Fix logging spillover

[vladsavelyev]

Fixes #2173

There were several sources of logging outside the main multiqc logger:

• Warnings about unknown to Python escape sequences (\d, \W, etc.) in regular expressions. To make it intentional and remove the warning, escape them with a raw specifier (r"").
• Using the logging module directly vs the logger object (in one place).
• A print leftover in the VEP module.

[ewels]

Great!

[ewels]

ngsderive is throwing a warning with colours, which is why that statement was being triggered:

|         ngsderive | Found 2 reports
|        mqc_colour | ngsderive_instruments_plot: Error getting colour: could not convert string to float: 'e'
|        mqc_colour | ngsderive_instruments_plot: Error getting colour: could not convert string to float: 'e'