Workflow Development Kit (wdk)

An open-source framework for defining Common Workflow Language (CWL) workflows using TypeScript and Java. wdk uses a construct-tree model inspired by the AWS CDK to let you define workflows as code, then synthesize them into standard CWL files that run on any compliant engine.

Quick Example

import { App, Workflow, Tool, ToolConfig, Input } from 'wdk-lib';

class Echo extends Tool {
  constructor(scope: Workflow) {
    super(scope, 'echo');
    ToolConfig.basic(this).withBaseCommand(['echo']);
    Input.string(this, 'message').withPosition(1);
  }
}

const app = new App();
const workflow = new Workflow(app, 'hello-wdk');
new Echo(workflow);
app.synth();

This produces a CWL CommandLineTool file in dist/hello-wdk/, ready to run with any CWL engine:

cwltool dist/hello-wdk/echo.clt.cwl --message "Hello, WDK!"

Installation

TypeScript / JavaScript

npm install wdk-lib

Java (via JSII, published to GitHub Packages)

<dependency>
  <groupId>com.biobam</groupId>
  <artifactId>wdk-lib</artifactId>
</dependency>

Repository: https://maven.pkg.github.com/biobam/wdk-lib

Key Concepts

wdk models workflows as a tree of constructs:

• App -- root of the tree, calls synth() to emit CWL files
• Workflow -- a CWL Workflow containing steps
• Tool -- a CWL CommandLineTool with typed inputs and outputs
• Input / Output -- typed ports that connect steps together
• Requirement -- Docker images, resource limits, environment variables

See Concepts for details and code examples.

Documentation

• Getting Started -- install, create your first workflow, run it
• Concepts -- the construct tree model and core abstractions
• TypeScript API Reference -- auto-generated from source
• Java API Reference -- auto-generated from source

Additional guides in docs/:

• FirstOrNullExpressionTool
• ToolOutputs

Examples

The src/examples/ directory contains working examples:

• CdHit workflow -- a multi-step pipeline with parameter generation, tool execution, and post-processing
• Pathway analysis -- tools for loading sequences and running pathway analysis
• EggNOG Mapper -- a workflow with Docker image configuration and database mounting
• PickFirst pattern -- merging optional outputs using FirstOrNullExpressionTool

Contributing

See CONTRIBUTING.md for setup, issues, and pull requests.

License

Apache License, Version 2.0