I would read in (with glob) the step_X_done file. Read its number, or 1 into a variable $already_done

for my $todo ($already_done .. $final_step){
    do_step1() if $todo == 1;
    do_step2() if (-e step_1_done);
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then wrap the code for each step in separate subs.

Now you can manually delete a "step-file" to have the job start from scratch, or at some spesific step, if you ever need that.