The “direction” doesn’t necessarily matter in that manifest, so long as it is all one, or all the other (forward or reverse) when importing single-end reads. Since you have demultiplexed reads, go ahead and import them as single-end, then trim the barcodes using q2-cutadapt. You might need to set up a few parameters in that step in order to catch the barcodes in both directions. Let us know how that goes for you! 