Importing & Exporting Workflows
BioNodulo can exchange supported workflow graphs with Snakemake, Nextflow, CWL, and Galaxy. Executable export currently covers a small set of tools. Importing a foreign pipeline creates a structural draft for review; it does not establish that the pipeline will execute with equivalent behavior.
Import a workflow
Press Ctrl+I, choose a format, and paste the source into Workflow source.
You can also use the file picker to load a saved workflow.
| Format | File | What is restored |
|---|---|---|
| BioNodulo JSON | .json | The native graph, parameters, layout, and metadata |
| Snakemake | .smk / Snakefile | Unchanged BioNodulo exports restore the original graph; simple foreign shell rules become a structural draft |
| Nextflow | .nf / main.nf | Unchanged BioNodulo exports restore the original graph; simple foreign DSL2 processes become a structural draft |
| CWL bundle | .cwl-bundle.json | A JSON file map containing workflow.cwl, referenced tools/*.cwl, and the BioNodulo round-trip manifest |
| Galaxy | .ga | Unchanged BioNodulo exports restore the original graph; foreign workflow JSON becomes a structural draft |
| PNG | .png | BioNodulo thumbnails embed the native workflow JSON |
Unchanged BioNodulo exports preserve node IDs, connections, parameters, positions, groups, annotations, and tool citation metadata. Their integrity marker is checked on import. If you edit the exported script or bundle, import returns an error instead of restoring stale graph metadata. Keep the native JSON as an editable backup.
Foreign workflows
Supported simple foreign rules, processes, or steps become generic_command
nodes with a review warning. Inspect every command, parameter, file binding, and
connection, then map the tools before running the draft. Source formats use
different execution semantics, and matching graph shapes is not proof of
equivalence.
For foreign CWL in the browser, supply a JSON file map with the workflow and its
referenced tool documents. A single .cwl file cannot supply missing tools.
Foreign JSON CWL imports only as a structural draft. YAML CWL, scatter,
conditionals, unsupported multiple-source bindings, and other complex constructs
are rejected. WDL is not supported.
If an import fails, the notice shows the reason and can be closed with OK or
Escape. The Import dialog stays open so you can correct the source and retry.
Export a workflow
Click Export or press Ctrl+E, choose a format, then Generate and
Download where applicable.
| Format | File | Current scope |
|---|---|---|
| PNG / JSON | .png / .json | Native workflow backup; PNG embeds the JSON |
| Snakemake | .smk | Executable FastQC and MultiQC graph with supported scalar options |
| Nextflow | .nf | The same tools as a DSL2 script, with one incoming edge per node |
| CWL bundle | .cwl-bundle.json | Executable Extract Columns, Filter Rows, Merge Tables, Normalize Data, and Replace Text nodes through the BioNodulo Python runner |
| Galaxy | .ga | Graph interchange; execution with installed Galaxy wrappers has not been verified |
| References | .ris, .bib, .csv | Citation metadata from the workflow’s tools |
Unsupported nodes, ports, options, and connections return an export error. Snakemake and Nextflow currently support one root read file for the FastQC to MultiQC graph. File-valued FastQC adapter, contaminant, and limits options are rejected until they can be staged correctly.
Run a supported export
Snakemake and Nextflow require FastQC and MultiQC on the execution host or in a
configured environment. Supply each root input using the exact key in the
generated script. For a FastQC node named qc:
snakemake --snakefile Snakefile --cores 1 --config qc_input=sample.fastq
nextflow run main.nf --qc_input sample.fastqThe exports preserve MultiQC’s Overwrite option. Generated output names are isolated from input files; Nextflow also stages inputs in a separate directory.
A CWL download is a JSON file map, not a standalone .cwl document. Unpack its
keys into one directory before executing workflow.cwl with your CWL job file.
The supported tools call the BioNodulo Python runner, so BioNodulo must be
installed in that execution environment.
The workflow portability guide contains the exact contracts and real-engine verification evidence. These checks cover deterministic fixtures for the listed tools; they do not validate arbitrary foreign workflows or every tool in the node library.