The results output is confusing.

[AdaZED]

Is your feature request related to a problem? Please describe.
In the results output, you get a "bamfiles" and a "consensus" folder.
If you stop at the description of the input parameters from the GitHub documentation page, you would think that the "bamfiles" folder is the output of the program itself.

-o OUTPUT, --output OUTPUT
Output directory, where barcode extracted FASTQ and BAM files will be placed in subdirectories 'fastq_tag' and 'bamfiles' respectively (dir will be created if they do not exist). [MANDATORY]

However, be aware that the "bamfiles" folder contain the bam files from the alignments by bwa sorted and indexed with samtools and NOT the one from consensus cruncher. The bam files resulting from consensus cruncher are in the "consensus" folder (there are more of them, up to 5). This is better explained after in the documentation so it's important to read the full documentation before using the program even though I think this part should be edited (in general users tend to go fast and stop reading at the description of the parameters).

Describe the solution you'd like

1. The output folders need to be definitively renamed to avoid any confusion for the users:
   "bamfiles" to "bamfiles from bwa-samtools"
   "consensus" to "bamfiles from consensus-cruncher"

2. And the GitHub documentation page should be edited too regarding the description of the parameters as this part will lead almost anyone to confusion.