anyone avail for this? thanks!

Not for now, but could you add this module directly to multiqc, so that the custom processing is not necessary?

Yes, I can do that, but still working on what's the best way to include rMATS results in multiQC. At the moment, I've just added the summary table. Any suggestion is very welcomed!

I have absolutely no idea what the tool outputs 😉 @Uri David Akavia I think was working on rmats modules, maybe he has some insight

Ok, so for the time beings, I won't include it in the report for rnasplice. I think it's better finishing the refactor which is being a lot of work and it's still not completed.

I glanced at the PR. This PR has refactoring, which is extensive, and the addition of RMATS. I would think it should be two separate PRs - if you want, I can review the RMATS related modules and files. However, if you're going to take it out of the PR for now, the question becomes moot

Ok, let me split into 2 PRs, so the most urgent is to fix the output dirs

yes, multiqc is generally sample based, that is true

I'll do thanks! And thanks for the review too! ☺️

some modules aren't sample based - eg. demultiplexing is lane-based

Great! Let me find some time to work on this module then. I'll have a look at demux to understand the best approach for RMATS. Thanks!

There's a new-ish skill in the repo that should help if you have an LLM at your disposal..