fix STAR known errors by printing error JSON

[morsecodist]

In order for the runner script to detect errors they must be printed as JSON as the last line of stderr. Maybe this constraint is not ideal but I think the best way to solve it for now is by printing errors. I took the code from our running of single pipeline steps:

    try:
        if args.step_class == "PipelineStepRunValidateInput":
            count_input_reads(input_files=step_instance.input_files_local,
                              max_fragments=step_instance.additional_attributes["truncate_fragments_to"])

        step_instance.validate_input_files()
        with open(f"{args.step_name}.description.md", "wb") as outfile:
            # write step_description (which subclasses may generate dynamically) to local file
            outfile.write(step_instance.step_description().encode("utf-8"))
        step_instance.run()
        step_instance.count_reads()
        step_instance.save_counts()
    except Exception as e:
        traceback.print_exc()
        exit(json.dumps(dict(wdl_error_message=True, error=type(e).__name__, cause=str(e), step_description_md=step_instance.step_description())))

and adapted it for our new utils.

[rzlim08]

This looks good, thanks for this! Yeah it seems like a challenge to convert the python exceptions to JSON, but this looks like a pretty good solution.