#' Run FastQC
#'
#' @description Runs the FastQC tool, a quality control tool for high throughput sequence data
#'
#' @param input List of all of the fastq files, forward and reverse, required
#' @param out.dir Name of the directory to write the FastQC results, required
#' @param threads Number of threads for FastQC
#' @param parallel Run in parallel, default set to FALSE
#' @param cores Number of cores/threads to use for parallel processing, default set to 4
#' @param execute Whether to execute the commands or not, default set to TRUE
#' @param fastqc Path to the FastQC program, required
#' @param version Returns the version number
#'
#' @return A list with the FastQC commands
#'
#' @examples
#' \dontrun{
#' fastqc.path <- "/software/FastQC-v0.11.8/fastqc"
#'
#' # Version
#' fastqc.version <- ""
#' fastqc.version <- run_fastqc(fastqc = fastqc.path,
#' version = TRUE)
#' fastqc.version
#'
#' # Run fastqc
#' reads.path <- "raw_reads"
#' mate1 <- list.files(path = reads.path, pattern = "*_R1_001.fastq.gz$", full.names = TRUE)
#' mate2 <- list.files(path = reads.path, pattern = "*_R2_001.fastq.gz$", full.names = TRUE)
#' # Merge the reads file names
#' all.reads <- c(mate1,mate2)
#'
#' out.dir <- "fastqc"
#'
#' fastqc.cmds <- run_fastqc(input = all.reads,
#' out.dir = out.dir,
#' fastqc = fastqc.path)
#' fastqc.cmds
#' }
#' @export
#'
run_fastqc <- function(input = NULL,
out.dir = out.dir,
threads = NULL,
parallel = FALSE,
cores = 4,
execute = TRUE,
fastqc = NULL,
version = FALSE){
# Check fastqc program can be found
sprintf("type %s &>//dev//null && echo 'TRUE' || echo 'FALSE'", fastqc)
# Version
if (isTRUE(version)){
fastqc.run <- sprintf('%s --version',
fastqc)
result <- system(fastqc.run, intern = TRUE)
return(result)
}
# Set the additional arguments
args <- ""
# Threads
if (!is.null(threads)){
args <- paste(args,"--threads",threads,sep = " ")
}
fastqc.run <- sprintf('%s %s -o %s %s',
fastqc,args,out.dir,input)
if (isTRUE(execute)){
if (isTRUE(parallel)){
cluster <- makeCluster(cores)
parLapply(cluster, fastqc.run, function (cmd) system(cmd))
stopCluster(cluster)
}
else{
lapply(fastqc.run, function (cmd) system(cmd))
}
}
return(fastqc.run)
}
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