nf-core_modules/modules/ensemblvep/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
params.use_cache = false
params.vep_tag = ""
process ENSEMBLVEP {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null)
if (params.use_cache) {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0"
} else {
container "quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0"
}
} else {
container "nfcore/vep:${params.vep_tag}"
}
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
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
dir_cache = params.use_cache ? "\${PWD}/${cache}" : "/.vep"
"""
mkdir $prefix
vep \\
-i $vcf \\
-o ${prefix}.ann.vcf \\
$options.args \\
--assembly $genome \\
--species $species \\
--cache \\
--cache_version $cache_version \\
--dir_cache $dir_cache \\
--fork $task.cpus \\
--format vcf \\
--stats_file ${prefix}.summary.html
rm -rf $prefix
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
END_VERSIONS
"""
}