Simply use the foreach loop to parse each file and redirect the output to output directory

my $output_dir = 'output/';

foreach my $file (@files) {
        print $file . "\n";
        #Parse the file here
        open(FH, '>>', $output_dir.$file ) or die "Unable to open the 
+file: $!";
        print FH "Output goes into output directory with the same file
+ name\n";
        close(FH);
}
[download]

I tried it that way, it doesnt work, The three folders code, input and output are in the same level in the directory structure (The folders are in a single folder ) and I need to output the result of the pipeline into the output folder with the names unchanged. sadly the code you provided is not working.

hi perlmonks007, could you please post the code you have tried ? so that I can assist you better.

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All is well