Yevis: System to support building a workflow registry with automated quality control

ELIXIR-Cloud AAI meeting 2022-08-31

Transcript

1. Yevis: System to support building a workflow registry
   with automated quality control
   Tazro Ohta, Ph.D.
   Database Center for Life Science, Japan
   2022/08/31
   

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2. Challenges on sharing workflows
   "Sharing resources helps science"
   Have you ever reused a public workflow?
   Had no issues?
   Really??
   Issues on reusing workflows
   Missing license
   Language syntax error
   Missing dependent materials
   Missing example input/output
   Missing test
   github.com/sapporo-wes/yevis-cli 2
   

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3. Workflows as processes challenge the FAIR principles by their structure, forms,
   versioning, executability, and reuse.
   Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober (2020): FAIR
   Computational Workflows. Data Intelligence 2(1):108–121 https://doi.org/10.1162/dint_a_00033 3
   

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4. Question: Who should take care?
   github.com/sapporo-wes/yevis-cli 4
   

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5. Case: WorkflowHub
   A FAIR workflow registry (in BETA)
   Asking submitters to maintain the workflow metadata
   https://workflowhub.eu 5
   

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6. Case: nf-core
   A Nextflow pipeline collection curated by community
   Ask submitter to join the community and maintain the uploads
   Not for 'bespoke' pipelines
   https://nf-co.re/ 6
   

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7. Trade-off: reliability vs diversity
   When published workflows are maintained by:
   Submitter
   Lower registry operation cost, expect higher diversity
   Reliability depends on developers' expertise
   Registry
   Expect better reliability
   With limitation on the coverage of workflow types
   github.com/sapporo-wes/yevis-cli 7
   

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8. Minor workflows matter
   Researchers need workflows specific to
   A biological species
   An experimental method
   A laboratory instrument
   A computing environment
   Smaller communities often have more difficulties on building common resources
   How we can make and keep minor but valuable resources reusable?
   github.com/sapporo-wes/yevis-cli 8
   

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9. Solution: lowering the cost of workflow maintenance
   Workflows are best maintained by their developers
   Domain knowledge is essential for managing contents
   BUT: Developers are often without extra time, skill, knowledge
   Provide an assistant for developers to lower the maintenance cost
   github.com/sapporo-wes/yevis-cli 9
   

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10. Yevis: A system to support building a registry
    Easily build one's own registry to share workflows in a reliable manner.
    Yevis metadata: assist developers to satisfy the requirements of 'reusable with
    confidence'
    Automatic validation and testing with CLI client and GitHub Actions
    Fully based on GitHub/Zenodo: no dedicated computing required
    Adapted the GA4GH TRS spec: promoting a distributed registry model
    github.com/sapporo-wes/yevis-cli 10
    

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11. Proposing criteria for workflows 'reusable with
    confident'
    Perspective Requirements
    Availability Main workflow description, Dependent materials, Testing materials, Open
    source license
    Validity Language type, Language version, Language syntax
    Traceability Authors and maintainers, Documentation, Workflow ID, Workflow
    metadata version
    github.com/sapporo-wes/yevis-cli 11
    

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12. The Yevis way
    github.com/sapporo-wes/yevis-cli 12
    

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13. yevis-web: registry browser
    github.com/sapporo-wes/yevis-cli 13
    

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14. Resources
    Examples
    Registry: https://github.com/ddbj/workflow-registry
    WebUI: https://ddbj.github.io/workflow-registry-browser/
    Repos
    CLI to deploy Yevis registry: https://github.com/sapporo-wes/yevis-cli
    WebUI for a Yevis registry: https://github.com/sapporo-wes/yevis-web
    Document
    https://sapporo-wes.github.io/yevis-cli/getting_started
    Publication
    https://www.biorxiv.org/content/10.1101/2022.07.08.499265v1
    github.com/sapporo-wes/yevis-cli 14
    

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