When I upload 10 pair-end sequencing sample, I missed a R2 for one sample, and uploaded after. How to put that sample in the right position in history? because later steps require multiple samples processing simultaneously, which accords to the order in history; this amended one mess up the order.
Recommended: Put the read data into a paired-end collection, and run that through the processing. You’ll set the pairing when the collection is created, so the order in the History won’t matter.
Hack: Use the “Copy Datasets” function under the History menu. You can do this a few times, putting copies into some other history in the order that you want them. Copies of your own data are “clones” and do not consume extra quota space. If the original history only contained those data, you could even purge it once everything is copied over, to clear up the clutter.
Hope one of those works out for you