[PKG] add comment
[TOPHAT][MOD] not specifying program name (for ngs-tophat script), add comment
[Tophat][MOD] if --out-dir is specified and only one project is input, use the give output directly.
[Tophat][MOD] use absolute import path
[Tophat][FIX] fix ref_name = 'unknown' typo
[PKG] change to version 0.0.4