R/parse_yaml_paths.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Parse YAML paths
#'
#' @description This function parses YAML paths
#'
#' @param file The file name of the YAML file containing the paths
#'   (default is "inst/paths.yaml")
#'
#' @return A list containing the paths specified in the YAML file
#'
#' @export
#'
#' @examples NULL
parse_yaml_paths <- function(file = system.file("extdata",
                               "paths.yaml",
                               package = "timaR"
                             )) {
  ## Read the YAML file containing the paths
  paths <- yaml::read_yaml(
    file = file
  )

  ## Set the working directory to the base directory specified in the YAML file
  setwd(paths$base_dir)

  ## Return the list of paths
  return(paths)
}