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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
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process DAMAGEPROFILER {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2"
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} else {
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container "quay.io/biocontainers/damageprofiler:1.1--hdfd78af_2"
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}
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input:
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tuple val(meta), path(bam)
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path fasta
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path fai
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path specieslist
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output:
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tuple val(meta), path("${prefix}"), emit: results
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path "versions.yml" , emit: versions
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def reference = fasta ? "-r $fasta" : ""
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def species_list = specieslist ? "-sf $specieslist" : ""
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"""
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damageprofiler \\
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-i $bam \\
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-o $prefix/ \\
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$options.args \\
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$reference \\
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$species_list
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
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END_VERSIONS
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"""
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}
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