mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e971f538a9
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Fix IQ tree * Fix picard markdup and merge sam * Fix plink/vcf version * Fix plink version output * Fix prokka version command * Fix pydamage * Try fixing markduplicates * Fix snpEff * Fix vcftools version * Fix pydamage and filtersamreads test run * Fix MarkDuplicates tests * Add missing unsorted checks * Remove MD5 sym due to stochasicity in BAM file
60 lines
2 KiB
Text
60 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.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: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
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
|
|
"""
|
|
}
|