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Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows

BACKGROUND: Many open-source workflow systems have made bioinformatics data analysis procedures portable. Sharing these workflows provides researchers easy access to high-quality analysis methods without the requirement of computational expertise. However, published workflows are not always guarante...

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Autores principales: Suetake, Hirotaka, Fukusato, Tsukasa, Igarashi, Takeo, Ohta, Tazro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944229/
https://www.ncbi.nlm.nih.gov/pubmed/36810800
http://dx.doi.org/10.1093/gigascience/giad006
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author Suetake, Hirotaka
Fukusato, Tsukasa
Igarashi, Takeo
Ohta, Tazro
author_facet Suetake, Hirotaka
Fukusato, Tsukasa
Igarashi, Takeo
Ohta, Tazro
author_sort Suetake, Hirotaka
collection PubMed
description BACKGROUND: Many open-source workflow systems have made bioinformatics data analysis procedures portable. Sharing these workflows provides researchers easy access to high-quality analysis methods without the requirement of computational expertise. However, published workflows are not always guaranteed to be reliably reusable. Therefore, a system is needed to lower the cost of sharing workflows in a reusable form. RESULTS: We introduce Yevis, a system to build a workflow registry that automatically validates and tests workflows to be published. The validation and test are based on the requirements we defined for a workflow being reusable with confidence. Yevis runs on GitHub and Zenodo and allows workflow hosting without the need of dedicated computing resources. A Yevis registry accepts workflow registration via a GitHub pull request, followed by an automatic validation and test process for the submitted workflow. As a proof of concept, we built a registry using Yevis to host workflows from a community to demonstrate how a workflow can be shared while fulfilling the defined requirements. CONCLUSIONS: Yevis helps in the building of a workflow registry to share reusable workflows without requiring extensive human resources. By following Yevis’s workflow-sharing procedure, one can operate a registry while satisfying the reusable workflow criteria. This system is particularly useful to individuals or communities that want to share workflows but lacks the specific technical expertise to build and maintain a workflow registry from scratch.
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spelling pubmed-99442292023-02-23 Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows Suetake, Hirotaka Fukusato, Tsukasa Igarashi, Takeo Ohta, Tazro Gigascience Research BACKGROUND: Many open-source workflow systems have made bioinformatics data analysis procedures portable. Sharing these workflows provides researchers easy access to high-quality analysis methods without the requirement of computational expertise. However, published workflows are not always guaranteed to be reliably reusable. Therefore, a system is needed to lower the cost of sharing workflows in a reusable form. RESULTS: We introduce Yevis, a system to build a workflow registry that automatically validates and tests workflows to be published. The validation and test are based on the requirements we defined for a workflow being reusable with confidence. Yevis runs on GitHub and Zenodo and allows workflow hosting without the need of dedicated computing resources. A Yevis registry accepts workflow registration via a GitHub pull request, followed by an automatic validation and test process for the submitted workflow. As a proof of concept, we built a registry using Yevis to host workflows from a community to demonstrate how a workflow can be shared while fulfilling the defined requirements. CONCLUSIONS: Yevis helps in the building of a workflow registry to share reusable workflows without requiring extensive human resources. By following Yevis’s workflow-sharing procedure, one can operate a registry while satisfying the reusable workflow criteria. This system is particularly useful to individuals or communities that want to share workflows but lacks the specific technical expertise to build and maintain a workflow registry from scratch. Oxford University Press 2023-02-22 /pmc/articles/PMC9944229/ /pubmed/36810800 http://dx.doi.org/10.1093/gigascience/giad006 Text en © The Author(s) 2023. Published by Oxford University Press GigaScience. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Suetake, Hirotaka
Fukusato, Tsukasa
Igarashi, Takeo
Ohta, Tazro
Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows
title Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows
title_full Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows
title_fullStr Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows
title_full_unstemmed Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows
title_short Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows
title_sort workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944229/
https://www.ncbi.nlm.nih.gov/pubmed/36810800
http://dx.doi.org/10.1093/gigascience/giad006
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