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41 lines
1.4 KiB
Text
41 lines
1.4 KiB
Text
process TBPROFILER_PROFILE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0' :
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'quay.io/biocontainers/tb-profiler:3.0.8--pypyh5e36f6f_0' }"
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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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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def input_reads = meta.single_end ? "--read1 $reads" : "--read1 ${reads[0]} --read2 ${reads[1]}"
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"""
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tb-profiler \\
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profile \\
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$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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"${task.process}":
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tbprofiler: \$( 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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