Pipeline doesn't build the right path to the vep cache files

[nschcolnicov]

Description of the bug

If running a command that uses the VEP cache files from "s3://annotation-cache/vep_cache" it fails to build the right path and raises this error: Files within --vep_cache invalid. Make sure there is a directory named caenorhabditis_elegans/110_WBcel235 in s3://annotation-cache/vep_cache/. https://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation It also fails for other genomes: Files within --vep_cache invalid. Make sure there is a directory named homo_sapiens/110_GRCh38 in s3://annotation-cache/vep_cache/. https://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation

Both of this files exist, but the path is not properly built: aws s3 ls s3://annotation-cache/vep_cache/ PRE 102_GRCm38/ PRE 108_GRCh38/ PRE 108_WBcel235/ PRE 109_GRCh38/ PRE 109_WBcel235/ PRE 110_GRCh37/ PRE 110_GRCh38/ PRE 110_WBcel235/

Command used and terminal output

For the frist error:
nextflow run ../../main.nf -profile bi,cluster --annotate_tools merge --outdir . -c config.config 

For the second error:
nextflow run ../../main.nf -profile bi,cluster --outdir . --annotate_tools merge --input https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet_full.csv -c ../config.config

Relevant files

First config.config file defines necesary reference files for running a WBcel235 sample Second config.config file defines necesary reference files for running GRCh38 sample

System information

dev branch

[bounlu]

Please see my PR for the fix.

[maxulysse]

This should now be fixed, sorry for the issues