Common Workflow Language Viewer: (Talk)

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

doi:10.7490/f1000research.1114453.1

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.
Project Website: https://view.commonwl.org/
Source Code: https://github.com/common-workflow-language/cwlviewer(https://doi.org/10.5281/zenodo.823535)
Software License: Apache License, Version 2.0
Submitted abstract: CWL Viewer: The Common Workflow Language Viewer
Poster: https://doi.org/10.7490/f1000research.1114375.1
Technical Report: Reproducible Research using Research Objects(https://doi.org/10.5281/zenodo.823295)

Original language	English
DOIs	https://doi.org/10.7490/f1000research.1114453.1
Publication status	Published - 22 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
workflows
scientific workflows
research object
visualization

Access to Document

10.7490/f1000research.1114453.1Licence: CC BY

BOSC_2017_paper_27Accepted author manuscript, 328 KBLicence: CC BY

http://slides.com/markrobinson/cwlviewerLicence: CC BY

Cite this

@conference{d4c2e0be3f4e436bab3ba4ad7fbaba04,

title = "Common Workflow Language Viewer: (Talk)",

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 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.Project Website: https://view.commonwl.org/Source Code: https://github.com/common-workflow-language/cwlviewer(https://doi.org/10.5281/zenodo.823535)Software License: Apache License, Version 2.0Submitted abstract: CWL Viewer: The Common Workflow Language ViewerPoster: https://doi.org/10.7490/f1000research.1114375.1Technical Report: Reproducible Research using Research Objects(https://doi.org/10.5281/zenodo.823295)",

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

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

note = "Robinson M, Soiland-Reyes S, Crusoe MR and Goble C. Common workflow language viewer [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1175 (slides) (doi: 10.7490/f1000research.1114453.1); Bioinformatics Open Source Conference (BOSC) 2017, BOSC ; Conference date: 22-07-2017 Through 23-07-2017",

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AU - Robinson, Mark

AU - Soiland-Reyes, Stian

AU - Crusoe, Michael R.

AU - Goble, Carole

N1 - Robinson M, Soiland-Reyes S, Crusoe MR and Goble C. Common workflow language viewer [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1175 (slides) (doi: 10.7490/f1000research.1114453.1)

PY - 2017/7/22

Y1 - 2017/7/22

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 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.Project Website: https://view.commonwl.org/Source Code: https://github.com/common-workflow-language/cwlviewer(https://doi.org/10.5281/zenodo.823535)Software License: Apache License, Version 2.0Submitted abstract: CWL Viewer: The Common Workflow Language ViewerPoster: https://doi.org/10.7490/f1000research.1114375.1Technical Report: Reproducible Research using Research Objects(https://doi.org/10.5281/zenodo.823295)

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 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.Project Website: https://view.commonwl.org/Source Code: https://github.com/common-workflow-language/cwlviewer(https://doi.org/10.5281/zenodo.823535)Software License: Apache License, Version 2.0Submitted abstract: CWL Viewer: The Common Workflow Language ViewerPoster: https://doi.org/10.7490/f1000research.1114375.1Technical Report: Reproducible Research using Research Objects(https://doi.org/10.5281/zenodo.823295)

KW - cwl

KW - workflows

KW - scientific workflows

KW - research object

KW - visualization

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

UR - https://www.youtube.com/watch?v=iB_0l-Bm4nA

U2 - 10.7490/f1000research.1114453.1

DO - 10.7490/f1000research.1114453.1

M3 - Abstract

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ER -

Common Workflow Language Viewer: (Talk)

Abstract

Conference

Keywords

Access to Document

Other files and links

Fingerprint

BioExcel

CWL Viewer: The Common Workflow Language Viewer

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

Cite this

Common Workflow Language Viewer: (Talk)

Abstract

Conference

Keywords

Access to Document

Other files and links

Fingerprint

Projects

BioExcel

Research output

CWL Viewer: The Common Workflow Language Viewer

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

Cite this