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16e8d21477
* add nanoplot * add Nanopore 100 read subset bam and fastq * add nanoplot module and sequencing_summary.txt * Update pytest_software.yml * Update main.nf * test directory path * testing one output file * Update main.nf * fix typo * remove path to test outputs (it worked locally) * use test_data.config in test * add meta.yml * allowing either summary.txt or fastq.gz inputs * fix linting and test.yml * test whether github check can catch the output * add summary.txt test output paths * check Nanoplot-report.html output
42 lines
1.5 KiB
Text
42 lines
1.5 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 NANOPLOT {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::nanoplot=1.32.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/nanoplot:1.32.1--py_0"
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} else {
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container "quay.io/biocontainers/nanoplot:1.32.1--py_0"
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}
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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 "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" :
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("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ''
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"""
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NanoPlot \\
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$options.args \\
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-t $task.cpus \\
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$input_file
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echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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