download_from_ena: Download FASTQ files from ENA's FTP

In almeidasilvaf/GEAtlas: Building Expression Atlas from RNA-Seq data

Download FASTQ files from ENA's FTP

Description

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()

download_from_ena(sample_info, fastqdir = fastqdir)

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.