Hands-on: Creating workflows from scratch

• 10 min
• Easy

Create workflows from local files

If you have a workflow that's not in any of the supported repositories (Galaxy, Git, WorkflowHub), you can still register it in LabID, by creating a workflow and version "from scratch".
This can be convenient for instance for some test workflow on your computer, or workflows for which version control systems are not appropriate (e.g binary files such as KNIME workflows).

To start creating a new workflow, go to the list of workflows page, then at the top left after clicking the New workflow , select New workflow.

Start by clicking the New Workflow button at the top left of the workflow list page

Step 1 : Fill-in workflow informations

The first step is the creation of a parent Workflow, to which a first Workflow Version will then be associated with a specific set of files.
The Workflow has rather minimal informations namely a name, an optional description and a Workflow Manager / programming language.
Additional options define user-permissions in LabID as for other registered entities.
Once the form is filled, click the button Save item at the top right corner, which will take you to the first Workflow Version for this Workflow.

First fill-in the information for the parent workflow

Step 2 : Edit the workflow version

The new workflow version has a default name and no associated files.
While you could start using this version right-away, associating it to Workflow Runs, it rather makes sense to edit it first, by clicking the Edit button at the top right corner.

Click the Edit button in the workflow version page

Edit metadata

It's a good idea to change the name to easily recognize it in the list of workflow versions, we recommend including the name of the parent workflow and a version indicator (such as "My KNIME workflow - v1").
You can also associate a license to this workflow version, or leave it for now. You can always edit the version later to edit it, or any other field.

Registering older versions

The workflow version has a field "is latest" to indicate if this version is the latest one.
This value is true by default when creating workflow versions, but you can set it to false, to create a version which would be anterior to a version previously registered in LabID.

Associate files to the version

At the bottom click the Browse button, or drag and drop files you would like to associate to this version.
Each file has an associated type (main, license...), this is used when exporting the workflow version as a Workflow RO-Crate or to Workflow Hub.
It's also of general use for someone who is not familiar with this type of workflow.
Once you are done, click the Save button at the top right.

What files should I select ?

Files associated to a workflow version should be the scripts and other files that compose this version and might change with new versions. You can add individual files but no directories.
Alternatively, if you need such kind of hierarchy you could add a zip file with the content of a directory.

About configuration files

Configuration files stored at the Workflow (version) level usually represent templates or examples to help users executing the workflow. The configuration files used when executing the workflow should be associated with workflow runs, just like inputs, outputs and logs/reports files.

Edit or add metadata about that specific version, and associate files composing this version

Releasing a workflow version

Before starting registering workflow runs with this workflow version, we recommend to first release this version in LabID.
To do so, exit the edit mode and click the Release button in the top right corner.
This freezes the workflow version and prevents the addition or removal of additional files. This ensures that each workflow run associated to this version refers to the exact same set of files.
Metadata such as file type, license, etc... remains editable even after the release.

Creating a new version

You cannot create additional versions of a workflow while the current version is not released !

What is the difference with "Publish"

The Publish button is used to publish the workflow version to Workflow Hub (or dev.workflowhub). See Export workflows to WorkflowHub.

Creating new versions

To create a new version, make sure to release the current version and click the + New version button at the top right. The new workflow version page is initialized with the set of files from the previous version. Make sure to rename the workflow version to something meaningful, as described in the section Edit metadata.
You can then replace those files with new versions, remove them if they became obsolete, and add new files as needed.
Once you start using this new version with imported workflow runs, don't forget to release it!

Overview of registered versions

From a workflow version page, click on Workflow to be taken to the parent workflow page. The workflow page lists all versions registered for this specific workflow.

Exporting workflow versions from LabID

Once you have created some workflow versions in LabID, you can share them with other LabID users, so they can register workflow runs with those. For this, simply adjust the visibility in the Sharing panel of the workflow and workflow version pages.
To share workflow versions with others out of LabID, you have 2 options :

• exporting the workflow version to workflow hub (or dev.workflow.hub)

• exporting the workflow version as RO-Crate. From the workflow version page in LabID, click RO-Crate to download a Workflow RO-Crate for this workflow version. This is basically a zip file containing all files composing the workflow, together with a json file describing the content of this zip.
  Such file can be used for instance to import the worflow version in another RO-Crate-capable software.

Note

You will find a similar "Export to RO-Crate" button for workflow runs.
This uses the Workflow Run RO-Crate profile, which is an extension to the Workflow RO-Crate profile mentioned above.