OxyMake

Next-generation workflow orchestration in Rust. The uv of computational workflows.

OxyMake is a fast, declarative workflow orchestration tool that combines the proven ideas of Snakemake (file-based rules, backward-chaining DAG, wildcards) with modern engineering: content-addressable caching, polyglot execution, in-memory data passing, and first-class support for both human and AI agent users.

Key Features

• Fast DAG resolution: 10K-job DAG resolved in 69 ms on M4 Max, 33.3× faster than Snakemake 7.32.4 (100K-job scaling out of scope for this benchmark wave; cold end-to-end is slower than Snakemake — an honest trade for content-addressable correctness)
• Content-addressable: no phantom re-runs from git checkout or file copies
• Polyglot: shell, Python, R, Julia — each rule chooses its language
• Daemon-free: ox run starts, works, exits. No server to manage.
• Agent-friendly: --json output, structured events, typed API
• Scales: same workflow on laptop, SLURM cluster, or Ray cluster (Kubernetes designed, not yet implemented)

Quick Example

# Oxymakefile.toml
ox_version = "0.1"

[config]
samples = ["A", "B", "C"]

[rule.process]
input = ["data/{sample}.csv"]
output = ["results/{sample}.json"]
shell = "python process.py {input} {output}"

[rule.report]
input = ["results/{sample}.json"]
output = ["reports/summary.html"]
shell = "python report.py {input} > {output}"

ox run                    # build everything
ox run -j 8               # 8 parallel jobs
ox status                 # what's running?
ox plan                   # what would run?