Renaming output folders

[vezzi]

pipeline_output folder contains the results of the pipeline. I recently started to append in front of the folders a number in order to have the folders automatically sorted in a chronological order, it is a really small detail but often allows to have an idea of the recipe that has been followed in few seconds.

Something like this:

00_logs
01_preliminary_alignment_qc
02_raw_alignments
03_merged_aligments
04_processed_alignments
05_final_alignment_qc
06_variant_calls
misc

[johandahlberg]

I'll fix this. No problem. Do you want this only under the working directory or under the delivery folder structure as well?

[vezzi]

For now in the working directory only the delivery structure, if I am not wrong, will contain only alignments ready and variant calls, so in this case is not necessary to add structure.

[johandahlberg]

Ok. Though at the moment the delivery folder structure also contains quality control information and the raw data.