Thanks for posting and welcome to the community! You’ve started us off with a really excellent question
To summarise (please correct me if I’m wrong), the problem here is that you want table-specific sample name cleaning. To clean + collapse sample names in General Stats, but not in other tables.
This is not currently possible within MultiQC, but it could be interesting to do. I think it’s basically the same as the ancient GitHub issue #542 from way back in 2017:
I suspect that this would be the best solution , @vlad.savelyev maybe we can take a fresh look at this and see if we can move it up the roadmap a little.
Another approach would be to look at how this data is getting into the report in the first place, from the nf-core/sarek pipeline. @maxulysse / @FriederikeHanssen - have you guys had any similar requests in the past, or any ideas on this topic?
, @vlad.savelyev maybe we can take a fresh look at this and see if we can move it up the roadmap a little.