Workflow Hub

Registry of COVID-19 workflows in workflowhub.eu

• Sub-topic of Workflows, FAIR Data, Ontology, Web Development

Several COVID-19 Workflows have already been identified and are being worked on in this BioHackathon.

The EOSC-Life Workflow Hub is in development to become a registry of life science workflows from multiple underlying repositories for many workflow systems. EOSC-Life participants include large EU-wide European Research Infrastructures like ELIXIR, but the Workflow Hub is developed as a separate open source community project.

This topic proposes to set up an early pre-production instance of the Workflow Hub, covid19.workflowhub.eu, to be a registry that gather the COVID-19 workflows and their metadata. Part of the tasks here is also to curate the existing workflows and help making them interoperable, reusable and reproducible.

The curated metadata will be in a FAIR format based on RO-Crate and BioSchemas annotations and maintained separate from the Workflow Hub; where possible contributed back to the workflow's origin GitHub repositories.

Skills

Desired (one or more):

• One or more workflow systems
• Ruby on Rails
• Python
• BioSchemas
• JSON-LD
• Linked Data
• Documentation writing

Coordinator

• Carole Goble

Participants

• Stian Soiland-Reyes
• Finn Bacall
• Stuart Owen
• Alan Williams
• Leyla Garcia
• Dan Fornika (GitHub, Twitter, Genomics Specialist @ BCCDC Public Health Laboratory)
• Frederik Coppens-
• Alban Gaignard
• Ignacio Eguinoa
• Vahid Kiani
• Bert Droesbeke
• Hervé Ménager
• José Mª Fernández
• Kiran K Telukunta
• Flora D'Anna
• Ambarish Kumar
• Robin Robertson
• Emmy Tsang
• Laura Rodriguez-Navas Anyone welcome! Add yourself above and join the biohackathon mailing list

Communication

The communication will be the same as for Workflow Hub community calls, just more frequent.

• Slack: #workflows on seek4science.slack.com
• Daily stand-up calls:
  • Biohackathon webinar: Sunday 2020-04-05 13.00 BST / 14.00 CEST
  • Kick-off: Monday 2020-04-06 09:00 BST / 10:00 CEST
  • Morning: 09:00 BST / 10:00 CEST roll call, task prioritizing
  • Afternoon: 16:00 BST / 17:00 CEST wrap-up and next steps
  • Call details and agenda.
  • Daily call: join with the Zoom client/app (recommended) or Web browser: https://zoom.us/j/719881989 or telephone, see https://zoom.us/u/ad8HBAhAeU meeting number 719-881-989, with SIP or Skype for Business: https://zoom.us/skype/719881989 (sip:[email protected] )
  • Final call: Thursday 2020-04-09 16:00 BST / 17:00 CEST
    • (Good Friday bank holiday in many countries)
  • Mid term webinar for all BioHackathon: Wednesday 13:00 BST / 14:00 CEST
    • Webinar call details, see https://groups.google.com/forum/#!forum/virtual-biohackathon
  • Wrap-up for all BioHackathon: Saturday wrap report.

Reporting

• Minutes and planning
• Mini-publication
• Mid-week slide

Tasksroll call, task prioritizing_

• Preparation
  • Register domain name Done
    • Shows COVID-19 programme view of WorkflowHub
  • Prepare pre-production Workflow Hub install
    • nginx and Let's Encrypt SSL
    • Prepare structure, e.g. separate Project for all workflows in https://github.com/galaxyproject/SARS-CoV-2
    • Single-sign-on with ELIXIR
  • Setup automatic, incremental backup, with offsite copies
• Workflow review
  • Augment existing lists of COVID-19 Workflows
  • Crosswalk to monitor workflow development in the Gene Expression Topic
• Induction
  • Workflow-RO-Crate making
  • Workflow metadata (Bioschemas Workflow Profile)
  • Workflow Hub current features
• Simple register of existing workflows (direct links)
  • Galaxy workflows
  • Nextflow workflows (nf-core)
  • others?
• Documentation
  • Document export/deposit instructions per workflow system
  • Document deposition API using Pasteur's Nextflow examples
• Curation and metadata
  • Curate existing workflows with structured RO-Crate metadata
  • Plan and test how to make per-workflow-git-repository to hold metadata
  • Register new versions in Workflow Hub (preserve IDs?)
  • Display more of metadata in WorkflowHub
  • Contribute RO-Crate metadata back to existing workflow git repos
  • Review Bioschemas Workflow Profile against experience (end of hackathon)
• Limited support for ad-hoc shell scripts
  • Deposit into GitHub via simple upload
  • Metadata curation and workflowisation?
• Contributor attribution and credit
  • Register DOI per workflow? (probably after hackathon?)
  • Review credit and contribution features.
• Collections
  • First class collection support (not just tag based search)

Resources

• (soon) http://covid19.workflowhub.eu/
  • Note: Separate dev-instance https://dev.workflowhub.eu/ is occasionally wiped but can be used for testing
• https://github.com/workflowhub-eu/about/wiki
• https://github.com/seek4science/seek/tree/workflow
• https://github.com/ieguinoa/cwl-from-galaxy

Existing COVID-19 workflows

Please add to this list!

• See also https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Workflows#workflows
• https://github.com/connor-lab/ncov2019-artic-nf
• https://github.com/galaxyproject/SARS-CoV-2
• https://github.com/INSaFLU/INSaFLU
• https://github.com/nf-core/viralrecon
• https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2
• https://github.com/pitagora-network/COVID-19-CWL
• https://cbg-ethz.github.io/V-pipe/
• https://github.com/common-workflow-lab/2020-covid-19-bh
• ..

Note that most of these are work in progress that will evolve during the Workflows topic at this Bio Hackathon