Rnohup: submit a bash commands into the qsub...
In ZhenWei10/RbashGEO: GEO raw data processing in bash.

1	Rnohup(command, output = "X")

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,"_hisat2") )
}