organizeRawSequenceData: Organize Raw Sequence Data

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

Organize Raw Sequence Data

Description

Moves raw sequence data into the correct subdirectory for the processing pipeline, renames files to include sequencer run ID, and untars sequence data if necessary.

Usage

organizeRawSequenceData(
  fn,
  metadata,
  outdir_sequence = NEONMICROBE_DIR_SEQUENCE(),
  verbose = TRUE
)

Arguments

fn	Character vector of full names (including path) of raw sequence files. Can include tarballs.
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_sequence	Default NEONMICROBE_DIR_SEQUENCE(). Directory where raw sequence files can be found before reorganizing.
verbose	If TRUE, prints message each time a file is reorganized.

Value

Character vector of the files (including files within tarballs) that were successfully reorganized. If no files were successfully reorganized, returns no value.

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