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Hi, greeting from <#C08E444AHSR|> channel:wave:. W...
# multiqc
y
Hi, greeting from #C08E444AHSR channel👋. We are currently porting DROP to a nf-core pipeline. In the original DROP pipeline, we have an internal tool to render qc plots in html report,s and this could be replaced nicely by multiqc. (I already played with multiqc custom contents and found it very nice!) I have one question ❓ though -- we have different groups in the samplesheet and different samples can belong to different groups (and trigger different tools) and ideally we would like to generate for each group ONE html report. But usually in nf-core pipelines, multiqc runs in the end and generate one report for all tools. Do you have any suggestion there?
j
There is no reason why you couldn't generate multiple multiqc reports per group
i.e. it's not a fixed rule to have a single report 🙂
You just need to batch the files appropriately in your channel so it runs multiople times (and make sure the name of the final report is distinct)
y
Makes sense! Will try it out. Thanks!
p
You could even do both - detailed per-sample reports and then a run-level one summarising key metrics
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m
You may want to look at the 
dev
branch of #C06PHJM0Y3D for inspiration. There we (actually just @Adrien Coulier) has already implemented a nice tag-based approach to group samples into multiple reports (e.g. per flow cell, per project or tag).
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❤️ 1
y
Hi, coming back to this thread 🙂 I was able to run MultiQC multiple times to get different reports. Thanks a lot for the comments and #C06PHJM0Y3D for inspiration. One thing I would like to have is an index page for my many many multiqc reports. So I came up the idea to use mutliqc again on all mutliqc report channels (mix all MULTIQC_x.out.report.toList()) and add 
_mqc
as suffix, so that it works with custom content. This all works but the page does look so great with the two navigation bars, and the right navi bar does not roll and is also not clickable to hide. It seems there is also no option in multiqc to hide it completely?
inception 5
doge inception 3
p
wow, I'm amazed that this works at all
No this is not a thing that is supported. MultiQC is designed specifically to be multi-sample, so combining single-sample reports kind of goes against that design philosophy
So my advice would be to instead combine all of the inputs and generate a single report with everything in it
I appreciate that it'll be difficult to get the navigation you're after, as you want multi-level hierarchy. Also if you're embedding images into the reports (looks like it) then the filesize could get huge and it might crash the browser.
So better to think about how to reshape the data and do plots that are human-readable for comparing multiple samples in the multi-sample report. More work, but the end result will be more useful.
y
thanks Phil. In #C08E444AHSR we make some plots just on group level and per subworkflow. So I made multiqc reports on all group/subworkflow combinations and they are all custom contents. That is why i initially think an index page would be nice. I agree this is indeed quite different from common multiqc usage.
p
Yup, understood 👍🏻
I think my advice still stands - in a perfect world, I'd argue that the pipeline-level report would have its own plots to give the best overview possible. Then people could dig into the group level reports for more detail if needed / as appropriate.
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s
if you need something more advanced than MultiQC then maybe its time to start thinking about building a formal web app for it. Something in R Shiny or Python Flask / Django etc. might be worth looking into...
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