mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
97fe899f79
* Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
51 lines
1.6 KiB
Text
51 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } 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
|
|
path specieslist
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}"), emit: results
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def reference = fasta ? "-r $fasta" : ""
|
|
def species_list = specieslist ? "-sf $specieslist" : ""
|
|
|
|
"""
|
|
damageprofiler \\
|
|
-i $bam \\
|
|
-o $prefix/ \\
|
|
$options.args \\
|
|
$reference \\
|
|
$species_list
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
|
|
END_VERSIONS
|
|
"""
|
|
|
|
}
|