validateIO: Validate Input/Output Arguments to DADA2 Wrappers

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

Validate Input/Output Arguments to DADA2 Wrappers

Description

Internal function for validating the input and output path arguments to any of the DADA2 wrapper functions. Keeps only existing input files. Output directory is modifiable by processing batches via NEONMICROBE_DIR_OUTPUTS.

Usage

validateIO(
  fn,
  in_subdir,
  out_subdir,
  in_explicitdir,
  out_explicitdir,
  targetGene = c("16S", "ITS"),
  validate_input_only = FALSE
)

Arguments

fn	Base names of input fastq files. If inputs are not base names (i.e. if they include directory paths), the directory paths will be removed. Files that do not exist will be ignored; however, if all files do not exist, this function will issue a warning.
in_subdir	Subdirectory name from which to retrieve input fastq files. Enter "raw" for raw sequence files, or any other character string to specify a subdirectory within NEONMICROBE_DIR_MIDPROCESS/16S. To specify a directory outside NEONMICROBE_DIR_MIDPROCESS/16S, use the 'in_explicitdir' argument.
out_subdir	Subdirectory name where output fastq files will be written. Enter any character string to specify a subdirectory within NEONMICROBE_DIR_MIDPROCESS/16S. If the directory does not exist, it will be created. To specify a directory outside NEONMICROBE_DIR_MIDPROCESS/16S, use the 'out_explicitdir' argument.
in_explicitdir, out_explicitdir	Directory names to use instead of 'in_subdir' and 'out_subdir', if static directory names or directories outside of NEONMICROBE_DIR_MIDPROCESS/16S are desired. Not recommended for use within processing batches.
targetGene	Either "16S" or "ITS".

Value

List.

• fn: Full paths to input files.

• fn_out: Full paths where each file will be written after processing.

• in_dir: Full path to input directory.

• out_dir: Full path to output directory.

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