Combining several MultiQC reports into one


Currently my pipeline generates MultiQC reports sample by sample. But for analysis purposes I would like to combine several MultiQC reports into one.

I believe that there is no current sollution for this request? Maybe you have it in development and will add this feature to 2.0 release?

Hi @quantumkisa,

You already came to the correct conclusion - no solution for this right now I’m afraid, apart from re-running MultiQC with the combined source log files. But it is planned, as part of a major refactoring:

It’s a massive task so it may take some time, so don’t hold your breath. But I’m hoping that we can get to it this year. Feel free to follow the GitHub issue to get updates on our progress.


Thank you!

I believe that using MegaQC will help me with that, but I am not sure if it is still in support. Last update was in 2020.

That’s not completely true, the last (non-cosmetic) commits were in June 2023: Commits · MultiQC/MegaQC · GitHub

MegaQC is in use by at least a handful of sites, but it is purely a community project at this point and is not officially supported by Seqera / anyone. It is somewhat functional, but very buggy and incomplete in places.

Thank you!