Build, validate, and execute reproducible bioinformatics workflows with DAG-based execution, AI-powered pipeline generation, first-class environment management, cluster scheduling, and reproducible reporting — all from a single, fast Rust binary.
Everything you need to build production-grade bioinformatics pipelines.
Automatic dependency resolution, topological sorting, cycle detection, and parallel execution. Built with petgraph — proven on 1,000-rule stress tests.
First-class support for conda, pixi, Docker, Singularity, Python venv, and HPC modules. Each rule declares its own isolated environment.
Resource-aware scheduling across SLURM, PBS, SGE, and LSF backends. Rules declare CPU, memory, GPU, and disk requirements; the scheduler enforces them.
Modular HTML/JSON report generation with Tera templates. Execution summaries, resource metrics, and output file browsers for each pipeline run.
Built-in axum server with versioned REST API, RBAC (Admin/User/Viewer), rate limiting, and security headers.
Export workflows to multi-stage Docker builds or Singularity images. Rootless containers with HEALTHCHECK support for portable, self-contained execution.
Contextual AI across the full workflow lifecycle: generate pipelines from natural language (Dashboard), get intelligent refinement suggestions (Editor), diagnose failures (Monitor), and interpret results (Report). Powered by Claude, OpenAI, DeepSeek, or local Ollama.
Shell injection prevention, path traversal protection, secret scanning, per-IP rate limiting, and #![forbid(unsafe_code)] across every crate.
Native binary — instant startup, fearless concurrency, zero-cost abstractions. Rust 2024 edition. 890 tests including 100 browser E2E scenarios.
Learn oxo-flow incrementally — from a one-rule hello-world to production-grade
multi-omics pipelines. Every example passes oxo-flow validate and is tested in CI.
From zero to running pipeline in a few commands.
Define your pipeline in clean, readable TOML. Wildcards like {sample}
are expanded automatically based on input file discovery or explicit configuration.
31 subcommands covering the complete workflow lifecycle —
run, validate, dry-run, graph,
cluster, serve, and more.
Three ways to get oxo-flow on your system.
cargo install oxo-flow-cli
# Linux (x86_64)
curl -LO https://github.com/Traitome/oxo-flow/releases/latest/download/oxo-flow-x86_64-unknown-linux-gnu.tar.gz
tar xzf oxo-flow-x86_64-unknown-linux-gnu.tar.gz
sudo mv oxo-flow /usr/local/bin/
# macOS (Apple Silicon)
curl -LO https://github.com/Traitome/oxo-flow/releases/latest/download/oxo-flow-aarch64-apple-darwin.tar.gz
tar xzf oxo-flow-aarch64-apple-darwin.tar.gz
sudo mv oxo-flow /usr/local/bin/
git clone https://github.com/Traitome/oxo-flow.git
cd oxo-flow
cargo build --release
# Binaries in target/release/
# oxo-flow (CLI)
# oxo-flow-web (Web server)
Built on battle-tested Rust crates and React 19. 890 tests including 100 browser E2E scenarios,
with #![forbid(unsafe_code)] enforced across all crates.
Open-source core with a dual-license model for the web interface. The core library and CLI are free and open-source under Apache 2.0.
| Component | License | Details |
|---|---|---|
oxo-flow-core |
Apache 2.0 | Free and open-source — use, modify, distribute without restriction |
oxo-flow-cli |
Apache 2.0 | Free and open-source — use, modify, distribute without restriction |
oxo-flow-web |
Dual — Academic / Commercial | Free for academic & non-commercial use; commercial use requires a paid license |
Contributions are welcome. Read the guides below, ensure make ci passes, then open a PR.
Security policy · Reproducibility guarantees · IQ/OQ/PQ validation · Change control
If you use oxo-flow in academic research, please cite our work:
Shixiang Wang
oxo-flow: compiled, memory-safe bioinformatics workflow orchestration
bioRxiv, 2026
doi:10.64898/2026.06.11.731578
Jia Ding, Yun Peng, Ruochen Wei, Boquan Wang, Jian-Guo Zhou, Shixiang Wang
BLIT: an R package for seamless integration of command-line bioinformatics tool universe
Bioinformatics Advances, Volume 6, Issue 1, 2026, vbag088
doi:10.1093/bioadv/vbag088
Read the documentation, explore the gallery, or dive straight into the source.