haplotyper-battle-royale/modules/efetch/main.nf

process EFETCH {
    tag "${genome}"
    label 'process_single'

    container 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1'

    input:
    val(genome)

    publishDir "${params.outdir}", mode: 'copy'

    output:
    path 'reference.fasta'

    script:
    """
    esearch \\
            -db nucleotide \\
            -query "${genome}" \\
        | efetch \\
            -format fasta \\
        > reference.fasta
    """
}