I generated a report containing custom content with supported Bakta and QUAST results that are generated by default. By default, modules are included in the report in the order specified in config.module_order. Any modules found that aren’t in this list are appended at the top of the report.
You can definitely set the order of custom config sections:
But whether you can mix them in amongst regular modules or not, I’m not sure off the top of my head. Worth investigating and potentially a nice feature request if not.
There is a report_section_order option that allows to put weight to each section in the report, or place it before/after certain sections: Customising Reports - MultiQC
E.g. in your case the config can look as following: