Question 2

Consistent reporting GUI is one reason, also reporting analysis / QC metrics from multiple tools for a single sample is likely still useful. Other things: • If you have MultiQC support, users can always run it manually after running the pipeline multiple times, outside of Nextflow • Doubly so when we get around to implementing standardised intermediate files • If the summary / QC data is in MultiQC, it's easier to use for downstream use. For starters, all metrics are dumped in a standardised format in

multiqc_data

(yaml/json/tsv) so nice and easy to load for downstream scripts. Also, soon Jupyter notebook integration should get nicer. Then there's MegaQC and whatever else might come one day in the future 🤫 • It's a nice place to report software versions used by the pipeline alongside any QC, as the template already produces MultiQC-compatible files for that.

Very cool, I am now sold on the idea! Also MegaQC is just a fantastic name for that webapp 😁