Welcome @scyllas1981
This is a good question!
Yes, MultiQC does some data massaging around sample keys. This happens wherever it is used (not just in Galaxy).
The tool expects that the first column is always a unique index key, the sample identifier. (It can also remove certain file extensions).
I can think of a few ways to get all lines displayed, and the easiest could be simply adding in an “index” column as the first column. The tools used could be:
Add column** to an existing dataset(with the Iterate? toggled to YES)- Then rearrange the columns with
Cut columns from a table- FAQ: Beware of Cuts – the
Advanced Cuttool will not work for this.
- FAQ: Beware of Cuts – the
You could also make the column more meaningful. The important part is that the key is unique. If you are new to Text Manipulation in Galaxy, these tutorials can help you to get oriented. Not all tools are included but you can usually search with common utility names then find help on the tool form directly. Please ask if you have questions!
I hope this helps and we can follow up more! 