General improvements to the code

[jonbra]

Possible improvements:

• Better documentation
• Make sure that all samples and runs are included (i.e. that the Nextclade mutation reports are found for all samples).
• Improve the way the various mutation classes are summarized.
• Better documentation to designate between successful analysis without any resistance findings, or if the sample has not been analysed.
• Maybe create separate tasks for these things.