fix multiqc plot rows and create simplified output

[cahn20]

• Added average methylation rate per group
  • fixed some scripts to accommodate for addition of average methylation rate
• Unify "uniq1" and "uniq2" to lower case
• re-order final output files
• keep detailed final output excel/tsv, with "raw_" prefix in the file name
• create simplified output file named "all_sample_comparisons.{tsv/xlsx}"
• fixed multiQC to use correct pair names in output plots