Altered code to upload all files to a common batch history (batch name pulled from parent directory). New histories are created to hold ONLY the output from each workflow run. Generating a run log which preserves the sample name and all files and parameters used in running the workflow.  Additioally, serializing history json objects to a file which will output all resulting histories for a batch run.  This will later be used to load the histories to report status and automate downloads.