download_from_ena: Download FASTQ files from ENA's FTP

View source: R/01_download_data.R

download_from_enaR Documentation

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/gead documentation built on April 26, 2023, 3:47 p.m.