A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Ambitious PR to add a new MultiQC variant.
<https://github.com/nf-core/modules/pull/9587>

So if I understand well, this is tiny modification on the regular MultiQC, on which you add an extra input channel and the plugin so that it can run nicely on the Illumina rundir

Yep, that’s it
Container including the plugin + new input and some staging magic to make it work

And we would probably want to include this in more than 1 repo

thinking about this convo -&gt; <https://nfcore.slack.com/archives/C06PKQ25BJT/p1761435629253459>

cc <@UE4L64T4G>, just wondering the same question again
For me if we manage to automate nicely the update, I wouldn't mind having multiple flavors of the multiQC with dedicated plugins, but it's a slippery slope

and what about multiqc with multiple plugins?

If it's just a different container (like it is for xenium) then I think a local patch to switch out the containers is fine

In this case, there needs to be a bunch of extra logic around inputs and data structuring for MultiQC to handle the report generation properly

So it sounded to me like a separate module was probably warranted, as that's a bit exceptional (usually MultiQC "just works" without any faffing around like this)

Whether it's a local or a shared module.. :man-shrugging::skin-tone-2:

> If it’s just a different container (like it is for xenium) then I think a local patch to switch out the containers is fine
There’s no need to patch, you can fix it in config