Better user Nextflow Configuration override

[madeline-scyphers]

Right now if a user needs to change anything about the NF default config, they have to copy the whole NF config. This is annoying for a number of reasons. The users should be able to just override 1 option if they want. It is also more fragile since if we change the default config, more people will have a very large configuration out there overriding defaults then just overriding 1 or 2 options.