nf-core_modules/modules/racon/main.nf
avantonder 977d96ed0b
Add Racon module to nf-core/modules (#949)
* add racon

* add racon

* add racon

* add racon module

* add racon module

* edit racon module

* edit racon module

* edit racon module

* edit racon module

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-10-29 13:33:38 +01:00

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Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process RACON {
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::racon=1.4.20" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1"
} else {
container "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
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
racon -t "${task.cpus}" \\
"${reads}" \\
"${paf}" \\
$options.args \\
"${assembly}" > \\
${prefix}_assembly_consensus.fasta
gzip -n ${prefix}_assembly_consensus.fasta
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( racon --version 2>&1 | sed 's/^.*v//' )
END_VERSIONS
"""
}