[TopHat][ADD] now default give gene annotation and extra args for Tophat
[TopHat][MOD] rewrite the part for reference determination
[Tophat][FIX] accept extra args and output err msg if tophat ends with error
Merge branch 'fix_tophat' into develop
[Tophat][FIX] Tophat crashes when a relative path to output dir is given
Merge branch 'fix_tophat' into develop
[Tophat][MOD] not show ref_name if it is guessed from SampleSheet.csv