to deal with the fact that there are now other directories in the $input_directory

Depends what you mean by "deal with". If you want to ignore directories, then code similar to what you have will work. If you want to recursively process the directories then you should probably use File::Find.

But without much luck

That's really not a very good description of the problems that you are having.

Piecing together your code:

opendir(DIR_A,"$input_directory") or die $!;

INNER_A:
while(my $job =readdir(DIR_A)){
  chomp;
  next unless -f $job;

  # other stuff I assume
}
[download]

Firstly, you're unnecessarily quoting the $input_directory variable in the "opendir" call.

Secondly, you're making the most basic error in your use of opendir/readdir. It's so basic that it's described in the documentation.

Oh, and what's that "chomp" there for? More cargo-cult programmming?

Please try to do a little bit of your own research before posting questions here. The Perl documentation set is really good. It _will_ answer a large proportion of your questions if you give it a chance.