mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
47 lines
1.8 KiB
Text
47 lines
1.8 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process DRAGONFLYE {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${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::dragonflye=1.0.4" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/dragonflye:1.0.4--hdfd78af_0"
|
|
} else {
|
|
container "quay.io/biocontainers/dragonflye:1.0.4--hdfd78af_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
|
|
output:
|
|
tuple val(meta), path("contigs.fa") , emit: contigs
|
|
tuple val(meta), path("dragonflye.log") , emit: log
|
|
tuple val(meta), path("{flye,miniasm,raven}.fasta") , emit: raw_contigs
|
|
tuple val(meta), path("{miniasm,raven}-unpolished.gfa"), optional:true , emit: gfa
|
|
tuple val(meta), path("flye-info.txt"), optional:true , emit: txt
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def memory = task.memory.toGiga()
|
|
"""
|
|
dragonflye \\
|
|
--reads ${reads} \\
|
|
$options.args \\
|
|
--cpus $task.cpus \\
|
|
--ram $memory \\
|
|
--outdir ./ \\
|
|
--force
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(dragonflye --version 2>&1 | sed 's/^.*dragonflye //' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|