setup_directories {demulticoder} | R Documentation |
Set up directory paths for subsequent analyses
Description
This function sets up the directory paths for subsequent analyses. It checks whether the specified output directories exist or creates them if they don't. The function also provides paths to primer and metadata files within the data directory.
Usage
setup_directories(
data_directory = "data",
output_directory = tempdir(),
tempdir_path = NULL,
tempdir_id = "demulticoder_run"
)
Arguments
data_directory |
Directory path where the user has placed raw FASTQ (forward and reverse reads), metadata.csv, and primerinfo_params.csv files. Default is "data". |
output_directory |
User-specified directory path for outputs. Default is tempdir(). |
tempdir_path |
Path to a temporary directory. If |
tempdir_id |
ID for temporary directories. The user can provide any helpful ID, whether it be a date or specific name for the run. Default is "demulticoder_run". |
Value
A list with paths for data, output, temporary directories, primer, and metadata files.