Is it possible to pipe inputs to trimmomatic. Similarly can I redirect the output to stdout ?
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In Unix-like operating systems it is possible to redirect any input or output; if the program is missing this option, simply use "/dev/stdin" and "/dev/stdout" as the filenames. The only problem is if the program needs to make multiple passes through the input or read it nonconsecutively, but I assume Trimmomatic doesn't. -
Well, the "problem", as it were, with Trimmomatic is that it wants to input 2 files (R1 pre, R2 pre) and output 4 files -- R1 post, R2 post, R1 unpaired, R2 unpaired. Given that 4 outputs are required then simple piping will not work. I have not tried it but you could probably set up FIFOs for the 4 files.Comment
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