Hi @fabrice
To input paired end data, try placing your data into a paired-end collection folder: List of Pairs. These smart folders can contain one or many samples. You can build that quickly now, then next time, you can load the data at the start inside of a collection.
How to is in a video here. ā Why collections?
Many of the updated tool forms will now require collections for samples based on paired data. This is for both scientific (confirming intact pairs) and technical reasons (parameter complexity).
But please know that we try to host all prior versions of tools ā and while you can navigate to these for reproducibly reasons (or reference them in workflows), you can also choose them if you just prefer how one of them functions.
-
We have had a few a prior discussions about this situation so far ā I just relabeled this one to make it easier to find. 
ā Bowtie2 -- Paired end samples? Use a List of Pairs collection! - #5 by wm75 -
Then, topics like this one have examples for more complex manipulations (not needed for what you are doing, but maybe a useful reference later?). ā Troubleshooting: fastq read content and shape. Collections, interlaced/interleaved reads, quality assurance - #8 by jennaj
Iām glad you asked about this! Please review the resources above and let us know if you have any questions or if you would like some assistance with getting your sample organized. Thanks! 