mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
process DAMAGEPROFILER {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2' :
|
|
'quay.io/biocontainers/damageprofiler:1.1--hdfd78af_2' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
path fasta
|
|
path fai
|
|
path specieslist
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}"), emit: results
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
def reference = fasta ? "-r $fasta" : ""
|
|
def species_list = specieslist ? "-sf $specieslist" : ""
|
|
"""
|
|
damageprofiler \\
|
|
-i $bam \\
|
|
-o $prefix/ \\
|
|
$args \\
|
|
$reference \\
|
|
$species_list
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
damageprofiler: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|