#' @title generate a command for trim_galore in R
#' @examples
#' arg_df <- data.frame(
#' Fastq_file_name = rep("SRR1744126",3),
#' trim_5 = c(16,16,0),
#' trim_3 = c(12,0,12),
#' output_name = paste0("SRR1744126_",1:3)
#' )
#'
#' for(i in 1:nrow(arg_df)) {
#' x = arg_df[i,]
#' Rhisat2(Fastq_file_name = x$Fastq_file_name,
#' trim_5 = x$trim_5,
#' trim_3 = x$trim_3,
#' output_name = x$output_name,
#' Fastq_directory = "/home/zhen/TREW_new_data") %>% Rnohup(.,paste0(x$output_name,"_trim") )
#' }
#'
#'
#' @export
#'
Rtrim_galore <-
function(GEO_accession = "SRR1234567",
fastq_end = ".fastq",
Paired = F,
Phred_cut = 20,
Phred = 33,
fastqc = T,
CLIP_5 = c(0,0),
CLIP_3 = c(0,0)) {
if (length(CLIP_5) == 1) CLIP_5 = c(CLIP_5,CLIP_5)
if (length(CLIP_3) == 1) CLIP_3 = c(CLIP_3,CLIP_3)
if(Paired == F){
Paired_dependent_chunk <- paste0("--clip_R1 ",CLIP_5[1]," --three_prime_clip_R1 ",CLIP_3[1]," ", GEO_accession,fastq_end)
}else{
Paired_dependent_chunk <- paste0("--clip_R1 ",CLIP_5[1],
" --clip_R2 ",CLIP_5[2],
" --three_prime_clip_R1 ",CLIP_3[1],
" --three_prime_clip_R2 ",CLIP_3[2],
" ", GEO_accession,"_1",fastq_end,
" ", GEO_accession,"_2",fastq_end)
}
paste0("trim_galore ","--quality ",Phred_cut," --phred",Phred,ifelse(fastqc," --fastqc "," "),Paired_dependent_chunk)
}
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