Hello! I want to use sarek to annotate my VCF via VEP. This is a human sample sequenced on GRCh38. I want to use --offline, so I need a VEP cache. Would love a sanity check to make sure I am doing this right:

nextflow run $SAREK \
	 -profile singularity \
	 --genome GATK.GRCh38 \
	 --vep_cache_version 110 \
	 --outdir "/projects/cache/out" \
	 --outdir_cache "/projects/cache" \
	 --tools vep \
	 --download_cache \
     --vep_version 115 \
     --vep_genome "GRCh38" \
	 --build_only_index \
	 --input false

Here is my full sarek command:

# Run nf-core/sarek
nextflow run $SAREK \
	 -profile singularity \
	 -c $CONFIG \
	 --input $INPUT \
	 --outdir $OUTDIR \
	 --genome GATK.GRCh38 \
	 --igenomes_base $iGENOMES \
	 --step annotate \
	 --tools vep \
     --vep_genome "GRCh38" \
	 --vep_cache_version 115 \
     --vep_cache "/projects/cache/out"
	 --vep_custom_args "--everything --per_gene --total_length --offline --format vcf"

I think offline is by default

I was under the impression that with --offline you still need a VEP cache as igenomes does not have one (or I cannot find it in the igenomes directory), but if that's not the case, then even better.

you do need a VEP cache