BioExcel Best Practice Guide: Creating workflows with Common Workflow Language
  • About this guide
  • Introduction
  • Pitfalls and limitations
  • Resources

Suggested development practice

  • 1. Establish workflow development practices
  • 2. Sketching out workflow
  • 3. Finding / creating tools
  • 4. Writing incremental tests
  • 5. Writing partial workflows
  • 6. Running and verifying workflow
  • 7. Ensuring workflow is portable and interoperable
  • 8. Ensuring workflow is scalable
  • 9. Asking for help
  • 10. Capture provenance from workflow runs
  • 11. Publishing in workflow repositories, documentation
  • Containers and packages
    • 1. Docker containers
    • 2. Conda and BioConda
Distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) ; except CWL examples where the creators have waived all copyrights according to CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.
BioExcel Best Practice Guide: Creating workflows with Common Workflow Language
  • Resources

Recommended resources

Recommended tutorials

  • https://www.commonwl.org/user_guide/
  • https://mmb.irbbarcelona.org/biobb/availability/tutorials/cwl

Other CWL best-practice guides

  • https://www.commonwl.org/user_guide/rec-practices/
  • https://docs.dockstore.org/en/develop/advanced-topics/best-practices/best-practices.html
  • https://doc.arvados.org/user/cwl/cwl-style.html

Recommended bibliography (reviews)

  • https://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html
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BioExcel Best Practice Guide: Creating workflows with Common Workflow Language
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