Restructuring the tool parameter specification within rules to allow for more parameters to be changed.

Discussion on: https://git.scicore.unibas.ch/zavolan_group/pipelines/zarp/-/wikis/Design-discussions#passing-tool-parameters.

New design that has:

• rule congif file with additional standard parameters
• read function within Snakefile to parse this config
• Additional parameter specified within each rule that contain a string specified from parsing the rule config with the read function