process SAMTOOLS_STATS {
    tag "$meta.id"
    label 'process_low'

    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"

    input:
    tuple val(meta), path(input), path(input_index)
    path fasta

    output:
    tuple val(meta), path("*.stats"), emit: stats
    path  "versions.yml"            , emit: versions

    script:
    def args = task.ext.args ?: ''
    def reference = fasta ? "--reference ${fasta}" : ""
    """
    samtools stats --threads ${task.cpus-1} ${reference} ${input} > ${input}.stats

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