Use --pack to create self-contained pipeline before execution.

[jorvis]

From mr-c on Gitter:
You can replace {{cwl_tools_dir}} with ../tools and it would still be valid CWL. If you want to deliver a single CWL file to your users you can use cwltool --pack workflows/prok-annotation-cheetah.cwl to combine them altogether

Once {{cwl_tools_dir}} is gone then you can show off fancy workflow visualizations like https://view.commonwl.org/workflows/github.com/common-workflow-language/workflows/blob/lobstr-v1/workflows/lobSTR/lobSTR-workflow.cwl