ox translate

Translate a Snakefile into OxyMake TOML.

The ox translate command parses a Snakemake Snakefile and emits an equivalent Oxymakefile.toml. Use it to migrate existing Snakemake workflows to OxyMake without rewriting rules by hand.

Usage

ox translate Snakefile                       # Writes Snakefile.translated.toml
ox translate Snakefile -o Oxymakefile.toml   # Writes a custom path

When -o is omitted, the translator writes two files next to the input:

<INPUT>.translated.toml — the generated Oxymakefile
<INPUT>.translated.toml.escalations.toml — written only when the IR contains escalations

Every run emits a one-line summary to stderr:

translated: N rules (X mechanical, Y with escalations); dropped: Z unsupported top-level constructs; includes: K files NOT followed

ox translate exits with status 2 when escalations were recorded so CI or shell scripts can gate on a clean translation. The files are still written; only the exit code changes.

Arguments

Argument	Description
`<SNAKEFILE>`	Path to the Snakefile to translate

Options

Flag	Description
`-o, --output <OUTPUT>`	Write the translated TOML to this path instead of the default `<INPUT>.translated.toml`. The escalation file lands at `<OUTPUT>.escalations.toml`.

Translation Notes

The translator handles the most common Snakemake patterns:

rule blocks → [[rule]] sections
input / output → inputs / outputs
expand() calls → OxyMake wildcard {sample} syntax
params → [rule.params]
shell → command

Complex Python logic inside Snakefiles (e.g., run: blocks, conditional inputs, lambda wildcards) may require manual adjustment after translation. Review the generated TOML and run ox lint to verify.

Examples

# Quick migration — produces Snakefile.translated.toml
ox translate Snakefile
ox lint -f Snakefile.translated.toml   # Verify the result
ox plan -f Snakefile.translated.toml   # Check execution plan

# Custom output path
ox translate Snakefile -o Oxymakefile.toml

# CI gate: fail the job when escalations were emitted
ox translate Snakefile || echo "needs manual review"

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