@Maxime Garcia for starting to track all the WARN messages in the nf-test snapshots. Would have not spotted this until much much later otherwise:

+ 94         "WARN: Access to undefined
                                         parameter `vep_phenotypes` -- Initiali
                                        se it to a default value eg. `<http://params.ve|params.ve>
                                        p_phenotypes = some_value`"            
  94     ]                                95     ]                             
  95 ]                                    96 ]

I knew this was going to be useful at some point

As in, you are tracking expected WARNING in case some change accidentally breaks them?

yes exactly. Or in this case, an unexpected WARNING showed up

Ah, so you are using something like

PROCESS.stderr

or some such rather than manually adding/removing expected errors

for all I know it's magic @Maxime Garcia what is happening behind the scenes?

nf-test, and checking stdout and stderr as nextflow doesn't usually publish in out