Change it to a while loop:

    while (@files) {
    ...
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That should fix your problem, cause it'll only loop as long as there are elements in @files. Whereas yours was actually looping *over* @files, which is a different thing, and not recommended if you're going to be modifying @files (which you did, by using shift).

Alternatively, though, you may want to try using splice:

    push @data, [ splice @files, 0, $num_cols ]
        while @files;
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splice grabs chunks of an array (and can also replace those chunks w/ a list) and increases/decreases the size of the array as necessary. Sounds good for your particular use.