloads: 11 Last month

Rankings

Stargazers count: 1.8%

Forks count: 3.7%

Dependent packages count: 10.0%

Dependent repos count: 11.6%

Average: 14.9%

Downloads: 47.6%

Maintainers (2)

mcrusoe tetron

Last synced: 5 months ago

conda-forge.org: cwl_runner

Homepage: https://github.com/common-workflow-language/common-workflow-language
License: Apache 2.0
Latest release: 1.0
published almost 7 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Stargazers count: 9.8%

Forks count: 11.4%

Average: 26.6%

Dependent repos count: 34.0%

Dependent packages count: 51.2%

Last synced: 5 months ago

cwl_runner

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Common Workflow Language

User Guide

Citation

Code of Conduct

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: cwlref-runner

Rankings

Maintainers (2)

proxy.golang.org: github.com/common-workflow-language/common-workflow-language

Rankings

pypi.org: cwl_runner

Rankings

Maintainers (3)

pypi.org: cwltool_service

Rankings

Maintainers (2)

conda-forge.org: cwl_runner

Rankings

Dependencies