Default to correct use of the configuration file
vigji opened this issue · comments
This will probably be solved in the testing branch, but
sashimi
from the terminal should just give the execution of whatever is set to be in the configuration, and should not require the additional inputs
sashimi --scanning ni
as is currently happening.
After we have merged #112 and #92 there will be a chance for a PR completely focused on command line entries, config file and thereof. Understandably, this sort of entry right now can be a source of annoyance. However, we must proceed in order. This will be addressed, alas, now it is not the time yet