revamp help command, rework ngs.sh to simplify registering new modules, bug fixes

* ngs.sh now uses an array to list all modules that are available.
* reworked handling of help text to allow for new module handling in
ngs.sh.
* restructured ngs.sh to be more clear (e.g. all functions grouped
together).
* fixed required number of args for SNP, SPAdes, Bowtie.
* Preparing for renaming of SPAdes to SPADES (all modules expected to
be uppercase).