#' @title submit bash commands by user defined number of chunks
#' @param Commands the vector of commands we want to submit (do not need to include nohup portion).
#' @param Chunk number of parallel processes.
#' @param Name the names of the script and output files.
#'
#' @examples
#'
#' file_names <- grep(".fq$", list.files("/home/zhen/PAR-CLIP/Trim"), value = T)
#' commands <- paste0("fastq_to_fasta -i ",file_names," -o ", gsub("fq","fa",file_names),"{\}n",
#' "fastx_collapser -i ",gsub("fq","fa",file_names)," -o ", gsub("trimmed.fq","collapsed.fa",file_names))
#' Chunk_submit(commands,6,"collapse")
#'
#' @export
Chunk_submit <- function(Commands,Chunk = 6,Name) {
mapply(function(x,y)write(x,y),
split(Commands,
cut(1:length(Commands),Chunk)),
paste0(Name,"_",1:Chunk,".sh"))
system("chmod +x *.sh")
commands_submit <- paste0("nohup ./",paste0(Name, "_",1:Chunk,".sh")," > ",paste0(Name, "_",1:Chunk,".out")," &")
sapply(commands_submit,system)
}
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