nf-core_modules/modules/damageprofiler/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

46 lines
1.4 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
output:
tuple val(meta), path("${prefix}"), emit: results
path "versions.yml" , emit: versions
script:
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
damageprofiler \\
-i $bam \\
-r $fasta \\
-o $prefix/ \\
$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
END_VERSIONS
"""
}