Add MultiQC as optional step

[niemasd]

It would be good to add MultiQC as an optional step:

• Main Website: https://multiqc.info/
• GitHub Repo: https://github.com/ewels/MultiQC
• Documentation: https://multiqc.info/docs/
• Paper: https://doi.org/10.1093/bioinformatics/btw354

This may require restructuring how the current tools are executed, as it seems to need the log files rather than the output files

[niemasd]

Actually, maybe I'll use SamBamViz instead