Move rule configuration values backwards into YAML config files

[TBradley27]

A lot of rule specific configuration at the moment (i.e. v.1.2.3) is achieved by manually editing relevant Snakefiles. This is not ideal as we don't ever really want the user to have go into the Snakefiles themselves and do some editing in order to reconfigure how FilTar is executed.

If we bring this configuration backwards, closer to the root, and into purpose-built YAML config files then this will make life a lot easier for the user. It is also a benefit to see the entire project configuration in a single or small number of YAML files rather than having to hunt for this information in nested file structures.