nf-core_modules/modules/mtnucratio/main.nf
louperelo a4943a9e57
Mtnucratio (#986)
* add new module samtools_depth

* fixed main.nf for samtools/depth

* add new module mtnucratio

* fix main.nf

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* layout in main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-29 15:02:02 +02:00

43 lines
1.4 KiB
Text

include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process MTNUCRATIO {
tag "$meta.id"
label 'process_low'
publishDir "${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::mtnucratio=0.7" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2"
} else {
container "quay.io/biocontainers/mtnucratio:0.7--hdfd78af_2"
}
input:
tuple val(meta), path(bam)
val(mt_id)
output:
tuple val(meta), path("*.mtnucratio"), emit: mtnucratio
tuple val(meta), path("*.json") , emit: json
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
mtnucratio \\
$options.args \\
$bam \\
$mt_id
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(mtnucratio --version 2>&1) | head -n1 | sed 's/Version: //')
END_VERSIONS
"""
}