Clearly define input format

[cb-Hades]

Clearly define the (tested) input format for the workflows, especially GFF, FASTA and annotated genomes files.

TODO:

• Identify file formats that are working
• Write the working formats at fitting places in the documentation of the workflows
• Write FAQ for fast access to this information
• write a note or hint that other formats might work as well, and if errors do occur, one option would be to write an issue or start a discussion to have a particular type of file added / to have the file handling adjusted