Importing & Exporting Workflows
BioNodulo converts workflows to and from the formats used by other pipeline systems, so you can bring an existing SnakeMake, Nextflow, CWL, or Galaxy pipeline onto the canvas — or export a BioNodulo workflow back out.
Import a workflow
Click Import in the top bar (or press Ctrl+I), pick a format tab, and
paste the workflow source into the text area. You can also load a file directly
with the file picker below the text area.
| Format | File | Notes |
|---|---|---|
| BioNodulo JSON | .json | Full-fidelity round trip; the native save format |
| SnakeMake | .smk / Snakefile | Rules become nodes |
| Nextflow | .nf / main.nf | DSL2 processes become nodes |
| CWL | .cwl | Workflow document plus its tools/ CommandLineTool files |
| Galaxy | .ga | Galaxy workflow JSON |
| PNG | .png | Workflow thumbnails exported by BioNodulo embed the full workflow JSON; importing the image restores the workflow |
After import, review the generated nodes before running: imported workflows get fresh node IDs and generic positions, and parameters may need manual cleanup.
What each importer does
- SnakeMake — parses each
ruleinto a node, with inputs, outputs, and theshellcommand carried over. Edges are inferred where one rule’s input matches another rule’s output. - Nextflow — parses
processdefinitions and theworkflowblock (DSL2). Container and conda directives,cpus, andmemoryare preserved where present. - CWL — reads a
workflow.cwland resolves each step’srunreference against the accompanyingtools/directory of CommandLineTool documents. - Galaxy — reads
.gasteps;data_input,data_collection_input, andparameter_inputsteps become input nodes, tool steps become regular nodes, andinput_connectionsbecome edges.
Export a workflow
Click Export in the top bar (or press Ctrl+E) and choose a format:
| Format | File | Notes |
|---|---|---|
| PNG thumbnail | .png | Canvas image with the workflow JSON embedded — doubles as a portable backup |
| SnakeMake | .smk | Snakefile with a rule all over terminal nodes and one rule per node |
| Nextflow | .nf | main.nf with one process per node, including container/conda/cpus/memory directives when the node declares them |
| CWL | .cwl | A workflow.cwl plus one CommandLineTool document per node under tools/ |
| Galaxy | .ga | Galaxy workflow JSON with steps in topological order and original canvas positions |
| References | .ris, .bib, .csv | A citation list built from the tools used in the workflow — RIS, BibTeX, or CSV |
Limitations
- Conversion is best-effort. Both importers and exporters work from the node graph and declared commands; free-form scripting inside a rule or process may not survive translation and should be reviewed after import.
- Export raises an error for node types that have no meaningful mapping in the target format (for example, Galaxy export rejects unsupported node types).
- Only BioNodulo JSON (and the PNG thumbnail, which embeds it) is guaranteed to round-trip without information loss.