depictio Depictio dashboard for sarek: your feedback wanted Hi all! 👋 I am building Depictio, an open-source platform from EMBL to explore pipeline results without writing a Shiny or Streamlit app each time. A pipeline gets a dashboard template: a short definition that turns the outputs of any run into an interactive dashboard. I am now sharing it more widely, so I would like the view of sarek users and developers. ✨ What it does • MultiQC reports (aggregated across runs) next to result tables, images, phylogenetic trees, maps... with linked filters • Reusable: point the template at any new run of the same pipeline and you get the same dashboard • Fully editable: modify any dashboard from the GUI or in YAML, so the template is a starting point, not a constraint • Versioned, with comments and annotations on any component • Runs as a Python package, with Docker Compose or on Kubernetes, and can serve as a companion web app for a publication 🔍 For sarek: coverage and sex check, variant yield per caller, call quality, concordance between callers, SnpEff consequences, the genes carrying the calls and a locus view, next to the MultiQC report. 👀 What I need: I have built 25 templates and want people who really use these pipelines to review and criticise them. What is useful? What is misleading? 👉 Dashboard: sarek dashboard (no account needed) 💬 Comment on the dashboard (Google sign-in) or in the GitHub discussion dedicated to sarek. ⭐ A star on the repo is welcome if you find it useful. Thanks! 🙏 🎤 In you're interested in the project, I was speaking about Depictio at the Nextflow Summit (session page), and the recording will be available in the coming weeks.

Hi, very nice! The sarek dashboard doesn't load though:

Hi @Tania Wyss! 🙂 thanks for noticing, I made a quick update yesterday and that changed the id of the dashboard, this is fixed!

How would samples of different type mix in the report? If you give the pipeline paired samples, it will process the germline samples individiually using germline. callers, but also does paired calling.

Hi @Rike Hanssen sorry for the delayed answer! 🙂 Good point. and was actually curious to get feedback on this! Thanks, that's exactly the case I was wondering about. Right now the dashboard it only covers germline, but I'd rather not split a mixed run into two dashboards, since it's the same patients and the same QC. I'm currently working on that but the plan would be: the germline calls (normals included) go in the germline tabs, the paired and tumour-only calls get somatic tabs that appear only when there are tumours, and every patient is labelled as paired, normal only or tumour only so you can filter by that. For paired patients, I'd add a tab putting the normal's germline calls next to the somatic ones. Would that work the way people usually look at these runs?

that sounds sensible to me. agreed that it shouldn't be two different dashboards as you would want to be able to quickly compare both

Hey folks 🙂 depictio loading The sarek dashboard just got an update @Maxime Garcia @Rike Hanssen 🔍 Genome browser (JBrowse 2), the main feature of 1.20: read depth and reads on one axis. Docs, with examples 🆕 Reworked Overview, gene UpSet coloured by caller, an (i) on each chart that explains how to read it, a colour key in the study card. The dashboard is now on the 3.11.0 template, with a new Structural variants tab. A second dashboard on a tumour/normal run opens the Somatic tabs (somatic calls, copy number & MSI, germline vs somatic). sarek dashboards: germline run and tumour/normal run @Rike Hanssen!

where can I see the jbrowse view?

In the Locus tab! 🙂

I expected it under coverage. It’s a bit hard to find

Happy to get feedback Rike ! 🙂 UX wise how would you like the JBrowse to be more easily accessible ? Floating + redirection to be always accessible ? Additional button to redirect to it ? Tab name change ?

I was thinking for a local usage on a secure ie offline cluster

Offline would work as well except for some tracks on Jbrowse that won't be displayed as fetched externally > this can be solved by caching/downloading them upfront and referencing the local paths