WorkflowHub project

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Project pages for developing and running the WorkflowHub, a registry of scientific workflows.

View the Project on GitHub workflowhub-eu/about

How to register your workflow(s) in WorkflowHub?

Prerequisites

Before you register a workflow, you need to ensure that you

Get started

To register a workflow, you can either click on the "contribute" icon in the WorkflowHub homepage, or in the "Workflow" option of the "Create" menu from any page of the application.

Supported workflow types

Following workflow types are tested to work well with WorkflowHub, click on them to find out more.

Galaxy (.ga)

    How to use Galaxy
    Information on how to use galaxy can be found on the Galaxy Training Network.

    Extract a workflow from the History
    This is the most easy way to generate a Galaxy workflow and is extensively explained here.

    Editing a Galaxy workflow
    Using the Galaxy workflow editor it is recommended to add tags and/or add for example the tutorial title as Annotation/Notes. Mor information on how to use the editor can be found here in the "The workflow editor" section.

    Galaxy to CWL abstract
    Galaxy workflows can easily be converted to CWL abstract with galaxy2cwl. This can be seen as a standardized summary of the workflow that can be interpreted by WorkflowHub. CWL abstract can also be used to generate a diagram.

    Uploading to WorkflowHub
    Since it is not possible to reference a workflow in a Galaxy instance, you either have to download the workflow file and upload it to WorkflowHub, or make an RO-crate following the steps below. You can still reference the workflow in the galaxy instance using the source property in the metadata of the registration.

Common Workflow Language (.cwl)
    More information will soon be available.
Nextflow (.nf)
    More information will soon be available.
SnakeMake (.snake)
    More information will soon be available.
KNIME (.knwf)
    More information will soon be available.

It is also possible to upload workflows from another type (for ex. bash scripts), these will be recognized as unknown workflow type. Note that at this moment only for CWL workflows it is possible to automatically generate a diagram.

Registering your workflow on WorkflowHub

After clicking on the "Contribute" icon or selecting "Create" and then "Workflow" from the navigation menu bar, you have 2 options for registering your workflow. For more information on the these options, please go to the corresponding pages:

Using the UI of WorkflowHub you upload or reference a workflow file along with optionally a CWL Description and/or a diagram.

- The advanced way: registering a workflow RO-crate

When you have created a workflow RO-crate of your workflow using the python package, and want to upload or reference it.

- [In development] Registering a workflow RO-crate using the API

We are working on a WorkflowHub API that will allow the user to automatically register workflow RO-crates. Not all features are yet developed, but a glimpse of the API can be found here.