Quartus complains a lot while building Yosys-generated Verilog:

• it fails some subjective lints (warnings 10270, 10763, 10935) that don't affect the semantics (modulo Yosys bugs).
• Quartus doesn't recognise certain attributes like src (warning 10335) generated by nMigen.
• Quartus will use its internal IP library whenever you instantiate a megafunction, and warn about it not being within the settings file (warning 12125).
• Quartus complains whenever you set NUM_PARALLEL_PROCESSORS to something which isn't all cores (warning 18236).
• Quartus Lite will also complain about unimportant features only being available when you buy Quartus (warning 292013).

These can be silenced through the creation of a .srf file (which in this case suppresses all message text with a given ID in quartus_suppressed_warnings).

Of these, all but 10335 are effectively harmless. Silencing 10335 has the potential to obscure a misspelt user attribute, so I could remove it if you'd prefer.