tbf this error message comes from https://github.com/nf-core/sarek/blob/e92242ead3dff8e24e13adbbd81bfbc0b6862e4c/subworkflows/local/samplesheet_to_channel/main.nf#L162 and https://github.com/nf-core/sarek/blob/e92242ead3dff8e24e13adbbd81bfbc0b6862e4c/subworkflows/local/annotation_cache_initialisation/main.nf#L50 which is not handeled by nf-validation

Yes, the error message related to VEP is fine. The problem is the one related to the sample-sheet.

which is also custom written by us (see first link)

A lot of improvements to error messages have been done in

nf-schema

so that will hopefully reduce the need for these custom messages. (although some of these will still not be possible as it checks the samplesheet based on some parameters given)

I see. Still annoying though

Perhaps a ticket should be made for fixing this in Sarek? (I looked for one, but didn’t find any.)

sure go ahead

Talking about misleading error messages from Nextflow/Sarek, has the problem with the misleading “join mismatch” error messages been solved?