Hands-on: Exporting a workflow version to WorkflowHub¶

15 min
Medium

To share a workflow version more broadly, you can publish it publicly to Workflow Hub, which is a recommended FAIR repository for workflow deposition.
LabID has a built-in integration with both Workflow Hub and its twin testing platform dev.workflowhub.de.
The instructions below are written for WorkflowHub, but works the same for the testing platform, only substitute the workflow hub account for an account on the testing platform.

The publication process requires creating an account on WorkflowHub and connecting it to your LabID user profile. This should be done once only, and is detailled in step 1 and 2 below.
You can jump to step3 if you already configured your WorkflowHub account in LabID.

Note

Under the hood, LabID will generate a so-called Workflow RO-Crate for the workflow version, with all the files and metadata composing this version, and export it to WorkflowHub.
The workflow version page in LabID also has an "Export ROCrate" button, that lets you directly download such crate, for instance to import the workflow version in another ROCrate-capable software. This export to ROCrate file is also available for workflow runs.

Step 1 : WorkflowHub account creation¶

While you can import public workflows from WorkflowHub, the publication of workflow versions requires having an account on WorkflowHub, and associating this account with LabID.
If you already have an account for one of the WorkflowHub repository, you can go to step 2.

Otherwise, to create an account, first go to Workflow Hub (or dev.workflowhub.de).
At the top right, click register then fill the informations required.
Once you completed the account activation, click on "Join or Create a Team" on your profile page, you might find a team for your lab or institution.

Step 2 : Setup LabID with your WorkflowHub token¶

Go to Workflow Hub, login and under your profile go to Actions > API tokens.
Then click on New API token, provide a meaningful name and validate.
Copy the token, go back to LabID, and navigate to your user dashboard.
There click on Configure WorkflowHub..., make sure the Instance is matching the one of your token, paste the token and save.
Your LabID account is now configured to publish workflow versions in WorkflowHub,

LabID dashboard where you can configure the WorkflowHub integration

WorkflowHub dialog in LabID — Enter your WorkflowHub token here, make sure the selected instance is the right-one for the token at hand

Step 3 : Export a workflow version¶

Once your WorkflowHub account is set up, you can now go to a workflow version you want to publish and make sure the following requirements are fulfilled:

the version needs a license, this can be either via the dedicated field in the version metadata, or by having a file with type LICENSE as part of the version.
among the associated files, a main file must be defined. This should be the main workflow file, or entry point script.
the Computer Language should be populated.

You can now click Publish at the top right, select your team in the pop-up dialog and validate.
The files composing the workflow version are then transferred to WorkflowHub, and the link of the published workflow on WorkflowHub is registered with the workflow version in LabID.

Only released versions can be published

Only workflow versions that are "released" within LabID can be published to WorkflowHub, this is to ensure the exact correspondence between the version published to WorkflowHub and registered in LabID.
Reminder : it is not possible to add or remove files associated to a released workflow version, only metadata can be edited.

Publish a workflow version — Click the Publish button at the top right of a released workflow version to publish it. Then select your team and hit "publish"