Rtrim_galore: generate a command for trim_galore in R
In ZhenWei10/RbashGEO: GEO raw data processing in bash.

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Rtrim_galore(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))

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") )
}