Common Workflow Language User Guide

This guide will introduce you to writing workflows using the Common Workflow Language (CWL) open standards. This guide describes the latest specification v1.2.

Contributions and Feedback are Welcome!

If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the project repository for this guide. You can also suggest changes directly in a Pull Request by clicking the “Edit this page” button at the right sidebar of each page.

Navigating the User Guide

If you are a beginner user get started with the Introduction section. For advanced users the subsections of the Core Concepts have detailed information about the most common topics for CWL.

The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar.

Table of Contents

• 1. Introduction
  • 1.1. Quick Start
  • 1.2. Prerequisites
  • 1.3. Basic Concepts
• 2. Topics
  • 2.1. YAML Guide
  • 2.2. Command Line Tool
  • 2.3. Expressions
  • 2.4. Inputs
  • 2.5. Additional Arguments and Parameters
  • 2.6. Parameter References
  • 2.7. Outputs
  • 2.8. Custom Types
  • 2.9. Expression Tool
  • 2.10. Workflows
  • 2.11. Operations
  • 2.12. Environment Variables
  • 2.13. Using Containers
  • 2.14. Creating Files at Runtime
  • 2.15. Staging Input Files
  • 2.16. Best Practices
  • 2.17. File Formats
  • 2.18. Metadata and Authorship
  • 2.19. Specifying Software Requirements
• 3. Tutorials
  • 3.1. Beginner Tutorials
  • 3.2. Advanced Tutorials
  • 3.3. Bioinformatics Tutorials
• 4. FAQ
  • 4.1. Non “File” types using evalFrom
  • 4.2. Rename an input file
  • 4.3. Rename an output file
  • 4.4. Setting self-based input bindings for optional inputs
  • 4.5. Model a “one-or-the-other” parameter
  • 4.6. Connect a solo value to an input that expects an array of that type
  • 4.7. Optional Inputs 💯
  • 4.8. Enum Inputs ⚜️
  • 4.9. Record Inputs 📀
  • 4.10. Setting Mutually Exclusive Parameters
  • 4.11. Setting Booleans
  • 4.12. Concating Strings in Inputs
  • 4.13. cwltool errors due to filenames with space characters inside
  • 4.14. CWL Parameter Reference error due to hyphen in input identifier
  • 4.15. Use CWL and cwltool with Singularity
  • 4.16. Debug JavaScript expressions
• 5. Licenses
  • 5.1. Instructional Material
  • 5.2. Software
  • 5.3. Trademark