nf-core_modules/software/samtools/flagstat/main.nf

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// Import generic module functions
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include { saveFiles; getSoftwareName } from './functions'
params.options = [:]
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process SAMTOOLS_FLAGSTAT {
tag "$meta.id"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
} else {
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
}
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input:
tuple val(meta), path(bam), path(bai)
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output:
tuple val(meta), path("*.flagstat"), emit: flagstat
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path "*.version.txt" , emit: version
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script:
def software = getSoftwareName(task.process)
"""
samtools flagstat $bam > ${bam}.flagstat
echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
"""
}