mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
36 lines
1,012 B
Text
36 lines
1,012 B
Text
process RSEQC_TIN {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
|
|
container "${ 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
|
|
|
|
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
|
|
"""
|
|
}
|