mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
47 lines
1.7 KiB
Text
47 lines
1.7 KiB
Text
// 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
|
|
"""
|
|
}
|