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https://github.com/MillironX/nf-core_modules.git
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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
44 lines
1.4 KiB
Text
44 lines
1.4 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process DIAMOND_MAKEDB {
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tag "$fasta"
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label 'process_medium'
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publishDir "${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:[:], publish_by_meta:[]) }
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// Dimaond is limited to v2.0.9 because there is not a
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// singularity version higher than this at the current time.
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conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0'
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} else {
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container 'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0'
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}
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input:
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path fasta
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output:
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path "${fasta}.dmnd", emit: db
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path "versions.yml" , emit: versions
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script:
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"""
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diamond \\
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makedb \\
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--threads $task.cpus \\
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--in $fasta \\
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-d $fasta \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
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END_VERSIONS
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"""
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}
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