I am thinking it might be nice for people to work out the command line flags they want for one type of analysis (like paired end dbotu), have that information stored somewhere, and call it again later with just one user-defined flag. I feel like storing it in the user.cfg file would be useful. Or maybe we just have a few commands (they could even be hidden from the general public) where it's like --enigma_merge_db_micro and it sets many of the command like flags to be the same every time. That way, although having all the flags are nice, within a lab or within ENIGMA, you could always use the same set of flags and parameters on similar data.
swo
commented
10 years ago
I am thinking it might be nice for people to work out the command line flags they want for one type of analysis (like paired end dbotu), have that information stored somewhere, and call it again later with just one user-defined flag. I feel like storing it in the user.cfg file would be useful. Or maybe we just have a few commands (they could even be hidden from the general public) where it's like --enigma_merge_db_micro and it sets many of the command like flags to be the same every time. That way, although having all the flags are nice, within a lab or within ENIGMA, you could always use the same set of flags and parameters on similar data.