Enhancement: provide control samples in a different directory

[khyox]

Suggested in #37 as possible enhancement when the dataset may contain a significative number of negative control samples. When a metagenomic/metatranscriptomic study has many controls, it may be a good idea to have them organized in a different directory, separated from the regular samples, so that you don't need to rename all of them to be able to use the -c option with the number of control samples.