CWL workflow with breakpoints for debugging

hello-world-with-debug.cwl

#!/usr/bin/env cwltool
cwlVersion: v1.2
class: CommandLineTool
inputs:
  message:
    type: string
outputs:
  outfile:
    type: File
    outputBinding:
      glob: output.txt
baseCommand: [bash, run.sh]
requirements:
  DockerRequirement:
    dockerImageId: hello-world
    dockerFile: |
      FROM python
  InitialWorkDirRequirement: 
    listing:
      - entryname: inputs.json
        entry: $(inputs)
      - entryname: cwl.py
        entry: |
          #!/usr/bin/env python
          import os
          import sys
          import time

          if sys.argv[1] == "pause":
            # normal print will be catched by cwltool
            with open("state", "a") as f:
              f.write("PAUSED")

            os.system(f"echo Debug mode enabled and workflow paused.")
            os.system(f"echo Access container: docker exec -it {os.environ["HOSTNAME"]} bash")
            os.system(f"echo Unpause container: docker exec -it {os.environ["HOSTNAME"]} python cwl.py next")
            
            paused = True
            while paused:
              time.sleep(1)
              paused = open("state", "r").read() == "PAUSED"
          elif sys.argv[1] == "next":
            with open("state", "a") as f:
              f.write("RUN")
      - entryname: run.sh
        entry: |
          #!/usr/bin/env bash
          echo hi
          python cwl.py pause
          echo hello, $(inputs.message) > output.txt

Run with cwltool hello-world-with-debug.cwl --message world . Remove python cwl.py pause to remove the break point.