mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
45 lines
1.4 KiB
Text
45 lines
1.4 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
params.options = [:]
|
||
|
|
options = initOptions(params.options)
|
||
|
|
|
||
|
|
process DAMAGEPROFILER {
|
||
|
|
tag "$meta.id"
|
||
|
|
label 'process_low'
|
||
|
|
publishDir "${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']) }
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/damageprofiler:1.1--hdfd78af_2"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(bam)
|
||
|
|
path fasta
|
||
|
|
path fai
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("${prefix}"), emit: results
|
||
|
|
path "*.version.txt" , emit: version
|
||
|
|
|
||
|
|
script:
|
||
|
|
def software = getSoftwareName(task.process)
|
||
|
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||
|
|
|
||
|
|
"""
|
||
|
|
damageprofiler \\
|
||
|
|
-i $bam \\
|
||
|
|
-r $fasta \\
|
||
|
|
-o $prefix/ \\
|
||
|
|
$options.args
|
||
|
|
|
||
|
|
|
||
|
|
echo \$(damageprofiler -v) | sed 's/^DamageProfiler v//' > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|