process SAMTOOLS_FLAGSTAT {
    tag "$meta.id"
    label 'process_single'

    conda 'modules/nf-core/samtools/flagstat/environment.yml'
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
        'biocontainers/samtools:1.17--h00cdaf9_0' }"

    input:
    tuple val(meta), path(bam), path(bai)

    output:
    tuple val(meta), path("*.flagstat"), emit: flagstat
    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}"
    """
    samtools \\
        flagstat \\
        --threads ${task.cpus} \\
        $bam \\
        > ${prefix}.flagstat

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    END_VERSIONS
    """

    stub:
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    touch ${prefix}.flagstat

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    END_VERSIONS
    """
}
