Thank you for this! I was able to demultiplex my paired-end sequences.
However, I had to change the file names of my files, A_R1.fastq.gz and A_R2.fastq.qz, to “forward.fastq.gz” and “reverse.fastq.gz”.
Are there any future plans to incorporate the ability to specify your forward and reverse files and be able to have them named whichever way?
We don’t have any concrete plans right now, but this is similar to the problem faced by multiplexed data, where we have a large directory we need to populate. I could see generalizing the concept of a manifest file being a possible option. Of course this situation would be much easier to design around if we had a proper graphical interface, but that’s also a ways off.
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