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e0d820f9f4
* 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>
57 lines
1.8 KiB
Text
57 lines
1.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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params.use_cache = false
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params.snpeff_tag = ""
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process SNPEFF {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
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if (params.use_cache) {
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1"
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} else {
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container "quay.io/biocontainers/snpeff:5.0--hdfd78af_1"
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}
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} else {
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container "nfcore/snpeff:${params.snpeff_tag}"
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}
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input:
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tuple val(meta), path(vcf)
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val db
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path cache
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output:
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tuple val(meta), path("*.ann.vcf"), emit: vcf
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path "*.csv" , emit: report
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def avail_mem = 6
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if (!task.memory) {
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log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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cache = params.use_cache ? "-dataDir \${PWD}/${snpeff_cache}" : ""
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"""
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snpEff -Xmx${avail_mem}g \\
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$db \\
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$options.args \\
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-csvStats ${prefix}.csv \\
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$cache \\
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$vcf \\
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> ${prefix}.ann.vcf
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echo \$(snpEff -version 2>&1) > ${software}.version.txt
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"""
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}
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