process ENSEMBLVEP { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' : 'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }" input: tuple val(meta), path(vcf) val genome val species val cache_version path cache output: tuple val(meta), path("*.ann.vcf"), emit: vcf path "*.summary.html" , emit: report path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep" """ mkdir $prefix vep \\ -i $vcf \\ -o ${prefix}.ann.vcf \\ $args \\ --assembly $genome \\ --species $species \\ --cache \\ --cache_version $cache_version \\ --dir_cache $dir_cache \\ --fork $task.cpus \\ --vcf \\ --stats_file ${prefix}.summary.html rm -rf $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') END_VERSIONS """ }