Added a param --filters which takes a string as an argument which can be comma separated list of filter condition. These condition are similar to what we can give in filter_vep.
As nextflow-vep can handle only VCF files the filter_vep arguments used here is also tailored for VCF file.
Test Example
nextflow -C ${repositories}/ensembl-vep/nextflow/nextflow.config run ${repositories}/ensembl-vep/nextflow/workflows/run_vep.nf \
--vcf $input_file \
--vep_config $vep_config \
--outdir $output_dir \
--output_prefix $output_prefix \
--filters "amino_acids not match X[A-Za-z*]?\/,Feature is ENST00000377918"
Added a param
--filterswhich takes a string as an argument which can be comma separated list of filter condition. These condition are similar to what we can give infilter_vep.As nextflow-vep can handle only VCF files the
filter_veparguments used here is also tailored for VCF file.Test Example
example variant to check this filter