Hi All, When running the following command for a mouse tumor-only sample using nf-core/sarek:

nextflow run nf-core/sarek -r 3.5.1 \
  -profile singularity \
  --input SAMPLE_SHEET \
  --outdir somatic_20 \
  --step mapping \
  --genome GRCm38 \
  --save_mapped \
  --tools mutect2,manta,vep \
  --vep_cache \
  --vep_species mus_musculus

I encountered the following error:

Path provided with VEP cache is invalid.
Make sure there is a directory named mus_musculus/102_GRCm38.

Could you please advise which command and parameters should be used to successfully execute VEP annotation for this sample? Thank you very much for your guidance.

to me it seems that you did not supply a path to the cache (

--vep-cache

takes the path to the cache as an argument). You can download the mouse cache to your machine and then point sarek to it. Is there a reason why you use such an old version (I think we are at 3.8.1 now)

My previous projects used version 3.5.1, so I’m hoping the same version was used here. Do you happen to have a download link for the mouse cache? Also, what does the parameter

--vep_species mus_musculus

represent?

Here you go: https://annotation-cache.github.io/vep_cache/ The

--vep_species

defines which subdirectory in the VEP cache is used. One could write code to derive this automatically from e.g.

--genome

, but then you would need table for every possible genome assembly for every species, so it easier and safer to let the user specify the correct string.

When running the following command for a mouse tumor-only sample using nf-core/sarek: nextflow run nf-core/sarek -r 3.5.1 \ -profile singularity \ --input SAMPLE_SHEET \ --outdir somatic \ --step mapping \ --save_mapped \ --genome GRCm38 \ --tools mutect2,cnvkit,vep \ --vep_cache /home/vep_cache \ --vep_species mus_musculus -resume I also download https://ftp.ensembl.org/pub/release-102/variation/indexed_vep_cache/mus_musculus_vep_102_GRCm38.tar.gz and then tar the file at the folder /home/vep_cache. Inside the outdir somatic folder, there are csv, multiqc, variant_calling, etc subfolders without annotation subfolder. However, the pipeline successfully completed the running without any error.

I am going to answer in the new thread you started.