nf-core_modules/modules/bamtools/stats/main.nf

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process BAMTOOLS_STATS {
tag "$meta.id"
label 'process_single'
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.stats"), emit: stats
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bamtools \\
stats \\
-in $bam \\
>${prefix}.bam.stats
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
END_VERSIONS
"""
}