R/run_trimmomatic.R

In uashogeschoolutrecht/structural_colours: Package For Project Structural Colour

#' This function uses trimmomatic to trim input fastq files and outputs them to the specified base dir. Please supply input as character type.
#'
#' @param mode Single end ("SE") or paired end ("PE") fastq file(s) input, default = "SE"
#' @param f1 Absolute path to fastq read one, supply single end file / direction one PE here
#' @param f2 Absolute path to fastq read two, only use for second paired end file not for single end file, default = "". (single end)
#' @param prefix Name of prefix for output files. Default = "trimmed"
#' @param phred Phred scale, e.g. 33 / 64. Default = "33"
#' @param minlen Minimum length of reads to keep, default = "90"
#' @param outdir Absolute path directory to store output files, default = "./trimmomatic". Directory will be made my script.
#' @param window Sliding window for quality trimming to use, default = "4:15"
#'
#' @return Creates trimming output files in specified directory
#' @export
#'
#' @examples
run_trimmomatic = function(mode = "SE",
                           f1,
                           f2 = "",
                           prefix = "trimmed",
                           phred = "33",
                           minlen = "90",
                           window = "4:15",
                           logfile = "trimmomatic_log.txt") {
  if (mode == "SE") {
    args = c('-jar', '/Trimmomatic-0.39/trimmomatic-0.39.jar',
             mode, f1, prefix, paste0("MINLEN:", minlen),
             paste0("SLIDINGWINDOW:", window),
             paste0("-phred", phred))
    log = sys::exec_internal("java", args)
    trim_stats = sys::as_text(log$stderr)[4]
  } else {
    args = c('-jar', '/Trimmomatic-0.39/trimmomatic-0.39.jar',
             mode, f1, f2, "-baseout", prefix, paste0("MINLEN:", minlen),
             paste0("SLIDINGWINDOW:", window),
             paste0("-phred", phred))
    log = sys::exec_internal("java", args)
    trim_stats = sys::as_text(log$stderr)[4]
  }
  return(trim_stats)
}