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7be60774b6
* add module for tbprofiler * Update test.yml * Update meta.yml Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
48 lines
1.8 KiB
Text
48 lines
1.8 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 TBPROFILER_PROFILE {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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::tb-profiler=3.0.8" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0"
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} else {
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container "quay.io/biocontainers/tb-profiler:3.0.8--pypyh5e36f6f_0"
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}
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("bam/*.bam") , emit: bam
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tuple val(meta), path("results/*.csv") , emit: csv, optional: true
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tuple val(meta), path("results/*.json"), emit: json
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tuple val(meta), path("results/*.txt") , emit: txt, optional: true
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tuple val(meta), path("vcf/*.vcf.gz") , emit: vcf
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path "versions.yml" , emit: versions
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script:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def input_reads = meta.single_end ? "--read1 $reads" : "--read1 ${reads[0]} --read2 ${reads[1]}"
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"""
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tb-profiler \\
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profile \\
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$options.args \\
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--prefix ${prefix} \\
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--threads $task.cpus \\
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$input_reads
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$(tb-profiler --version 2>&1) | sed 's/TBProfiler version //')
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END_VERSIONS
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"""
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}
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