G'day NewLondonPerl1,
This looks like a simple assignment to me:
#!/usr/bin/env perl
use 5.010;
use strict;
use warnings;
use Getopt::Long;
my %opts;
GetOptions(\%opts, qw{conf|c=s});
my $master_conf = $opts{conf};
say $master_conf;
Here it is in action:
$ pm_getopt_var.pl --conf conf_value
conf_value
Depending on where you do the assignment, you may want:
$master_conf = $opts->{conf};
The only place in your posted code that you mention $master_conf is in what appears to be a standalone piece of code with no obvious connection to other parts of your script:
my $json_data = extract_json("$master_conf");
Where were you intending to declare this variable? Where were you intending to assign it a value? I suspect one problem you have here is that you can't see the wood for the trees: probably 80% of the code you've posted has nothing to do with the issue at hand. Try making a simple, cut-down version of the script; when that's working, add in more complexity.
From the code you've posted, my best guess as to what you want is something like this:
# shebang and use <whatever> lines here
my $opts = getoptions();
my $master_conf = $opts->{conf};
# do something with $master_conf here (validation perhaps)
my $json_data = extract_json($master_conf);
my $decoded_json_obj = decode_json($json_data);
# do something with $decoded_json_obj here
# subroutine definitions here
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