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oxo-flow export#

Export a workflow to a container definition (Dockerfile, Singularity definition, Docker Compose) or a standalone TOML file.

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, compose, 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 Docker Compose#

oxo-flow export pipeline.oxoflow -f compose -o compose.yml

Export to standalone TOML#

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

Output#

oxo-flow v0.15.0 — Rust-native bioinformatics pipeline engine
# Auto-generated by oxo-flow for workflow: file-pipeline
FROM ubuntu:22.04

LABEL org.opencontainers.image.title="file-pipeline"
LABEL org.opencontainers.image.version="1.0.0"

# System dependencies
RUN apt-get update && apt-get install -y \
    curl wget git build-essential \
    && rm -rf /var/lib/apt/lists/*
...

When writing to a file with -o, the definition is saved and a confirmation message is printed instead: ✓ Exported docker to <path>.

Notes#

  • Container exports include all environment requirements specified in the workflow
  • TOML export bundles all includes into a single, standalone workflow file (equivalent to the format command without its --check mode)
  • Useful for archiving workflows or deploying to restricted environments