nf-core_modules/software/snpeff/main.nf
Maxime U. Garcia e0d820f9f4
Add snpeff (#546)
* feat: add snpeff

* fix: linting

* fix: tests

* fix: add csv output

* fix: add params information

* fix: improve script

* Update software/snpeff/environment.yml

* Update software/snpeff/environment.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-06 13:40:55 +01:00

57 lines
1.8 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } 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 "*.version.txt" , 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
echo \$(snpEff -version 2>&1) > ${software}.version.txt
"""
}