Unclear docu on non-human genomes

[d4straub]

Description of the bug

Hi there, thanks for the great pipeline! I am working with non-model organisms and attempted to use a bacterial reference genome. However, the docu was imperfect:

• In section "No igenomes reference files are used" of usage.md the recommended command lacks the required --outdir and doesnt mention --tools (which seems so important, without it no variants are called?)
• --fasta in https://nf-co.re/sarek/3.5.1/parameters/#fasta does not explain that --genome null --igenomes_ignore are also required when avoiding human altogether. A hint would be great at that place.

Command used and terminal output

Relevant files

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System information

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