RNA-seq pipelines (long-, small- and rampage) v2.3.3

All changes contained in this release will produce results that are compatible back to v2.2 (or further).

This release include the following minor changes:

1. long-RNA-seq RSEM quantification now includes a ScriptSeq vs. TruSeq parameter.
2. small-RNA-seq STAR alignment now allows for alternate clipping models for ENCODE 2 data.
3. All alignments that concatenate mutiple fastq files, have a better naming scheme for the result.