I’m so tired of the irrelevant error messages like “The sample-sheet only contains …“. An example from today from Sarek v3.4.3 :

The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ascat
The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ascat, controlfreec, mutect2
Path provided with VEP cache is invalid.
Make sure there is a directory named homo_sapiens/111_GRCh38 in /ngc/shared/nf_tools/references/vep_cache./nPlease refer to <https://nf-co.re/sarek/docs/usage/#how-to-customise-snpeff-and-vep-annotation> for more information.

The actual error is the last mentioned error related to VEP. I’m sure this is confusing for inexperienced users of sarek. I don’t know what is causing those misleading error messages, but I suspect nf-validation. Will that problem be solved with the replacement of nf-validation with nf-schema?

Please ask in #C056RQB10LU

Also switching to #C056RQB10LU will only be possible when #CE5LG7WMB is released

ok. I’ll post the question in nf-schema.

Hi these are not

nf-validation

or

nf-schema

custom errors, but rather seem like some custom errors used via the

errorMessage

schema option.