nf-core_modules/modules/medaka/main.nf
avantonder 8d9e8ae839
Add Medaka module (#992)
* add racon

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* Indentation

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update main.nf

* Update main.nf

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:26:37 +00:00

47 lines
1.5 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process MEDAKA {
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::medaka=1.4.4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0"
} else {
container "quay.io/biocontainers/medaka:1.4.4--py38h130def0_0"
}
input:
tuple val(meta), path(reads), path(assembly)
output:
tuple val(meta), path("*.fa.gz"), emit: assembly
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
medaka_consensus \\
-t $task.cpus \\
$options.args \\
-i $reads \\
-d $assembly \\
-o ./
mv consensus.fasta ${prefix}.fa
gzip -n ${prefix}.fa
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( medaka --version 2>&1 | sed 's/medaka //g' )
END_VERSIONS
"""
}