nf-core_modules/modules/snpeff/main.nf

60 lines
1.9 KiB
Text
Raw Normal View History

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
params.use_cache = false
params.snpeff_tag = ""
process SNPEFF {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
if (params.use_cache) {
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1"
} else {
container "quay.io/biocontainers/snpeff:5.0--hdfd78af_1"
}
} else {
container "nfcore/snpeff:${params.snpeff_tag}"
}
input:
tuple val(meta), path(vcf)
val db
path cache
output:
tuple val(meta), path("*.ann.vcf"), emit: vcf
path "*.csv" , emit: report
path "versions.yml" , emit: versions
script:
def avail_mem = 6
if (!task.memory) {
log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
cache = params.use_cache ? "-dataDir \${PWD}/${snpeff_cache}" : ""
"""
snpEff -Xmx${avail_mem}g \\
$db \\
$options.args \\
-csvStats ${prefix}.csv \\
$cache \\
$vcf \\
> ${prefix}.ann.vcf
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
END_VERSIONS
"""
}