Hi! I was wondering about the plan to reintroduce MultiQC https://github.com/nf-core/oncoanalyser/issues/81 Is this still the plan? and if so, any idea of when?

Hi @Eva Caceres, there is still a plan for reintroducing MultiQC and some work has already been done for this

For me MultiQC is central in the nf-core ecosystem, especially for bioinformatics pipelines

Got it, very much agree on all those points! And if there are any tool outputs / metrics that might be especially useful, please let us know

Hi thanks for the info! these are great news 🌟 Our internal automated QC checks for the different pipelines we support rely on the output from multiqc. It’s quite standard and makes things simpler. So it would be great to have this. We use quite standard metrics but I will check the ones we currently use and let you know. Thanks a lot 🫶

Hi folks, just echoing the support for MultiQC! Glad to see discussion around its integration. From our side, MultiQC support would be very valuable for standardizing QC reporting, and it would be a key factor in adopting oncoanalyser in our pipelines.

@Stephen Watts I finally had the time to look into this, we are interesting in metrics coming from the following files:

- purple/*puple.qc
- purple/*purple.purity.tsv
- amber/*amber.qc
- bamtools/*_bamtools/*bam_metric.summary.tsv
- bamtools/*_bamtools/*bam_metric.flag_counts.tsv

Then we are also interested in other metrics that are not computed at the moment but that would be relevant, like for example to assess AT/GC biases.

Thanks @Eva Caceres, as a starting point, does this provide the general information you would be interested in?

definitely! this is great 🌟

Looking good

Thanks for pointing that out, I’ll make sure to include this information!

This is a great start!

Eva, Ben -- do you have one QC report for both tumor and normal samples? We've been going back and forth on this. As the expected metrics are so different it makes it difficult to identify outliers at a glance.

Hi! we currently have one QC report for all samples, including: tumor and normal samples for TN analyses and only tumor samples for TO

Jon has implemented sample based MultiQC reports in #CE8SSJV3N, and we have tag based MultiQC reports in #C06PHJM0Y3D, so definitely doable

Hi, our use case may be a little different, we separate T+N and TO. But regardless of how we run them, there is just one report for all samples for that run.

Thanks for the feedback, I’ll aggregate metrics / information into a single report as the first pass

Hi! This would be great to have! Do you have a timeline for when this will be implemented?

hi @Stephen Watts, I'm sure you must have many things on your plate, but am wondering if it is reasonable to think that MultiQC integration would be included in the next release?

Signs are looking positive but I'll leave that for Stephen

It’s been implemented and is planned to be included in the next release

Fantastic, thank you Stephen!