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A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Request Feature · Report Bug · ⭐ Consider starring the repo! ⭐

🎨 Features

• sprocket analyzer Run Sprocket as a LSP server for IDE integration.
• sprocket check Performs static analysis on WDL documents.
• sprocket explain Explain lint rules.
• sprocket format Formats WDL documents.
• sprocket lint Performs static analysis on WDL documents with additional linting rules enabled.

Guiding Principles

• Provide a high-performance workflow execution engine capable of orchestrating massive bioinformatics workloads (the stated target is 20,000+ concurrent jobs).
• Develop a suite of modern development tools that brings bioinformatics development on par with other modern languages (e.g., wdl-lsp).
• Maintain an community-focused codebase that enables a diverse set of contributors from academic, non-profit, and commercial organizations.
• Build on an open, domain-tailored standard to ensure the toolset remains singularly focused on unencumbered innovation within bioinformatics.
• Retain a simple and accessible user experience when complexity isn't warranted.

📚 Getting Started

Installation

Before you can install sprocket, you'll need to install Rust. We recommend using rustup to accomplish this. Once Rust is installed, you can install the latest version of sprocket by running the following command.

cargo install sprocket

🖥️ Development

To bootstrap a development environment, please use the following commands.

# Clone the repository
git clone [email protected]:stjude-rust-labs/sprocket.git
cd sprocket

# Build the crate in release mode
cargo build --release

# Run the `sprocket` command line tool
cargo run --release

🚧️ Tests

Before submitting any pull requests, please make sure the code passes the following checks (from the root directory).

# Run the project's tests.
cargo test --all-features

# Run the tests for the examples.
cargo test --examples --all-features

# Ensure the project doesn't have any linting warnings.
cargo clippy --all-features

# Ensure the project passes `cargo fmt`.
cargo fmt --check

# Ensure the docs build.
cargo doc

🤝 Contributing

Contributions, issues and feature requests are welcome! Feel free to check issues page.

📝 License and Legal

This project is licensed as either Apache 2.0 or MIT at your discretion. Additionally, please see the disclaimer that applies to all crates and command line tools made available by St. Jude Rust Labs.

Copyright © 2023-Present St. Jude Children's Research Hospital.