nf-core_modules/modules/dragonflye/main.nf
Robert A. Petit III 608bb22598
Update dragonflye to latest version (#1442)
* Update dragonflye to latest version

* trigger ci
2022-03-24 14:56:32 -04:00

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1.5 KiB
Text

process DRAGONFLYE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' :
'quay.io/biocontainers/dragonflye:1.0.11--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
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def memory = task.memory.toGiga()
"""
dragonflye \\
--reads ${reads} \\
$args \\
--cpus $task.cpus \\
--ram $memory \\
--outdir ./ \\
--force
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dragonflye: \$(dragonflye --version 2>&1 | sed 's/^.*dragonflye //' )
END_VERSIONS
"""
}