nf-core_modules/modules/minia/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process MINIA {
tag "$meta.id"
label 'process_high'
publishDir "${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::minia=3.2.4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0"
} else {
container "quay.io/biocontainers/minia:3.2.4--he513fc3_0"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.contigs.fa'), emit: contigs
tuple val(meta), path('*.unitigs.fa'), emit: unitigs
tuple val(meta), path('*.h5') , emit: h5
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
echo "${reads.join("\n")}" > input_files.txt
minia \\
$options.args \\
-nb-cores $task.cpus \\
-in input_files.txt \\
-out $prefix
echo \$(minia --version 2>&1) | sed 's/^.*Minia version //; s/ .*\$//' > ${software}.version.txt
"""
}