[RAP-318] Additional cleanup of leftover files by e.g. Toil

Frits Sweijenrequested to merge
RAP-318 into master

Addresses a few leftover files that Toil leaves behind even on successful runs as outlined in RAP-318. Changes include:

  • --bypass-file-store is only used in combination with Slurm.
  • --stats removed since that interferes with Toil cleaning up temporary files (I don't think output of this is used?).
  • ToilRunner's teardown method now parses Toil's worker logs to clean up their temporary directories unless the run is in debug mode.

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