Add instructions about creating and using the samples list and a reference transcriptome

[SantosRAC]

@felipevzps @capuccino26 our current pipeline does not have a "references" folder.
We must create it, add a reference transcriptome (for P. putida, matching our test data) and add instructions ! (explain what the references folder have). I would also explain what the samples.csv is and add instructions on how to create one.