I'd go for xargs -P here. Except that it can't do input redirection. Perhaps your fastqc tool has an option for that?

# untested
# launches 42 processes at a time
open my $xargs, '|-', qw(xargs -0 -P 42 -n 2),
  qw($fastqc_folder/fastqc)
  or die $!;

for my $file (@files) {
  print $xargs join("\000",
    "--outdir=$fastqc_output_folder",
    "$input_folder/$file"), "\000";
}
close $xargs;
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