2. Topics

• 2.1. YAML Guide
  • 2.1.1. Contents
  • 2.1.2. Key-Value Pairs
  • 2.1.3. Comments
  • 2.1.4. Maps
  • 2.1.5. Arrays
  • 2.1.6. JSON Style
  • 2.1.7. Reference
• 2.2. Command Line Tool
• 2.3. Expressions
• 2.4. Inputs
  • 2.4.1. Essential Input Parameters
  • 2.4.2. Array Inputs
  • 2.4.3. Advanced Inputs
• 2.5. Additional Arguments and Parameters
• 2.6. Parameter References
• 2.7. Outputs
  • 2.7.1. Returning Output Files
  • 2.7.2. Capturing Standard Output
  • 2.7.3. Array Outputs
• 2.8. Custom Types
• 2.9. Expression Tool
• 2.10. Workflows
  • 2.10.1. Writing Workflows
  • 2.10.2. Nested Workflows
  • 2.10.3. Scattering Steps
  • 2.10.4. Conditional workflows
• 2.11. Operations
• 2.12. Environment Variables
• 2.13. Using containers
  • 2.13.1. Running tools inside Docker
• 2.14. Creating files at runtime
• 2.15. Staging input files
• 2.16. Best practices
• 2.17. File formats
  • 2.17.1. Sample Parameter Files
• 2.18. Metadata and authorship
  • 2.18.1. Extended Example
• 2.19. Specifying software requirements