Added additional report step

- Added an alignment multiqc step that gathers all qualimap and bismark alignment QC reports (Step 9b)
- Added trimgalore reports to trimmed multiqc report
- Added report suffixes (GLMethylSeq) to all multiqc reports
- Updated multicore specification from "4" to "NumberOfThreads"
- Updated filename specifications to more specifically call out the different filenames bismark generates for paired-end/single-end, bowtie2/hisat2
- Moved generation of nucleotide frequencies file from alignment step to genome reference generation step
- Updated R library versions

Author: bnovak32