nf-core_modules/software/damageprofiler/main.nf

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// 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
"""
}