Hands-on: Importing workflows

• 10 min
• Easy

LabID supports importing workflows from various sources, including git repositories, WorkflowHub and galaxy.
By Workflow here we include traditional ones from workflow platforms (Nextflow, Snakemake, Galaxy) but also scripts and notebooks, which can be equally registered in LabID.

To import a workflow, from the left menu, navigate to Workflows > Workflow.
On the top left of the page, click on New workflow to see the different import options.

Workflows can be imported from various sources or created from scratch

Import from git

Workflows can be imported from a public (GitHub, GitLab...) or privately hosted (e.g institutional) git repo.

Warning

To import workflows from an institutional repository, your admin needs to configure authentication via ssh.

From the list of options under New workflow (see above), select Import from git to start the import from a git repository.

After pasting the URL to the repository, LabID automatically fetches information from the last release and automatically lists some files from the repository based on filenames (main workflow file, license, readme, config).
The dropdown menu Workflow version commit lets you select older released versions (or specific commits) if needed.
Note that versions already imported in LabID are tagged as such.

The default list of files and associated types may be incomplete, or the type attributed might not reflect reality, and should be reviewed. Additional files can be selected by clicking the on the bottom left.
It is also possible to remove files that are not relevant, or change their associated type.
Note that here "removing" does not mean removing files from the original repository but only skipping their annotation in LabID. Indeed, only key files (main workflow file, license, readme, config) from the repository needs to be annotated with a type. This can always be modified later.
Once all files of interest are selected, clicking Import version x.x.x will create a corresponding Workflow version in LabID.
A parent Workflow will also be created if this is the first version imported from this repository.

Importing a workflow from git

Info

The parent Workflow keeps a reference to the original Git repository, while the associated Workflow versions have a reference to the original commit hash.

Resulting workflow and associated workflow versions in LabID

Import from a workflow repository (ex : WorkflowHub, Galaxy...)

Workflows can also be imported from workflow repositories such as WorkflowHub (and dev.WorkflowHub) and galaxy instances.
The repositories you can import from need to be configured by an admin (see WorkflowHub Integration of the admin documentation).

To import from a workflow repository, first go to the Workflows section of LabID, then click New workflow on the top left of the page, and select the corresponding Import from ... option.
If this option is missing, your LabID instance is not configured to import from that repository, in this case an administrator needs to add it following these instructions.

Importing workflows in LabID

You can either search across the workflow repository using the built-in search functionality of LabID or paste the URL to a public workflow in that repository.

To import workflows you can either use the direct URL to the workflow or search the workflow repository with a query

Import using the URL to a workflow

If you already identified the workflow you want to import, you can directly copy/paste its URL in the corresponding field of the import dialog (see below). This is possible for public workflows only.

Importing a workflow from its URL

Info

When importing from a WorkflowHub URL, the main URL of the workflow page (ex : workflowhub.eu/workflows/1325/) cannot be used directly for import, as it does not point to a specific version, rather to the last available version at the time the link is visited.
LabID enforces here the use of version-specific URL (ex : workflowhub.eu/workflows/1325?version=3) to ensure reliable identification of imported workflow versions.
Such version-specific links are available under Version history on the WorkflowHub page, simply copying the hyperlink under the version identifier.

Example workflow from WorkflowHub. Make sure to use the link to a specific version for import (as shown)

Info

Workflow version imported from WorkflowHub are packaged as Workflow RO-Crate.
This ROCrate is associated to the Workflow Version in LabID via the Attachements functionality, so you can always download the original crate for this workflow version.
The link to the workflow on WorkflowHub is also stored in LabID as an Annotation.

Searching the workflow repository from LabID

Besides using the URL to a workflow, LabID supports searching the workflow repository using a custom search query. Below an example searching through the EU Galaxy instance.
This functionality lets you then import a specific version, when multiple versions of a workflow are available.

Searching for a workflow from LabID, here within the Galaxy EU repository

Resulting workflow and workflow version in LabID

If the import is successfull, a new Workflow and Workflow Version entity are created in LabID. Click on the button in the notification window informing about the successfull import to be taken to the workflow page.

Both the Workflow and Workflow version retain the original link to the workflow repository.
The workflow version in LabID will also have a copy of the main galaxy file (.ga) when importing from galaxy, while when importing from WorkflowHub, the Workflow ROCrate is saved as an attachment.

Workflow versions imported from Workflow Hub retain the link to the workflow page and a copy of the imported Workflow ROCrate

Workflow and workflow version after importing workflow from a galaxy instance