Pipeline: auto-documentation improvements #311
Description
The tinyRNA pipeline allows users to repeat analyses on prior outputs using the recount and replot subcommands. It also provides copies of configuration files from each run for auto-documentation. Currently, there is too much overlap between these features. Users must make copies of configuration files before editing them for resume runs, or otherwise lose documentation of the prior run's configurations. (To be exact, the Features Sheet is an exception).
An additional output subdirectory, which holds a copy of all configuration files, will be added to the Run Directory during each run/resume. It will be timestamped just like other output directories during resumed runs to keep run documentation separate. The configuration files in the root of the Run Directory can then be modified freely between runs without loss of documentation.