added parameters for indatadir, outdatadir, reposdir, tmpdir and amended file nodes to use them.

Unless components of path to transcriptome are given as parameters, the --transcriptome-index flag for the tophat2 command will not be used
enhancements to handling substitutions in array refs
Merge pull request #2 from dozy/devel

Devel
Merge pull request #1 from wtsi-npg/devel

Devel