nf-core_modules/modules/rseqc/readduplication/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process RSEQC_READDUPLICATION {
tag "$meta.id"
label 'process_medium'
publishDir "${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']) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else {
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
}
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*seq.DupRate.xls"), emit: seq_xls
tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls
tuple val(meta), path("*.pdf") , emit: pdf
tuple val(meta), path("*.r") , emit: rscript
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
read_duplication.py \\
-i $bam \\
-o $prefix \\
$options.args
read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt
"""
}