prepare_design.R: Added biological_replicate_number and technical_replicate_number to file name in design

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
prepare_design.R: Now use a specie argument instead of always using Hosa

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>