mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
65 lines
2 KiB
Text
65 lines
2 KiB
Text
// 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: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
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)}: \$(vep --help 2>&1)
|
|
END_VERSIONS
|
|
"""
|
|
}
|