CWL Viewer: The Common Workflow Language Viewer

Mark Robinson; Stian Soiland-Reyes; Michael R. Crusoe; Carole Goble

doi:10.7490/f1000research.1114375.1

CWL Viewer: The Common Workflow Language Viewer

Mark Robinson, Stian Soiland-Reyes, Michael R. Crusoe, Carole Goble

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Common Workflow Language project

Research output: Contribution to conference › Poster › peer-review

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Abstract

The Common Workflow Language (CWL) project emerged from the BOSC 2014 Codefest as a grassroots, multi-vendor working group to tackle the portability of data analysis workflows. It’s specification for describing workflows and command line tools aims to make them portable and scalable across a variety of computing platforms.

At its heart CWL is a set of structured text files (YAML) with various extensibility points to the format. However, the CWL syntax and multi-file collections are not conducive to workflow browsing, exchange and understanding: for this
we need a visualization suite.

CWL Viewer is a richly featured CWL visualization suite that graphically presents and lists the details of CWL workflows with their inputs, outputs and steps. It also packages the CWL files into a downloadable Research Object Bundle including attribution, versioning and dependency metadata in the manifest, allowing it to be easily shared. The tool operates over any workflow held in a GitHub repository. Other features include: path visualization from parents and children nodes; nested workflows support; workflow graph download in a range of image formats; a gallery of previously submitted workflows; and support for private git repositories and public GitHub including live updates over versioned workflows.

The CWL Viewer is the de facto CWL visualization suite and has been enthusiastically received by the CWL community

Original language	English
Number of pages	1
DOIs	https://doi.org/10.7490/f1000research.1114375.1
Publication status	Published - 6 Jul 2017
Event	Bioinformatics Open Source Conference (BOSC) 2017 - ISMB/ECCB 2017, Prague, Czech Republic Duration: 22 Jul 2017 → 23 Jul 2017 http://www.open-bio.org/wiki/BOSC_2017

Conference

Conference	Bioinformatics Open Source Conference (BOSC) 2017
Abbreviated title	BOSC
Country/Territory	Czech Republic
City	Prague
Period	22/07/17 → 23/07/17
Internet address	http://www.open-bio.org/wiki/BOSC_2017

Keywords

cwl
workflow
research object
scientific workflows

Access to Document

10.7490/f1000research.1114375.1Licence: CC BY

BOSC_2017_paper_27Accepted author manuscript, 328 KBLicence: Other

Cite this

@conference{b60c4d3c303b4b5494f09cb1e9059b20,

title = "CWL Viewer: The Common Workflow Language Viewer",

abstract = "The Common Workflow Language (CWL) project emerged from the BOSC 2014 Codefest as a grassroots, multi-vendor working group to tackle the portability of data analysis workflows. It{\textquoteright}s specification for describing workflows and command line tools aims to make them portable and scalable across a variety of computing platforms. At its heart CWL is a set of structured text files (YAML) with various extensibility points to the format. However, the CWL syntax and multi-file collections are not conducive to workflow browsing, exchange and understanding: for thiswe need a visualization suite. CWL Viewer is a richly featured CWL visualization suite that graphically presents and lists the details of CWL workflows with their inputs, outputs and steps. It also packages the CWL files into a downloadable Research Object Bundle including attribution, versioning and dependency metadata in the manifest, allowing it to be easily shared. The tool operates over any workflow held in a GitHub repository. Other features include: path visualization from parents and children nodes; nested workflows support; workflow graph download in a range of image formats; a gallery of previously submitted workflows; and support for private git repositories and public GitHub including live updates over versioned workflows. The CWL Viewer is the de facto CWL visualization suite and has been enthusiastically received by the CWL community",

keywords = "cwl, workflow, research object, scientific workflows",

author = "Mark Robinson and Stian Soiland-Reyes and Crusoe, {Michael R.} and Carole Goble",

note = "Abstract submitted to BOSC 2017. After peer review, accepted as poster and talk. Poster published in F1000Research. Won F1000Research Poster Award at ISMB/ECCB 2017. How to cite this poster: Robinson M, Soiland-Reyes S, Crusoe MR and Goble C. CWL Viewer: the common workflow language viewer [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1075 (poster) (doi: 10.7490/f1000research.1114375.1); Bioinformatics Open Source Conference (BOSC) 2017, BOSC ; Conference date: 22-07-2017 Through 23-07-2017",

year = "2017",

month = jul,

day = "6",

doi = "10.7490/f1000research.1114375.1",

language = "English",

url = "http://www.open-bio.org/wiki/BOSC_2017",

}

TY - CONF

T1 - CWL Viewer

T2 - Bioinformatics Open Source Conference (BOSC) 2017

AU - Robinson, Mark

AU - Soiland-Reyes, Stian

AU - Crusoe, Michael R.

AU - Goble, Carole

N1 - Abstract submitted to BOSC 2017. After peer review, accepted as poster and talk. Poster published in F1000Research. Won F1000Research Poster Award at ISMB/ECCB 2017. How to cite this poster: Robinson M, Soiland-Reyes S, Crusoe MR and Goble C. CWL Viewer: the common workflow language viewer [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1075 (poster) (doi: 10.7490/f1000research.1114375.1)

PY - 2017/7/6

Y1 - 2017/7/6

N2 - The Common Workflow Language (CWL) project emerged from the BOSC 2014 Codefest as a grassroots, multi-vendor working group to tackle the portability of data analysis workflows. It’s specification for describing workflows and command line tools aims to make them portable and scalable across a variety of computing platforms. At its heart CWL is a set of structured text files (YAML) with various extensibility points to the format. However, the CWL syntax and multi-file collections are not conducive to workflow browsing, exchange and understanding: for thiswe need a visualization suite. CWL Viewer is a richly featured CWL visualization suite that graphically presents and lists the details of CWL workflows with their inputs, outputs and steps. It also packages the CWL files into a downloadable Research Object Bundle including attribution, versioning and dependency metadata in the manifest, allowing it to be easily shared. The tool operates over any workflow held in a GitHub repository. Other features include: path visualization from parents and children nodes; nested workflows support; workflow graph download in a range of image formats; a gallery of previously submitted workflows; and support for private git repositories and public GitHub including live updates over versioned workflows. The CWL Viewer is the de facto CWL visualization suite and has been enthusiastically received by the CWL community

AB - The Common Workflow Language (CWL) project emerged from the BOSC 2014 Codefest as a grassroots, multi-vendor working group to tackle the portability of data analysis workflows. It’s specification for describing workflows and command line tools aims to make them portable and scalable across a variety of computing platforms. At its heart CWL is a set of structured text files (YAML) with various extensibility points to the format. However, the CWL syntax and multi-file collections are not conducive to workflow browsing, exchange and understanding: for thiswe need a visualization suite. CWL Viewer is a richly featured CWL visualization suite that graphically presents and lists the details of CWL workflows with their inputs, outputs and steps. It also packages the CWL files into a downloadable Research Object Bundle including attribution, versioning and dependency metadata in the manifest, allowing it to be easily shared. The tool operates over any workflow held in a GitHub repository. Other features include: path visualization from parents and children nodes; nested workflows support; workflow graph download in a range of image formats; a gallery of previously submitted workflows; and support for private git repositories and public GitHub including live updates over versioned workflows. The CWL Viewer is the de facto CWL visualization suite and has been enthusiastically received by the CWL community

KW - cwl

KW - workflow

KW - research object

KW - scientific workflows

UR - https://view.commonwl.org/

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

UR - https://www.open-bio.org/w/images/4/42/BOSC2017-complete-program-compressed.pdf

UR - https://zenodo.org/record/826827

U2 - 10.7490/f1000research.1114375.1

DO - 10.7490/f1000research.1114375.1

M3 - Poster

Y2 - 22 July 2017 through 23 July 2017

ER -

CWL Viewer: The Common Workflow Language Viewer

Abstract

Conference

Keywords

Access to Document

Other files and links

Fingerprint

Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Common Workflow Language Viewer: (Talk)

CWL Viewer v1.0: common-workflow-language/cwlviewer

F1000Research Poster Award

Cite this

CWL Viewer: The Common Workflow Language Viewer

Abstract

Conference

Keywords

Access to Document

Other files and links

Fingerprint

Research output

Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Common Workflow Language Viewer: (Talk)

CWL Viewer v1.0: common-workflow-language/cwlviewer

Prizes

F1000Research Poster Award

Cite this