This function uses the NCBI SRA Toolkit via
system2() to download files
from SRA and convert them to fastq.gz. To process files in parallel, register
a parallel backend, e.g., using
that intermediate files created by fasterq-dump are uncompressed and could
require hundreds of gigabytes if files are processed in parallel.
fetch( accessions, outputDir, overwrite = FALSE, keepSra = FALSE, prefetchCmd = "prefetch", prefetchArgs = NULL, fasterqdumpCmd = "fasterq-dump", fasterqdumpArgs = NULL, pigzCmd = "pigz", pigzArgs = NULL )
Character vector of SRA run accessions.
String indicating the local directory in which to save the files. Will be created if it doesn't exist.
Logical indicating whether to overwrite files that already exist in
Logical indicating whether to keep the ".sra" files.
String indicating command for prefetch, which downloads ".sra" files.
Character vector indicating arguments to pass to prefetch.
String indicating command for fasterq-dump, which uses ".sra" files to create ".fastq" files.
Character vector indicating arguments to pass to fasterq-dump.
String indicating command for pigz, which converts ".fastq" files to ".fastq.gz" files.
Character vector indicating arguments to pass to pigz.
A list. As the function runs, it updates a tab-delimited log file in
outputDir called "progress.tsv".