prepare_sample_sheet.R: Added a param to set specie name instead of always using Hosa

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
prepare_sample_sheet.R: Fixed a bug where SINGLE_END was added to the first line when there was no single-ended file

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
prepare_sample_sheet.R: Solved a bug where the FASTQ1 and FASTQ2 name of the last line were copied at every other lines

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