Fixed file configurations for VEP plugins

[kubranarci]

Description of the bug

The config file to run VEP tool points out to exact file names, which should be removed since plugins are optional in the first place. Although, if ranking scripts at the end depends on these, they have to be mandatory.

Command used and terminal output

Relevant files

withName: 'ENSEMBLVEP_SNV' { ext.prefix = { "${meta.prefix}_vep_${meta.scatterid}" } ext.args = { [ '--dir_plugins vep_cache/Plugins', '--plugin LoFtool,LoFtool_scores.txt', '--plugin pLI,pLI_values.txt', '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz', '--distance 5000', '--buffer_size 20000', '--format vcf --max_sv_size 248956422', '--appris --biotype --cache --canonical --ccds --compress_output bgzip', '--domains --exclude_predicted --force_overwrite', '--hgvs --humdiv --no_progress --numbers', '--polyphen p --protein --offline --regulatory --sift p --symbol --tsl', '--uniprot --vcf' ].join(' ') } }

System information

No response