Creating workflows with Common Workflow Language

This best practice guide outlines the development process for writing a workflow using the Common Workflow Language (CWL), from creating and selecting tools like BioBB, through early experimentation, reuse and testing, to optimization and ensuring reproducibility before publication in workflow repositories.

• About this guide
• Introduction
• Pitfalls and limitations
• Resources
• Suggested development practice
  • Establish workflow development practices
  • Sketching out workflow
  • Finding / creating tools
  • Writing incremental tests
  • Writing partial workflows
  • Running and verifying workflow
  • Ensuring workflow is portable and interoperable
  • Ensuring workflow is scalable
  • Asking for help
  • Capture provenance from workflow runs
  • Publishing in workflow repositories, documentation
  • Containers and packages
    • Docker containers
    • Conda and BioConda