nf-core_modules/modules/seqtk/rename/main.nf

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

    conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
        'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"

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

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

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

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def extension = "fasta"
    if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
        extension = "fastq"
    }
    """
    seqtk \\
        rename \\
        $args \\
        $sequences \\
        $prefix | \\
        gzip -c --no-name > ${prefix}.renamed.${extension}.gz

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