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

    conda "bioconda::fastqc=0.11.9"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
        'biocontainers/fastqc:0.11.9--0' }"

    input:
    tuple val(meta), path(reads)

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

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    // Make list of old name and new name pairs to use for renaming in the bash while loop
    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
    def rename_to = old_new_pairs*.join(' ').join(' ')
    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
    """
    printf "%s %s\\n" $rename_to | while read old_name new_name; do
        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
    done

    fastqc \\
        $args \\
        --threads $task.cpus \\
        $renamed_files

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
    END_VERSIONS
    """

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

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
    END_VERSIONS
    """
}
