Improve output of resutls

[evezeyl]

Output of results is a bit messy

• incl. NUCDIFF Results - that output the last result directory - > needs to be supressed
• sort the files we really need as output

[evezeyl]

• result directory ok
• Sorting files that are really necessary will be done at the end ... when we have analysed all

[evezeyl]

I think the most important to be organized are:

• bakta annotation results into directory -> ok
• nucdiff results into directory -> ok (because can be reused)
• vcf annotator - uncertain if want to use now

The rest are temporary output files - they can be removed from output