Download FASTQ files from ENA's FTP

Usage

download_from_ena(
  sample_info = NULL,
  urls = NULL,
  fastqdir = "results/01_FASTQ_files",
  method = "auto",
  link_from = "api"
)

Arguments

sample_info: Data frame of sample metadata created with the function create_sample_info.
urls: Character vector returned by get_url_ena() with the URLs to each file in the ENA's FTP repository. If NULL, this function will run get_url_ena() to get the URLs before downloading.
fastqdir: Path to the directory where .fastq files will be stored. Default: results/01_FASTQ_files.
method: Method to be used for downloading files. One of "internal", "libcurl", "wget", "libcurl", "curl", "wininet" (Windows only), or "auto".
link_from: Method to extract the URL to each FASTQ file in the ENA's ftp repository. One of 'api' or 'iterative'. Default: 'api'.

Value

A data frame as returned by fastq_exists.

Examples

data(sample_info)
fastqdir <- tempdir()
# \donttest{
download_from_ena(sample_info, fastqdir = fastqdir)
#> Downloading file ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_1.fastq.gz
#> Downloading file ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_2.fastq.gz
#>          Run Status
#> 1 SRR1039508     OK
# }