[Tophat][ADD] In Sample mode, manual <out_dir> means the root result dir of all samples
[Tophat][ADD] --resume if possible
[Tophat][MOD] -r now is not a required parameter
[Tophat][FIX] In Sample mode, shared args variable may create wrong <out_dir>. copy args as well like Project mode
[Tophat][FIX] shows resume no log found when --resume, no error when skip successful end but resumed samples
[Tophat][MOD] update argument help, rename main tophat run function
Merge branch 'develop'

* develop:
  [Tophat][FIX] shows resume no log found when --resume, no error when skip successful end but resumed samples
  [Tophat][MOD] update argument help, rename main tophat run function
  [Tophat][ADD] In Sample mode, manual <out_dir> means the root result dir of all samples
  [Tophat][ADD] --resume if possible
  [Tophat][MOD] -r now is not a required parameter
  [Tophat][FIX] In Sample mode, shared args variable may create wrong <out_dir>. copy args as well like Project mode