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

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process RSEQC_TIN {
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), path(bai)
path bed
output:
tuple val(meta), path("*.txt"), emit: txt
tuple val(meta), path("*.xls"), emit: xls
path "versions.yml" , emit: versions
2022-02-04 08:53:32 +00:00
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
tin.py \\
-i $bam \\
-r $bed \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
rseqc: \$(tin.py --version | sed -e "s/tin.py //g")
END_VERSIONS
"""
}