Pit Wiper

• major cleanup and refactoring of wrappers and code structure (but not rules)
• scRNAseq workflow added
• using yaml config files all over, ie.
  1. all wrappers write out a config yaml
  2. Snakefile configuration only depends on provided '--configfile'
• better handling and and more usage of common_functions
• all genome config files converted to yaml, function to load genome information
• own genome file can be provided instead of only pre-configured ones
• paths config file converted to yaml
• eliminate organism specific t2g and symbol files, they are now created by rule from gtf
• check that sleuth is only run if replicates are available
• bugfix: only provided wrapper arguments overwrite either defaults or configfile options, before
  a not provided wrapper option (but in config file provided) would be overwritten by default,
  now there is true hierachy: defaults -> configfile -> wrapper !