nf-core_modules/modules/rseqc/readduplication/main.nf
2022-02-04 09:53:32 +01:00

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process RSEQC_READDUPLICATION {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
'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 "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}"
"""
read_duplication.py \\
-i $bam \\
-o $prefix \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
rseqc: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g")
END_VERSIONS
"""
}