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Workflows in LabID

LabID provides support for computational workflows by allowing you to track the provenance of your data throughout the computational analysis process.

Creating Workflows

Manual creation of Workflow entities

The UI allows you to create a Workflow entry and upload existing workflow files from your local computer. This is an alternative to creating a GitHub repository for your workflow. You can input the details that are minimally required for a RO-Crate Workflow profile and upload relevant workflow files to a WorkflowVersion. These files can be annotated to indicate their type within the workflow, e.g., main entry point, config file, etc. A user can have multiple WorkflowVersions with different WorkflowFiles, allowing you to track the evolution of your workflow over time. You can view the different WorkflowVersions and their associated git hashes.

RO-Crate Format

RO-Crate is a community standard for packaging research data with their metadata using JSON-LD and schema.org vocabulary.

Figure 1: Manual creation of workflow and version

Manual creation of workflow and version
Figure 1: Manual creation of workflow and version

The following flow is supported:

  1. Create a new Workflow and a new WorkflowVersion, and a Git repository is initialized.

  2. Upload WorkflowFiles and annotate them accordingly (using a predefined list of types) on the WorkflowVersion detail page.

  3. Save this state to continue later, to add or modify files.

  4. When the WorkflowVersion is ready, "release" the version and the files are committed to the underlying git repository. After "release", adding/removing new files is not possible, only changing their type is possible. Several fields of the WorkflowVersion remain modifiable.

  5. A new WorkflowVersion can be created, initialized with the same files as the previous version. These files can be re-annotated, removed, or updated with newer versions. Additional files can also be added. Only upon another release are the changes committed again to the git repository; before that, they are "staged".

Importing Workflows

Import Sources

LabID supports importing workflows from multiple sources:

  • Git repositories: Import from GitHub, GitLab, and other Git hosting platforms
  • Galaxy: Import workflows from Galaxy servers (see Workflow Integrations for details)
  • WorkflowHub: Import workflows from the WorkflowHub registry (see Workflow Integrations for details)

Import Workflows from remote git repositories

Figure 2: Import Workflow from remote git repository

Import Workflow from remote git repository
Figure 2: Import Workflow from remote git repository

On the workflow list page, you will find a Add workflow button at the top left. Select the option Import from git to import a Workflow from a remote git repository (GitHub, GitLab...). LabID supports importing from both public repositories and privately hosted repositories (e.g. in your organization).
For information about accessing restricted repositories, please see the administrator documentation.
The following import flow is implemented:

  1. Paste a URL.

  2. The server checks if the repository can be reached and lists the found commits, tags, and associated files.

  3. Select the desired version to import.

  4. Select and annotate files you find important.

  5. Upon "import", the Workflow and WorkflowVersion are created based on the information from the git repository. The git repository is cloned to the local disk.

  6. You can then modify the WorkflowFiles' types and change metadata on the Workflow and WorkflowVersion.

  7. A new version can be imported by clicking "new version", which will start a similar flow.

Note: When a workflow has is_remote set to true, only selected files will be stored as workflow files in LabID; other files will remain in the Git repository on disk.