downloadRawSequenceData: Download NEON Marker Gene Sequencing Raw Data

In claraqin/neonMicrobe: Downloading, Pre-processing, and Assembling NEON Soil Microbe Marker Gene Sequence Data

Download NEON Marker Gene Sequencing Raw Data

Description

Downloads NEON raw sequence data files to the specified filepath, by referencing URLs in the metadata output from downloadSequenceMetadata.

Usage

downloadRawSequenceData(
  metadata,
  outDir = NULL,
  overwrite = FALSE,
  ignore_tar_files = TRUE,
  checkSize = TRUE,
  verbose = FALSE
)

Arguments

metadata	The output of downloadSequenceMetadata. Must be provided as either the data.frame returned by downloadSequenceMetadata or as a filepath to the csv file produced by downloadSequenceMetadata.
outDir	Location where output files are saved and sorted into target gene-specific subdirectories. By default (NULL), this is NEONMICROBE_DIR_SEQUENCE().
overwrite	Default FALSE. If TRUE, overwrites existing files.
ignore_tar_files	If TRUE (default), does not download tar files. Each tar file is a batch containing an entire sequence run of fastq files. The tar file structure will soon be deprecated.
verbose	If TRUE, prints status messages associated with file downloads (in addition to default progress bars).

Value

Returns (invisibly) a list of integer codes: 0 indicates success of downloads and a non-zero integer indicates failure. See the help page for download.file for more details.

claraqin/neonMicrobe documentation built on April 11, 2024, 11:47 a.m.