Needed updates on "PEMA's output files.md"

[JustinePa]

To facilitate use and understanding of PEMA by external users (e.g. future Tesseract users), the file PEMA's output files.md needs a few updates and more details:

• "Pre-processing steps": the names of the folders are not the same anymore, update to the new ones
• "7.gene_dependent": information regarding 18S and ITS are missing (even if there are similarities with 16S and COI, there are also differences that should be explained) for COI and 16S, many file names changed and some are missing each file that is found in the PEMA output needs to be described here (or in another place that you consider is best, where users can easily find it), along with an explanation of how it is obtained
• add description of "8.outputPerSample" folder and checkpoints folder

A new user should be able to understand what each file/folder corresponds to without having to dive in the depths of the PEMA code.

[hariszaf]

Hi @JustinePa Thanks for the issue. v.2.1.5 will have in general a different output structure but it is still valid input . Please feel free to write these descriptions you describe if you feel convenient with PEMA's output and open a PR so you can be acknowledged as a contributor. 🤓

[JustinePa]

Thanks @hariszaf for your answer. I will work on an update of this file then!