Decide on how output directories should be created/handled

[chasemc]

I'm not sure if this is the reason I'm seeing weird behavior when trying to resume an interrupted job, but regardless, this is making it difficult to track down files. I am navigating to params.outdir expecting to see the generated files but instead have to navigate two more sub-directories. The workflow.sessionId is also not obvious to an end user, as this does not appear to be a user-defined input.

Could we keep params.out and discard params.interim_dir? Then for each metagenome provided, a sub-directory in params.out containing all of the metagenome's respective files could be created. This would make looking up a particular genome much easier.

Originally posted by @WiscEvan in #157 (comment)

[evanroyrees]

This looks like a duplicate of #160 --> I'll link to this in that issue so we can consolidate these