analysis step awarness

[dizak]

f4d4887

Proposed feature

mothulity know each step of analysis from each other. This might be achieved with few steps:

• Enclosing particular mothur commands, instead of keeping them in a plaing text in the template. The question is: to what extent the logic from templates should be removed?
• Once the command is passed to mothulity, it should know how the files would be named after each step. If it's done - resolving Checkpointing feature #9 is straightforward.
• mothulity already creates the hidden logfile. It can be used as the cache.

[dizak]

The simplest way of re-running the analysis could be done in a similar way to calling mothulity for running the analysis phase.