WILDS WDL Library Documentation

Technical documentation for a centralized collection of bioinformatics WDL infrastructure providing reusable, well-tested components for genomics research.

Welcome to the WILDS WDL Library Documentation

This site provides comprehensive technical documentation for all WDL modules, vignettes, and workflows in the WILDS WDL Library. Use the sidebar navigation to explore available components and view detailed task descriptions, inputs/outputs, and usage examples.

Navigating This Documentation

Modules - Foundational building blocks

Tool-specific collections of reusable WDL tasks
Each module page shows available tasks with complete parameter documentation
Includes test workflows demonstrating basic usage

Vignettes - Integration examples

Compact workflows combining 2-3 modules into common analysis patterns
Demonstrates how modules work together
Serves as templates for custom workflows

Workflows - Production pipelines

Complete, publication-ready analysis pipelines
Complex workflows combining multiple modules
Ready for production use with minimal customization

Quick Start: Using Components

Importing Modules into Your Workflows

All components can be imported directly via GitHub URLs:

import "https://raw.githubusercontent.com/getwilds/wilds-wdl-library/refs/heads/main/modules/ww-sra/ww-sra.wdl" as sra_tasks
import "https://raw.githubusercontent.com/getwilds/wilds-wdl-library/refs/heads/main/modules/ww-star/ww-star.wdl" as star_tasks

workflow my_analysis {
  call sra_tasks.fastqdump { input: sra_id = "SRR12345678" }
  call star_tasks.star_align_two_pass {
    input: sample_data = { "name": "sample1", "r1": fastqdump.r1_end, "r2": fastqdump.r2_end }
  }
}

Benefits of GitHub imports:

No local cloning required - use modules directly
Pin to specific commits or tags for reproducibility
Easy version switching by changing the URL
Import only the modules you need

Running Components Locally

# Clone the repository
git clone https://github.com/getwilds/wilds-wdl-library.git
cd wilds-wdl-library

# Run a module test workflow (no inputs needed)
cd modules/ww-star
sprocket run testrun.wdl

# Run a vignette (update inputs.json as needed)
cd ../../vignettes/ww-sra-star
sprocket run ww-sra-star.wdl inputs.json

# Run a full workflow (update inputs.json as needed)
cd ../../workflows/ww-leukemia
sprocket run ww-leukemia.wdl inputs.json

Library Architecture

The WILDS WDL Library is organized into three complementary tiers:

Modules (`modules/`)

Purpose: Foundational building blocks for larger workflows Content: Individual bioinformatics tools (STAR, BWA, GATK, etc.) Testing: Unit tests ensure each task functions correctly Usage: Import tasks into custom workflows or run demonstration workflows

Vignettes (`vignettes/`)

Purpose: Educational examples of module integration Content: 2-3 modules combined into standard analysis patterns Testing: Integration tests verify modules work together Usage: Templates for common workflows or learning examples

Workflows (`workflows/`)

Purpose: End-to-end analyses suitable for research publications Content: Complex workflows combining multiple modules and custom logic Testing: Comprehensive validation with realistic datasets Usage: Production analyses requiring minimal customization

Supported WDL Executors

All components are tested with multiple WDL executors to ensure broad compatibility:

Cromwell - Production-grade workflow engine
miniWDL - Lightweight local execution
Sprocket - Modern WDL executor with enhanced features

Container Images

All tasks use versioned, tested Docker images from the WILDS Docker Library, ensuring reproducible execution across different computing environments.

Getting Help

Documentation Issues: Found something unclear or incorrect? Report an issue
General Questions: Contact the Fred Hutch Data Science Lab at wilds@fredhutch.org
Additional Resources:
- WILDS Guide - Comprehensive guides and best practices
- Contributing Guidelines - How to contribute
- GitHub Repository - Source code and development

Ready to explore? Use the sidebar to browse available modules, vignettes, and workflows. Each component page provides complete technical documentation including task signatures, parameter descriptions, and usage examples.

WILDS WDL Library