WIP. Porting bash pipeline script to python.

Added code to load environment modules from within a python script. Also general bugfixes and additional functionality. Still a work in progress, so is not yet complete.
Ah yes - Mario mentioned something about this.. https://github.com/ewels/miRNA_processing/blob/ca9a05d1c1ce69822debc5a8c4129a5303e70ff8/pipeline.py#L44