Portable workflow and tool descriptions with the CWLCitation formats

  • External authors:
  • Peter Amstutz
  • Nebojša Tijanić
  • John Kern
  • Luka Stojanovic
  • Tim Pierce
  • John Chilton
  • Maxim Mikheev
  • Samuel Lampa
  • Hervé Ménager
  • Scott Frazer
  • Venkat Sai Malladi
  • Michael R. Crusoe

Standard

Portable workflow and tool descriptions with the CWL. / Amstutz, Peter; Tijanić, Nebojša; Soiland-Reyes, Stian; Kern, John; Stojanovic, Luka; Pierce, Tim; Chilton, John; Mikheev, Maxim; Lampa, Samuel; Ménager, Hervé; Frazer, Scott; Malladi, Venkat Sai; Crusoe, Michael R.

2015. Abstract from Bioinformatics Open Source Conference, Dublin, Ireland.

Research output: Contribution to conferenceAbstractpeer-review

Harvard

Amstutz, P, Tijanić, N, Soiland-Reyes, S, Kern, J, Stojanovic, L, Pierce, T, Chilton, J, Mikheev, M, Lampa, S, Ménager, H, Frazer, S, Malladi, VS & Crusoe, MR 2015, 'Portable workflow and tool descriptions with the CWL', Bioinformatics Open Source Conference, Dublin, Ireland, 10/06/15 - 11/06/15. <https://github.com/common-workflow-language/2015-bosc/blob/master/bosc_abstract/cwl_abstract_bosc.md>

APA

Amstutz, P., Tijanić, N., Soiland-Reyes, S., Kern, J., Stojanovic, L., Pierce, T., Chilton, J., Mikheev, M., Lampa, S., Ménager, H., Frazer, S., Malladi, V. S., & Crusoe, M. R. (2015). Portable workflow and tool descriptions with the CWL. Abstract from Bioinformatics Open Source Conference, Dublin, Ireland. https://github.com/common-workflow-language/2015-bosc/blob/master/bosc_abstract/cwl_abstract_bosc.md

Vancouver

Amstutz P, Tijanić N, Soiland-Reyes S, Kern J, Stojanovic L, Pierce T et al. Portable workflow and tool descriptions with the CWL. 2015. Abstract from Bioinformatics Open Source Conference, Dublin, Ireland.

Author

Amstutz, Peter ; Tijanić, Nebojša ; Soiland-Reyes, Stian ; Kern, John ; Stojanovic, Luka ; Pierce, Tim ; Chilton, John ; Mikheev, Maxim ; Lampa, Samuel ; Ménager, Hervé ; Frazer, Scott ; Malladi, Venkat Sai ; Crusoe, Michael R. / Portable workflow and tool descriptions with the CWL. Abstract from Bioinformatics Open Source Conference, Dublin, Ireland.1 p.

Bibtex

@conference{f71e169b8724458086d6e621077d8c74,
title = "Portable workflow and tool descriptions with the CWL",
abstract = "Bioinformatics workflow platforms provide provenance tracking, execution and data management, repeatability, and an environment for data exploration and visualization. Example F/OSS bioinformatics workflow platforms include Arvados, Galaxy, Mobyle, iPlant DiscoveryEnvironment, Apache Taverna and Yabi. Each one presently represent workflows using different vocabularies and formats, and adding new tools requires different procedures for each system.Neither the description of the workflows nor the descriptions of the tools that power them are usable outside of the platforms they were written for. This results in duplicated effort, reduced reusability, and impedes collaboration.Three engineers (Peter Amstutz, John Chilton, and Nebojsa Tijanic) from leading bioinformatics platform teams (Curoverse, Galaxy Team, and Seven Bridges Genomics) and a tool author (Michael R. Crusoe / khmer project) started working together at the BOSC 2014 Codefest with an initial focus on developing a portable means of representing, sharing and invoking command line tools which was then the basis for portable workflow descriptions. The group placed high value on re-using existing formats and ontologies; they governed themselves with a lazy consensus / do-ocracy approach.On March 31st, 2015 the group released their second draft of the Common Workflow Language specification. The serialized form is a YAML document that is validated by an Apache Avro schema and can be interpreted as an RDF graph using JSON-LD. The documents are also valid Wf4Ever 'wfdesc' descriptions after a simple transformation. Future drafts will include the use of the EDAM ontology to describe the tools enabling discovery via the ELIXIR tool registry.Seven Bridges Genomics, the Galaxy Project, and the organization behind Arvados (Curoverse) have started to implement support for the Common Workflow Language, with interest from other projects and organizations like Apache Taverna, BioDatomics and the Broad Institute. Developers on the Galaxy Team are exploring adding CWL tool description support with plans to add support for the CWL workflow descriptions. Tool authors and other community members will benefit as they will only have to describe their tool and workflow interfaces once. This will enable scientists, researchers and other analysts to share their workflows and pipelines in an interoperable and yet human readable manner.",
keywords = "workflow, Scientific workflows, bioinformatics, cwl",
author = "Peter Amstutz and Neboj{\v s}a Tijani{\'c} and Stian Soiland-Reyes and John Kern and Luka Stojanovic and Tim Pierce and John Chilton and Maxim Mikheev and Samuel Lampa and Herv{\'e} M{\'e}nager and Scott Frazer and Malladi, {Venkat Sai} and Crusoe, {Michael R.}",
year = "2015",
month = jul,
day = "10",
language = "English",
note = "Bioinformatics Open Source Conference, BOSC ; Conference date: 10-06-2015 Through 11-06-2015",
url = "http://www.open-bio.org/wiki/BOSC_2015",

}

RIS

TY - CONF

T1 - Portable workflow and tool descriptions with the CWL

AU - Amstutz, Peter

AU - Tijanić, Nebojša

AU - Soiland-Reyes, Stian

AU - Kern, John

AU - Stojanovic, Luka

AU - Pierce, Tim

AU - Chilton, John

AU - Mikheev, Maxim

AU - Lampa, Samuel

AU - Ménager, Hervé

AU - Frazer, Scott

AU - Malladi, Venkat Sai

AU - Crusoe, Michael R.

N1 - Conference code: 2015

PY - 2015/7/10

Y1 - 2015/7/10

N2 - Bioinformatics workflow platforms provide provenance tracking, execution and data management, repeatability, and an environment for data exploration and visualization. Example F/OSS bioinformatics workflow platforms include Arvados, Galaxy, Mobyle, iPlant DiscoveryEnvironment, Apache Taverna and Yabi. Each one presently represent workflows using different vocabularies and formats, and adding new tools requires different procedures for each system.Neither the description of the workflows nor the descriptions of the tools that power them are usable outside of the platforms they were written for. This results in duplicated effort, reduced reusability, and impedes collaboration.Three engineers (Peter Amstutz, John Chilton, and Nebojsa Tijanic) from leading bioinformatics platform teams (Curoverse, Galaxy Team, and Seven Bridges Genomics) and a tool author (Michael R. Crusoe / khmer project) started working together at the BOSC 2014 Codefest with an initial focus on developing a portable means of representing, sharing and invoking command line tools which was then the basis for portable workflow descriptions. The group placed high value on re-using existing formats and ontologies; they governed themselves with a lazy consensus / do-ocracy approach.On March 31st, 2015 the group released their second draft of the Common Workflow Language specification. The serialized form is a YAML document that is validated by an Apache Avro schema and can be interpreted as an RDF graph using JSON-LD. The documents are also valid Wf4Ever 'wfdesc' descriptions after a simple transformation. Future drafts will include the use of the EDAM ontology to describe the tools enabling discovery via the ELIXIR tool registry.Seven Bridges Genomics, the Galaxy Project, and the organization behind Arvados (Curoverse) have started to implement support for the Common Workflow Language, with interest from other projects and organizations like Apache Taverna, BioDatomics and the Broad Institute. Developers on the Galaxy Team are exploring adding CWL tool description support with plans to add support for the CWL workflow descriptions. Tool authors and other community members will benefit as they will only have to describe their tool and workflow interfaces once. This will enable scientists, researchers and other analysts to share their workflows and pipelines in an interoperable and yet human readable manner.

AB - Bioinformatics workflow platforms provide provenance tracking, execution and data management, repeatability, and an environment for data exploration and visualization. Example F/OSS bioinformatics workflow platforms include Arvados, Galaxy, Mobyle, iPlant DiscoveryEnvironment, Apache Taverna and Yabi. Each one presently represent workflows using different vocabularies and formats, and adding new tools requires different procedures for each system.Neither the description of the workflows nor the descriptions of the tools that power them are usable outside of the platforms they were written for. This results in duplicated effort, reduced reusability, and impedes collaboration.Three engineers (Peter Amstutz, John Chilton, and Nebojsa Tijanic) from leading bioinformatics platform teams (Curoverse, Galaxy Team, and Seven Bridges Genomics) and a tool author (Michael R. Crusoe / khmer project) started working together at the BOSC 2014 Codefest with an initial focus on developing a portable means of representing, sharing and invoking command line tools which was then the basis for portable workflow descriptions. The group placed high value on re-using existing formats and ontologies; they governed themselves with a lazy consensus / do-ocracy approach.On March 31st, 2015 the group released their second draft of the Common Workflow Language specification. The serialized form is a YAML document that is validated by an Apache Avro schema and can be interpreted as an RDF graph using JSON-LD. The documents are also valid Wf4Ever 'wfdesc' descriptions after a simple transformation. Future drafts will include the use of the EDAM ontology to describe the tools enabling discovery via the ELIXIR tool registry.Seven Bridges Genomics, the Galaxy Project, and the organization behind Arvados (Curoverse) have started to implement support for the Common Workflow Language, with interest from other projects and organizations like Apache Taverna, BioDatomics and the Broad Institute. Developers on the Galaxy Team are exploring adding CWL tool description support with plans to add support for the CWL workflow descriptions. Tool authors and other community members will benefit as they will only have to describe their tool and workflow interfaces once. This will enable scientists, researchers and other analysts to share their workflows and pipelines in an interoperable and yet human readable manner.

KW - workflow

KW - Scientific workflows

KW - bioinformatics

KW - cwl

UR - http://www.commonwl.org/

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

M3 - Abstract

T2 - Bioinformatics Open Source Conference

Y2 - 10 June 2015 through 11 June 2015

ER -