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

    conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
        'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"

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

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

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    lofreq indelqual \\
        $args \\
        -f $fasta \\
        -o ${prefix}.bam \\
        $bam

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