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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
62 lines
1.9 KiB
Text
62 lines
1.9 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.vep_tag = ""
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process ENSEMBLVEP {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null)
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if (params.use_cache) {
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0"
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} else {
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container "quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0"
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}
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} else {
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container "nfcore/vep:${params.vep_tag}"
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}
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input:
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tuple val(meta), path(vcf)
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val genome
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val species
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val cache_version
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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 "*.summary.html" , 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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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dir_cache = params.use_cache ? "\${PWD}/${cache}" : "/.vep"
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"""
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mkdir $prefix
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vep \\
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-i $vcf \\
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-o ${prefix}.ann.vcf \\
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$options.args \\
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--assembly $genome \\
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--species $species \\
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--cache \\
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--cache_version $cache_version \\
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--dir_cache $dir_cache \\
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--fork $task.cpus \\
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--format vcf \\
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--stats_file ${prefix}.summary.html
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rm -rf $prefix
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echo \$(vep --help 2>&1) > ${software}.version.txt
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"""
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}
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