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1840289068
* initiate agrvate module * remove todos [ci skip] * remove todos and fix containers [ci skip] * ready for testing Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
39 lines
1.4 KiB
Text
39 lines
1.4 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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process AGRVATE {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::agrvate=1.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/agrvate:1.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/agrvate:1.0--hdfd78af_0"
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}
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary
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path "${fasta.baseName}-results" , emit: results_dir
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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agrvate \\
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$options.args \\
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-i $fasta
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echo \$(agrvate -v 2>&1) | sed 's/agrvate //;' > ${software}.version.txt
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"""
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}
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