Remove redundant sequencing runs argument

generation.sh

@@ -19,5 +19,6 @@ fastq=".fastq"
 filename="sequence"
 prefix="curesim_"
 
-Rscript src/repertoire.r "$sequences" && java -jar tools/CuReSim.jar -n "$sequencing_runs" -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
+Rscript src/repertoire.r "$sequences" "$sequencing_runs"
+java -jar tools/CuReSim.jar -n "$sequencing_runs" -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
 rm "$data_directory/log.txt"

src/repertoire.r

@@ -22,8 +22,7 @@ process_data <- function(repertoire) {
     "d_sequence_alignment", "j_sequence_alignment"
   )
   data <- repertoire[, columns]
-  dna_sequence <- Biostrings::DNAStringSet(data$sequence)
+  data$sequence <- Biostrings::reverseComplement(data$sequence)
-  data$sequence <- Biostrings::reverseComplement(dna_sequence)
   save_data(data)
 }
 
@@ -35,6 +34,6 @@ parse_cli_arguments <- function() {
   return(args[1])
 }
 
-args <- parse_cli_arguments()
+arguments <- parse_cli_arguments(commandArgs(trailing))
-repertoire <- generate_repertoire(number_of_sequences = as.integer(args[1]))
+repertoire <- generate_repertoire(number_of_sequences = arguments[1])
 process_data(repertoire)