nf-core_modules/modules/ensemblvep/main.nf
2022-06-16 16:25:54 +02:00

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process ENSEMBLVEP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::ensembl-vep=105.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' :
'quay.io/biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }"
input:
tuple val(meta), path(vcf)
val genome
val species
val cache_version
path cache
path fasta
path extra_files
output:
tuple val(meta), path("*.ann.vcf") , optional:true, emit: vcf
tuple val(meta), path("*.ann.tab") , optional:true, emit: tab
tuple val(meta), path("*.ann.json") , optional:true, emit: json
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 file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf'
def prefix = task.ext.prefix ?: "${meta.id}"
def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
def reference = fasta ? "--fasta $fasta" : ""
"""
vep \\
-i $vcf \\
-o ${prefix}.ann.${file_extension} \\
$args \\
$reference \\
--assembly $genome \\
--species $species \\
--cache \\
--cache_version $cache_version \\
--dir_cache $dir_cache \\
--fork $task.cpus \\
--stats_file ${prefix}.summary.html \\
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
END_VERSIONS
"""
}