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Custom Workflows

Save and reuse common processing pipelines as custom workflow nodes. A custom workflow encapsulates a multi-step pipeline into a single reusable node.

Saving a Workflow

  1. Build a pipeline on the canvas as usual.
  2. Enter a name in the Workflow Name input field above the canvas.
  3. Click Save Workflow in the actions bar. If the name already exists, the existing workflow is updated.

Using a Custom Workflow

  1. Saved workflows appear in the My Workflows section of the tool menu.
  2. Drag a custom workflow onto any workspace to use it as a single reusable node.
  3. Double-click the custom workflow node to configure parameters for each internal step. Use the arrow buttons to navigate between steps.

Managing Custom Workflows

  • Click the pencil icon next to a saved workflow to edit it in a new workspace.
  • Click the X icon to delete a workflow (with confirmation). Deleting also removes instances from all workspaces.
  • Custom workflows are stored in your browser's localStorage and persist across sessions.
  • At export time, custom workflow nodes are expanded into their constituent processing steps in the generated CWL.

Staged Changes & Comparison

When you're editing a saved custom workflow, the Save Workflow button changes to Staged Changes. Clicking it opens a diff modal that shows exactly what has changed since the last save:

  • Metadata changes — workflow name or output name modifications
  • Node changes — added, removed, or modified nodes with details on Docker version, parameters, conditionals, expressions, scatter settings, and notes
  • Edge changes — added, removed, or modified edge mappings

Changes are color-coded: +Added (green), -Removed (red), ~Modified (orange).

The modal provides two actions:

  • Update Workflow — saves all changes to the custom workflow
  • Revert Changes — discards all changes and restores the workflow to its last saved state