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Workspaces & Export

Workspaces

  • Each workspace is an independent canvas with its own nodes and edges.
  • Create a new workspace with New Workspace, clear the current one with Clear Workspace, or remove it with Remove Workspace.
  • Navigate between workspaces using the page tabs at the bottom of the screen.
  • Workspace state is automatically saved in your browser storage.

Output Name

Set the exported filename using the Output input field in the toolbar. This name is used for the CWL workflow file and the downloaded bundle.

Generate Workflow

Click Generate Workflow to download a .crate.zip bundle containing everything needed to run your pipeline:

  • workflows/pipeline.cwl — CWL workflow definition
  • workflows/pipeline_job.yml — job template pre-filled with your configured parameter values
  • cwl/ — individual tool CWL files with pinned Docker image versions
  • Dockerfile + run.sh — one-command execution via Docker
  • Singularity.def + run_singularity.sh — for HPC environments using Singularity/Apptainer
  • prefetch_images.sh — pre-pull all required container images
  • ro-crate-metadata.json — JSON-LD metadata for FAIR compliance and WorkflowHub discovery
  • README.md — setup and execution instructions

Tip

The exported bundle is a CWL v1.2 Workflow RO-Crate. Run it with any CWL-compliant engine (e.g., cwltool, Toil) or use the included Docker/Singularity scripts.