Full containerization

v2.0 (Breaking changes introduced to to configuration files and the ways parameters are used).
This set of changes did a bit to modernize the pipeline:

• All steps are now available with containerized execution
• Created separate pipeline Snakefile_downstream_only which works from a list of report files to only un the downstream analysis steps.
• Included a small test dataset and better test execution
• Various code and README/manual changes
• License file added

A mostly finished pipeline

v1.0

uhgg processing bugfix