This is not "modified code" since the code you have presented is not Perl at all. However here is just one of the many, many ways to achieve this in Perl.

#!/usr/bin/env perl
use strict;
use warnings;
use Path::Tiny;

my @r = path (shift)->lines;
s/(.*),$/.$1($1),/ for @r[1..$#r];
$r[-1] =~ s/,$/);/;
print @r;
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And if you save it to a file called double.pl here is how it runs:

$ cat input.txt 
module abc(
rist_top_tck,
rist_top_tdi,
rist_top_tdo,
$ ./double.pl input.txt
module abc(
.rist_top_tck(rist_top_tck),
.rist_top_tdi(rist_top_tdi),
.rist_top_tdo(rist_top_tdo));
$
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See the docs for Path::Tiny, s/// and print for more.