Make rule for each command

[percyfal]

Make a separate rule file for each command so that atomic includes possible. Tentative setup:

gatk

• settings.rules
• IndelRealigner.rule
• UnifiedGenotyper.rule
• ...

Each *.rule would inherit basic settings from gatk (config_default setup in current file) and just define the rule. This goes along the lines of the examples in the common workflow language setup (see https://github.com/common-workflow-language/workflows/tree/master/tools).

[percyfal]

This is not as general is I first thought. For some tools, such as GATK, picard, alignment, this makes sort of sense. For others, such as zinba, bismark, where only a few commands that depend heavily on oneanother are run, it makes more sense to group commands in one rules file. Suffix should determine multiplicity of contained rules though.