nf-core_modules/modules/nanoplot/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process NANOPLOT {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::nanoplot=1.38.0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0"
}
input:
tuple val(meta), path(ontfile)
output:
tuple val(meta), path("*.html"), emit: html
tuple val(meta), path("*.png") , emit: png
tuple val(meta), path("*.txt") , emit: txt
tuple val(meta), path("*.log") , emit: log
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" :
("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ''
"""
NanoPlot \\
$options.args \\
-t $task.cpus \\
$input_file
echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//' > ${software}.version.txt
"""
}