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?).teardown
method now parses Toil's worker logs to clean up their temporary directories unless the run is in debug mode.This reverts commit a5d2e908.