Missing documentation for ordering of config loading

[harper357]

Describe the bug See Slack thread. In short, nf-core pipelines tend to load conf/modules AFTER profiles conf files. This means if you add a custom profile and add it to the list of profiles, you can't change any of the options in conf/modules. The easiest way to get around this is to load a config file (-c) on the command line. This is not very intuitive (in my opinion)

To Reproduce Steps to reproduce the behavior:

Add a custom profile to the profiles section of a nextflow.config with some options that are also in a conf/modules config. The options in the custom profile will get overwritten.

Expected behavior A clear and concise description of what you expected to happen.

Ideally, a custom profile will take priority. Minimally, it would be great to add this loading ordering into the documentation.