9. Clean up

##Clean-up:

There are a large number of files, both large and small, that are produced during the running of the pipeline, and most should be deleted straight after a successful run to save disk space (and keep your account under control – trust me). Fortunately, the pipeline will do most of this for you - at least the 'temp' directory.

You do still need to do some housekeeping between runs of the pipeline. The log folder for the run (typically created in the RedDog directory) should be deleted in entirety.
DO NOT DELETE THIS LOG FOLDER WHILE THE PIPE IS RUNNING!

At the end of each run, there is one file, "finish.deleteDir.Success", that does need to be removed - especially so if the run will be merged with other read sets later. (The pipe will not launch unless this file has already been removed from the 'out_merge_target' folder)

Note: In the RedDog directory after the run, you can ignore the *.pyc files. They are small, and recreated at the start of each run, so deleting them is an exercise in futility. (Though most times I can't help myself...)

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