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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Misleading info in error message concerning invalid path to VEP-cache #1326

Open asp8200 opened 10 months ago

asp8200 commented 10 months ago

Description of the bug

Observed on Sarek 3.3.2 (and on dev 51c7676c0947849d191359bf2c66bf32b10dc88b) :

The error message for invalid VEP-cache contains some seeming misleading info about invalid sample-sheet.

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/110_GRCh38 in /home/ubuntu/dev/./nPlease refer to https://nf-co.re/sarek/docs/usage/#how-to-customise-snpeff-and-vep-annotation for more information.

My guess is that the lines about the invalid sample-sheet comes from nf-validation.

Command used and terminal output

nextflow run main.nf -profile test_full,docker --vep_cache /some/invalid/path --outdir foo

Relevant files

No response

System information

No response

FriederikeHanssen commented 10 months ago

Canyou check whether this is still relevant on dev? Pretty sure a bunch of stuff was fixed around this

FriederikeHanssen commented 10 months ago

OK found the corresponding slack thread, and it is also present on dev

asp8200 commented 10 months ago

Canyou check whether this is still relevant on dev? Pretty sure a bunch of stuff was fixed around this

I also wrote in the description of the issue that I check it on dev.

bounlu commented 1 month ago

I confirm that this issue still persists in version 3.4.3.