Hello @Orange_Pomeranian
Yes, MultiQC is very picky and does some automatic interpretations of the sample file names that isn’t super obvious. This happens everywhere, not just Galaxy, so you’ll find lots of discussion online with a search like “multiqc missing samples”.
I have a demonstration workflow that performs this correctly. Would you like to compare to see what I did?
- Flattening before FastQC is the import part, since that avoid the “duplicated” sample names issues.
- You’ll also want to run through a step to rename the element identifiers in either your “original” OR “trimmed” read collections to avoid a conflict at that level. I did the latter.
- A bit complicated! But you’ll see what I did and understand better with the example.
You can also search at the UseGalaxy servers with that same term under the Activity bar → Workflows → Public workflows tab to find it. If you are working someone else, you can still review it in context. Download a copy, then import at your other server.
Hope this helps! 