Tophat: fastq.gz and generic paired names

[rjpbonnal]

Task in biongs which make the mapping using tophat, has the parameter fastq.
The procedure can not handle smoothly if the user has fastq.gz file but must importantly generic names for paired end file.
The convention is to have filename called _forward and _reverse but generally speaking from Illumina forward is named R1 and reverse R2. So an update is required.