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🏠 Overview

This extension provides support developing bioinformatics workflows via the Workflow Description Language. It does this by leveraging the sprocket command line tool (and the wdl family of crates).

📚 Getting Started

To get started, follow the instructions outlined in the documentation.

🎨 Features

• Syntax highlighting. The extension uses both a complete TextMate grammar and semantic syntax highlighting via the LSP integration. Notably, this syntax highlighting also drives GitHub's syntax highlighting of WDL.
• Document formatting. Full formatting of documents using the underlying sprocket format command is integrated such that it can be applied on-demand or automatically on save/paste.
• Static analysis. Static analysis of WDL documents is provided via the LSP and is configurable for both validation and lint warnings.
• Code completion. Various completions are available, including completion of standard library functions and context-aware completion of variables.
• Hover support. Hovering a variable or standard library function gives a modal with documentation regarding that item.
• Go to definition. Navigating from a symbol to its definition is supported in all known contexts.
• Find all references. Similarly, navigating from a symbol to all known references is supported in all known contexts.
• Rename symbol. Symbols may be seamlessly refactored and renamed using the built-in VSCode shortcuts.
• Workspace and document symbols. Symbols within WDL documents and symbols are surfaced via your code editor's default facilities. This generally includes an outline of symbols in a document and workspace-wide symbol search at a minimum.
• Code snippets for common WDL constructs and conventions.

All major functionality for the Sprocket VSCode extension has been completed. If you have things you want us to consider included, please file an issue.

Configuration

The extension provides the following configuration options:

• sprocket.server.checkForUpdates: Whether to check for updates to the automatically installed sprocket tool when the extension starts.
• sprocket.server.path: The path to the sprocket command line tool. Use this to specify a custom installation of sprocket.
• sprocket.server.verbose: Configures the verbosity of sprocket output. Valid values are Verbose, Information, and Quiet; defaults to Quiet.
• sprocket.server.lint: Passes the --lint flag to sprocket; this enables additional linting checks that are not enabled by default.
• sprocket.server.maxRetries: Sets the maximum number of retries before the extension bails out.

Known Issues

None at present.

Development

Setup

To build the extension, Node.js, npm, and yarn must be installed.

To install Node.js, follow these instructions.

To install yarn, run the following command:

npm install -g yarn

Finally, install the project dependencies by running the following command:

yarn install

Ensure the Yarn binaries directory is on your path by adding the following to your shell profile:

export PATH="$(yarn global bin):$PATH"

Building

To build the extension, run the following command:

yarn compile

This command will automatically be run when you start the extension in the development environment or when packaging the extension.

Running The Development Extension

To run the extension, open this directory in VS Code and press F5.

This will open a new VS Code window with the extension automatically loaded.

Installing The Extension

To install the extension, you can package it as a .vsix file and install it.

To package the extension, install the vsce tool:

yarn global add @vscode/vsce

Then package the extension by running:

vsce package --yarn

This will generate a sprocket-vscode-<version>.vsix file that you can install in VS Code using the Extensions: install from VSIX command.

🤝 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. Additionally, please see the disclaimer that applies to all crates and command line tools made available by St. Jude Rust Labs.

Copyright © 2024-Present St. Jude Children's Research Hospital.