R/run_fastqc.R

In GREP2: GEO RNA-Seq Experiments Processing Pipeline

#' QC report for each fastq files using FastQC
#'
#' \code{run_fastqc} HTML report of each fastq files using FastQC.
#' You need to install FastQC from
#' \url{https://www.bioinformatics.babraham.ac.uk/projects/fastqc/} 
#'
#' @param destdir directory where all the results will be saved.
#' @param fastq_dir directory of the fastq files.
#' @param n_thread number of cores to use.
#'
#' @return HTML report of the fastq files under fastqc directory.
#' 
#' @examples
#'
#' fastq_dir=system.file("extdata","", package="GREP2")
#' \donttest{
#' run_fastqc(destdir=tempdir(),fastq_dir=fastq_dir,
#' n_thread=2)
#' }
#'
#' @export
run_fastqc <- function(destdir, fastq_dir, n_thread ) {
    cat(paste("Running FastQC... ",Sys.time(),"\n",sep=""))
    fastq_files = list.files(fastq_dir, pattern=".fastq$", full.names=TRUE)

    if(!dir.exists("fastqc")){
        system(paste0("mkdir ",destdir,"/fastqc"))
    }
    system(paste0("fastqc -o ",destdir,"/fastqc/ --threads ",n_thread," ",
        fastq_files))
}