bioinformatics next-generation-sequencing ngs wdl wdl-workflow workflow workflow-engine

wdl

Rust crates for working with Workflow Description Language (WDL) documents.
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📚 Getting Started

The wdl family of crates consists of (a) a number of component crates (any crate that is not explicitly wdl) that are developed and versioned independently, and (b) a convenience crate (the wdl crate) that exists to ease syncing compatible component crates versions. Component crates can be enabled using features and are generally re-exported crates without the wdl- (or wdl_) prefix.

This repository contains crates that can be used to work with WDL within your own Rust projects—if you're looking for a command-line tool built on top of these crates instead, you should check out sprocket.

Convenience Crate

Most users should prefer selecting a version of the convenience crate and enabling features as they wish. For example,

cargo add wdl --features grammar

and then

use wdl::grammar;

Component Crate(s)

You are free to include component crates directly. For example,

cargo add wdl_grammar

and then

use wdl_grammar;

Be aware, however, that versions between component crates are explicitly not compatible. In other words, if you choose not to use the convenience crate, it is not simple to derive which crate versions are compatible, and you'll need to manually sync those. We highly recommend using the convenience crate if you intend to use more than one component crate in conjunction.

Minimum Supported Rust Version

The minimum supported Rust version is currently 1.79.0.

There is a CI job that verifies the declared minimum supported version.

If a contributor submits a PR that uses a feature from a newer version of Rust, the contributor is responsible for updating the minimum supported version in the Cargo.toml.

Contributors may update the minimum supported version as-needed to the latest stable release of Rust.

To facilitate the discovery of what the minimum supported version should be, install the cargo-msrv tool:

cargo install cargo-msrv

And run the following command:

cargo msrv --min 1.79.0

If the reported version is newer than the crate's current minimum supported version, an update is required.

✨ The `wdl` CLI tool

The wdl CLI tool provides commands to assist in the development of the wdl family of crates.

The wdl CLI tool can be run with the following command:

cargo run --bin wdl --features cli -- $ARGS

Where $ARGS are the command line arguments to the wdl CLI tool.

The wdl CLI tool currently supports three subcommands:

parse - Parses a WDL document and prints both the parse diagnostics and the resulting Concrete Syntax Tree (CST).
check - Parses, validates, and analyzes a WDL document or a directory containing WDL documents. Exits with a status code of 0 if the documents are valid; otherwise, prints the validation diagnostics and exits with a status code of 1.
lint - Parses, validates, and runs the linting rules on a WDL document. Exits with a status code of 0 if the file passes all lints; otherwise, prints the linting diagnostics and exits with a status code of 1.
analyze - Parses, validates, and analyzes a single WDL document or a directory containing WDL documents. Prints a debug representation of the document scopes and exits with a status code of 0 if the documents are valid; otherwise, prints the validation diagnostics and exits with a status code of 1.

Each of the subcommands supports passing - as the file path to denote reading from STDIN instead of a file on disk.

🖥️ Development

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

# Clone the repository
git clone git@github.com:stjude-rust-labs/wdl.git
cd wdl

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

# List out the examples
cargo run --release --example

🚧️ 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`.
# Currently this requires nightly Rust
cargo +nightly fmt --check

# Ensure the docs build.
cargo doc

🤝 Contributing

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

📝 License

This project is licensed as either Apache 2.0 or MIT at your discretion.

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Rust crates for working with Workflow Description Language (WDL) documents.