nextflow-io/nextflow

process download_reads {
    /*
    This process downloads fastq.gz files from ENA accessions. I run enaDataGet for accessions which point to
    only one sequencing lane, i.e. one pair of fastq files. It fails for accessions that point to multiple
    lanes, so in that case I use enaGroupGet instead. Both of these utilities are supplied by ENA:
    https://github.com/enasequence/enaBrowserTools
    */
    tag "$accession"
    publishDir 'reads', mode: 'symlink'
    cpus 1
    time '1h'
    errorStrategy 'retry'
    maxRetries 3
    memory {8.GB * task.attempt}
    time {1.hour * task.attempt}


    input:
    val accession from accessions

    output:
    set accession, file('**.fastq.gz') into downloaded_reads

    script:
    """
    enaDataGet -f fastq $accession || enaGroupGet -f fastq $accession
    """

}