mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
process RACON {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::racon=1.4.20" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1' :
|
|
'quay.io/biocontainers/racon:1.4.20--h9a82719_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads), path(assembly), path(paf)
|
|
|
|
output:
|
|
tuple val(meta), path('*_assembly_consensus.fasta.gz') , emit: improved_assembly
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
racon -t "$task.cpus" \\
|
|
"${reads}" \\
|
|
"${paf}" \\
|
|
$args \\
|
|
"${assembly}" > \\
|
|
${prefix}_assembly_consensus.fasta
|
|
|
|
gzip -n ${prefix}_assembly_consensus.fasta
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
racon: \$( racon --version 2>&1 | sed 's/^.*v//' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|