Fixed an issue where an aggregate output file was being inappropriately compounded with other file names.  Fixed an error message typo.  Clarified a debug message.
Added verboseOverMe output to the sequence reading.  Corrected a potential issue with skipping commented lines when it comes to reading fastq files.
Improved the --help output and improved an error message.
Initial check-in of pipeline script.
Removed old run_cff.sh script.