process IVAR_TRIM {
    tag "$meta.id"
    label 'process_medium'

    conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' :
        'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }"

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

    output:
    tuple val(meta), path("*.bam"), emit: bam
    tuple val(meta), path('*.log'), emit: log
    path "versions.yml"           , emit: versions

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    ivar trim \\
        $args \\
        -i $bam \\
        -b $bed \\
        -p $prefix \\
        > ${prefix}.ivar.log

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