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The whole process is now automated. The script create_json.py will create a json file, upload to s3, launch an instance that executes the workflow, sends logs to s3 and self-terminates. It uses the .tibanna.config file for storing relatively invariant parameters (e.g. reference bucket name, AMI, keyname, etc) and takes input files, parameters, etc as command-line options. It also adds the launched instance information to a job_list file to enable easier tracking.
minor change in the json format. (the previous format may not work especially for a multi-layer cwl)