nf-core_modules/modules/unicycler/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process UNICYCLER {
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::unicycler=0.4.8' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3"
} else {
container "quay.io/biocontainers/unicycler:0.4.8--py38h8162308_3"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.scaffolds.fa'), emit: scaffolds
tuple val(meta), path('*.assembly.gfa'), emit: gfa
tuple val(meta), path('*.log') , emit: log
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
"""
unicycler \\
--threads $task.cpus \\
$options.args \\
$input_reads \\
--out ./
mv assembly.fasta ${prefix}.scaffolds.fa
mv assembly.gfa ${prefix}.assembly.gfa
mv unicycler.log ${prefix}.unicycler.log
echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//' > ${software}.version.txt
"""
}