Feature/DIMS_v3.5_harmonize_Rscripts

[mraves2]

The R scripts for the DIMS pipeline (main scripts for every step of the pipeline and the function scripts in folders export and preprocessing) have been cleaned up:

• variables have logical and self-explanatory names
• obsolete or redundant variables have been removed
• docstrings outside the function; variables in docstrings match those used
• same order in main scripts: libraries, arguments, source functions, initialize, load objects
• setting the number of digits has been added for every script in which calculations are performed.
  In addition, the variable outdir is no longer necessary and has been removed. The output files which start with outlist* have been renamed peakgroup_list*.
  The function seqToIntervals has been removed from peak_finding_functions.R since the package R.utils is incorporated in docker image v1.4 and an alternative function has been used for gaussfunc. All NF scripts now use the updated docker image.

Argument parsing is part of another feature branch and can be ignored in this PR. Also, GenerateExcel.R and generate_excel_functions.R have been refactored in feature DIMS_DrugDB. The log2 operation has been removed from generate_violin_plots_functions.R.