Refactored R-scripts

According to https://github.com/molgenis/molgenis-pipelines/wiki/R-guidelines

To do's:
- adapt the protocol.sh files that call the R-scripts (now: ./r_script.R)
-- chmod +x R-scripts
- Validate refactored R-scripts and fix if necessary 
- install package argparse on cluster to deal with command line args?