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oxo-flow export#

Export a workflow to a container definition or standalone TOML.

Usage#

oxo-flow export [OPTIONS] <WORKFLOW>

Arguments#

Argument Description
<WORKFLOW> Path to the .oxoflow workflow file

Options#

Option Short Default Description
--format -f docker Export format (docker, singularity, toml)
--output -o stdout Output file path

Examples#

Export to Dockerfile#

oxo-flow export pipeline.oxoflow -f docker

Export to Singularity definition#

oxo-flow export pipeline.oxoflow -f singularity -o Singularity.def

Export to standalone TOML#

oxo-flow export pipeline.oxoflow -f toml -o bundle.oxoflow

Output#

oxo-flow 0.6.1 — Bioinformatics Pipeline Engine
✓ Exported docker to stdout
FROM ubuntu:22.04
RUN apt-get update && apt-get install -y ...
...

Notes#

  • Container exports include all environment requirements specified in the workflow
  • TOML export bundles all includes into a single, standalone workflow file
  • Useful for archiving workflows or deploying to restricted environments