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https://github.com/MillironX/nf-core_modules.git
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77d5dd60eb
* added bamtools stats module and tested * added bamtools stats module and tested * fixing prettier complaints * changed process tag to single
35 lines
974 B
Text
35 lines
974 B
Text
process BAMTOOLS_STATS {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
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'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.stats"), emit: stats
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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bamtools \\
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stats \\
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-in $bam \\
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>${prefix}.bam.stats
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
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END_VERSIONS
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"""
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}
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