WorkflowHub is a new FAIR workflow registry sponsored by the European RI Cluster EOSC-Life and the European Research Infrastructure ELIXIR. It is workflow management system agnostic: workflows may remain in their native repositories in their native forms.
This website describes the open source project for developing and running WorkflowHub.
For more details, see About WorkflowHub, FAIR Computational Workflows, Outreach and Publications.
This project has a Code of Conduct to ensure interactions are friendly, respectful and inclusive. You can contact info@esciencelab.org.uk if you have any concerns or questions.
- 2022-01-26: The WorkflowHub Usability study is looking for volunteers to help improve the usability of WorkflowHub
- 2022-01-22: WorkflowHub now has deeper Git support, when making a New Version it is possible to link an entry to a GitHub repository
- What is WorkflowHub
- How to register
- Logging-in
- How to join a team
- How to find and retrieve workflows from WorkflowHub
- How to register your workflow in WorkflowHub
- Updating a registered workflow
- Making a workflow citable with a DataCite DOI
For any kind of questions or suggestions on using WorkflowHub, feel free to join our community!
- Workflow RO-Crate spec
- How to make a workflow RO-Crate
- The Global Alliance for Genomics and Health (GA4GH) Tool Registry Service (TRS) API
- RO-Crate Submission API
For developer questions such as on REST APIs, RO-Crate, or setting up your own instance of WorkflowHub, feel free to join our community!
- Production instance: https://workflowhub.eu/
- Dev instance https://dev.workflowhub.eu/ (use for testing; occasionally wiped)
- Source: seek4science/seek branch
workflow - API documentation: https://workflowhub.eu/api
- Outreach and Publications
- Tasks:
- WorkflowHub roadmap
- WorkflowHub implementation https://github.com/seek4science/seek/projects/3 (SEEK)
- General WorkflowHub https://github.com/workflowhub-eu/about/issues
- Mailing list:
workflowhub😊elixir-europe.org(subscribe/archive) - Slack chat: #workflows on seek4science.slack.com (join)
- Google Drive (to request write-access, ask in Slack channel)
- Slides/posters:
- WorkflowHub - a registry for workflows, Carole Goble, ECCB 2020, 2020-09-02
- Poster: The WorkflowHub, a registry for Life Science Workflows, Ambarish Kumar, ISMB, 2020-07-13
- WorkflowHub Introduction slides, Carole Goble, 2020-03-25
- Weekly meeting: Rolling Minutes / call details
Regular meeting: WorkflowHub Club - all welcome!
Anyone is welcome to join the weekly WorkflowHub Club calls using Zoom.
- When: Alternate Wednesdays 10:00 GMT / 11:00 CET
- Agenda/telcon details: https://s.apache.org/workflowhub-minutes
See the list of club members on the acknowledgement page.
FAIR Computational Workflows workshop (2020-09-02)
The WorkflowHub team organized the Workshop on FAIR Computational Workflows at the 19th European Conference on Computational Biology (ECCB 2020).
Organizers: Ignacio Eguinoa, Björn Grüning, Frederik Coppens, Carole Goble, Stian Soiland-Reyes, Salvador Capella-Gutierrez
Talks included:
- A review on the FAIR principles for computational workflows (Sarah Cohen-Boulakia)
- Toward defining and implementing FAIR for research software (Mateusz Kuzak)
- WorkflowHub - a registry for workflows (Carole Goble)
- Common Workflow Language and CWLProv (Michael R. Crusoe)
- Packaging workflows with RO-Crate (Stian Soiland-Reyes)
- Testing workflows: Life Monitor and OpenEBench (Simone Leo & Salvador Capella-Gutierrez)
- FAIR Computational Workflows & OpenEBench (Salvador Capella-Gutierrez)
- FAIR computational data analysis with Galaxy (Björn Grüning)
- Nextflow and nf-core (Alex Peltzer)
The workshop organizers aim to make all slides available later.
BCC2020 CollaborationFest (2020-07-22 / 2020-07-23)
WorkflowHub was one of the working clusters at the BCC2020 CollaborationFest as part of Bioinformatics Community Conference 2020.
Activities included a Bring your own Workflow session to register more workflows at https://workflowhub.eu/.
Improving support for Galaxy workflows worked closely with Galaxy developers at BCC and the topic Exporting RO-Crate/BioCompute-Object packaged workflows from Galaxy which made a first release of the RO-Crate Python library and alignments with BioCompute Object.
Metadata and BioSchemas aligned and released BioSchemas ComputationalWorkflow profile 0.5 which was also aligned with the next version of RO-Crate.
IWC for Galaxy Workflows looked at API for workflow registration and created an open source license drop-down list for workflows.
More:
COVID-19 BioHackathon (2020-04-05 / 2020-04-11)
WorkflowHub was one of the topics at the Virtual COVID-19 BioHackathon, attracting more than 30 developers. The participants also collaborated with the Workflows and FAIR Data topics.
Thanks to the collaborative effort WorkflowHub could be launched early at https://covid19.workflowhub.eu/ in a "pre-beta" stage. The COVID-19 workflows registered at the hackathon now appear as part of https://workflowhub.eu/
More:
Planning documents
These planning documents are from the WorkflowHub Google Drive. Check their edit history, these may be incomplete or drafts.
- Methods of submitting to WorkflowHub
- WorkflowHub User Requirements
- Minimal Viable Product - leading to https://dev.workflowhub.eu/
- Minimum Information for the Registration of a Computational Workflow (MIRCW) lead to Workflow RO-Crate
- Workflow RO-Crate a profile of RO-Crate for exchange of workflows with WorkflowHub; based on BioSchemas Workflows profile
- Primer on standards for workflow packaging and metadata draft
Related resources
- SEEK is the underlying platform used by the WorkflowHub
- RO-Crate is a metadata/packaging mechanism, used by WorkflowHub for exchange of workflows
- BioSchemas Workflows - a suggested new
schema.orgtype for describing computational workflows - Common Workflow Language (CWL) is an executable workflow language, which WorkflowHub use primarily for descriptive functions
Workflow repositories
WorkflowHub intends to harvest workflows from existing workflow repositories, including:
- myExperiment was a workflow repository that inspired WorkflowHub
- nf-core - a community-developed colletions of bioinformatics workflows for Nextflow
- https://usegalaxy.eu/
workflowhub.eu lead development is part of EOSC-Life, funded by European Union’s Horizon 2020 programme under grant agreement 824087.
We are also grateful for contributions from ELIXIR Europe,
FAIRDOM (BB/M013189/1),
BioExcel-2 (823830),
IBISBA (730976,
871118),
SYNTHESYS+ (823827),
FAIR Workflows and others.
See a complete list on the acknowledgement page.