Try replying again now.
And a note: it is hard to tell what is going on in a workflow without seeing the actual shared workflow. The graph is just one part of it. See my example for the renaming portions. The graphic in the direct message was missing some steps compared to the one I shared – in particular, the element renaming steps. Be sure to notice how I applied those names – the common ways people may rename will be part of what I meant here:
Example: “trim” added on will get removed, but something like “trimx” will pass through.
How this works is how it would work if these files were all in folders on your computer that are run through the tool, so this is not Galaxy specific, it is part of how the underlying tools parse data to be “helpful”.
Also, be sure to run my workflow on at least two samples so you can see how the results come out. The hidden files will contain all of the intermediate steps in action.
From here, please try to reply again and to include shared data for review. The input + output data along with the workflow runs is a good idea. So, that could be two shared workflow invocations: one for my workflow, and one for yours.
Thanks!