3.0.0: GA-pre-scan

Changes:

replaced kaiju with kraken2
new GA-pre-scan stage
putative reads will now be scanned by centrifuge + kraken2 to determine likely taxa in sample
MetaPro will now craft a custom subset of ChocoPhlAn to speed up GA (BWA+BLAT) steps
ability to rename stages
ability to change the name of the bypass log
debug_stop_flag to stop MetaPro at a specific stage
Bugfixes:

output_per_read_score now writes to bypass log