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External Workflow System Integrations

LabID can integrate with several popular external workflow systems to import workflows and workflow runs. This page documents how to use these integrations as an end user.

Administrator Setup Required

These integrations must be configured by your LabID administrator before they can be used. See the Workflow Configuration guide for setup instructions.

Git Repository Integration

LabID supports importing workflows directly from Git repositories, including both public and organizational repositories.

Supported Repository Types

  • Public repositories: Available via both HTTPS and SSH
  • Organizational repositories: Available via SSH with proper authentication setup

For details on repository access requirements and setup, see the Git Repository Import section in the administrator documentation.

WorkflowHub Integration

Importing Workflows from WorkflowHub

Figure 1: Import Workflow from WorkflowHub

Import Workflow from WorkflowHub
Figure 1: Import Workflow from WorkflowHub

To import a workflow from WorkflowHub:

  1. Click the "Import" button on the Workflow list page
  2. Select "Import from WorkflowHub"
  3. Search for workflows by name or paste a WorkflowHub workflow URL
  4. Select the version to import
  5. Review and confirm the import

Public Workflows Only

This feature is limited to publicly available workflow versions. Only one version can be imported at a time.

Exporting Workflows to WorkflowHub

Figure 2: Publish Workflow to WorkflowHub

Publish Workflow to WorkflowHub
Figure 2: Publish Workflow to WorkflowHub

To export a workflow to WorkflowHub:

  1. Navigate to the workflow version you want to export
  2. Click the "Publish" button
  3. Search for the WorkflowHub Team you want to publish the workflow to
  4. Confirm the export

Export Requirements

  • Only released/published versions of workflows can be exported to WorkflowHub
  • Workflows previously imported from WorkflowHub or Galaxy cannot be published to WorkflowHub
  • You must first set up your WorkflowHub credentials in your user profile settings

ROCrate Export

Any workflow in LabID can be exported as a Research Object Crate (ROCrate). ROCrate is a community standard for packaging research data with their metadata using structured data standards.

Exporting Workflows to ROCrate

To download a workflow as an ROCrate:

  1. Navigate to the workflow version you want to export
  2. Use the download option to get the ROCrate archive

Exporting WorkflowRuns to ROCrate

WorkflowRuns can also be exported as ROCrates, which include both the workflow definition and execution metadata:

  1. Navigate to the workflow run you want to export
  2. Use the download option to get the run ROCrate archive

ROCrate Contents

  • Workflow ROCrates contain the workflow files, metadata, and version information
  • WorkflowRun ROCrates additionally contain execution details, input/output data references, and run-specific metadata

Galaxy Integration

Importing Workflows from Galaxy

To import a workflow from Galaxy, click "Import" on the Workflow list page and select "Import from Galaxy". You can either paste a Galaxy Workflow URL/ID for direct import or search workflows by name in the configured Galaxy server. Matching workflows will display their metadata, a link to the Galaxy workflow page, and an import button for selection.
You can find a step-by-step tutorial in the training section.

Importing Workflow Invocations from Galaxy

Figure 3: Galaxy WorkflowInvocation import to WorkflowRun

Galaxy WorkflowInvocation import to WorkflowRun
Figure 3: Galaxy WorkflowInvocation import to WorkflowRun

To import a workflow run from Galaxy:

  1. Click the "Import from Galaxy" button on the workflow run list page
  2. Enter a Galaxy Workflow Invocation ID/URL (which can be found on the Galaxy WorkflowInvocation page)
  3. Review and confirm the import

This will import the Galaxy Workflow Invocation metadata as a LabID Workflow Run. Input datasets that can be traced back to existing datasets in LabID will be automatically associated.
Have a look at Hands-on : Importing a workflow invocation from Galaxy for a more detailed step-by-step tutorial.

Galaxy Datasets

Currently, Galaxy datasets are not imported automatically. Only workflow invocation metadata and dataset associations are imported.

Additional Resources