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37 lines
1.2 KiB
Text
37 lines
1.2 KiB
Text
process NANOPLOT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? 'bioconda::nanoplot=1.39.0' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/nanoplot:1.39.0--pyhdfd78af_0' :
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'quay.io/biocontainers/nanoplot:1.39.0--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(ontfile)
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output:
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tuple val(meta), path("*.html"), emit: html
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tuple val(meta), path("*.png") , emit: png
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tuple val(meta), path("*.txt") , emit: txt
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tuple val(meta), path("*.log") , emit: log
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" :
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("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ''
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"""
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NanoPlot \\
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$args \\
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-t $task.cpus \\
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$input_file
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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nanoplot: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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