you mean something like this:

#!/usr/bin/perl

use strict; 
use warnings;

open DIR, "/path/to/dir/" or die "cannot read directory\n";
while (my $file = readdir DIR) {
    if ($file =~ /Run\d+_(BC\d+--BC\d+).fastq/) {
        my $barcode = $1;
        my $new_file = $file;
        $new_file =~ s/\.fastq/_edit.fastq/;
        warn "ediiting $file with barcode $barcode in $new_file\n";
        open (my $in, "<", $file) or die "cannot read $file\n");
        open (my $out, ">", $new_file) or die "cannot write $new_file\n";
        while (<$in>) {
            s/^@/\@Barcode$barcode\_/;
            print $out $_;
        }
        close $in;
        close $out;
    }
}
closedir DIR;