[fastaguy88]

As a scientist who cares about reproducibility, the big difference between the "useless cat" and providing the input file name on the command line is that, in the latter case, the program can capture that file name and reproduce it. That is harder when using stdin.

Many of my programs and scripts start output with the line: # cmd arg1 arg2 arg3 ...

and simply echo back lines that start with '#'. That way, I have an internal record of the program that was run and the data file that was read (as well as previous parts of the analysis chain).

And, 'R' ignores lines starting with '#', so the record is there, but does not affect later analyses.