prepare_sample_sheet.R: Added a new script to prepare SampleSheets using ENCODE metadata

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
prepare_sample_sheet.R: The script no longer crash when there is no paired end files

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