and what's the default kraken2 db in viralrecon?

if I understand the workflow correctly, it's using a human only database then keeping anything that is unclassified (non-human).

@Ammar Aziz right now the default functioning of kraken2 in viralrecon is set through these params:

kraken2_db                   = '<s3://ngi-igenomes/test-data/viralrecon/kraken2_human.tar.gz>'
    kraken2_db_name              = 'human'
    kraken2_variants_host_filter = false
    kraken2_assembly_host_filter = true

This means that: • For mapping+variant calling it WON'T remove host reads, just perform kraken2 to calculate host reads statistics, for example to know how well or bad amplicon primer enrichment worked. You can change this behaviour by changing

kraken2_variants_host_filter = false

to

true

• For de novo assembly, it WILL remove host reads prior to assembly (keeping anything that is unclassified) • The default host database is human, but by providing another kraken2 database through

kraken2_db

, you can use anyother host genome. You can even create a multiple host genomes database. For arboviruses we use a mixture of mosquitoes and vero (African Green monkey) genomes, as they are extracted from mosquitoes and then cultivated, and we find both genomes in the sequencing reads. Hope this solves your doubt!

That does help thanks. I'm not running amplicon data (probe data), actually similar to Sam above I am running twist. @Sam Wilkinson what did you end up suggesting to collaborators?

They seemed to be getting reasonable results with viralrecon so they stuck with it I think

That's good to know at least. I wish the more params were exposed...

I've been thinking about that! @Ammar Aziz @Sam Wilkinson. nf-core/bacass contains several

<software>_args

params github.com/nf-core/bacass/blob/…/nextflow.config#… that can be use through CLI. If it makes viralrecon easier for the community I can think about the most important and customizable softwares through the pipeline and expose their params in a more general way, along with the already defined specific ones (min_depth, min_allele_frequency...). I'll try to think about a good way to do it and discuss it in the next viralrecon development meeting!

Hello team! Tomorrow we have the viralrecon regular meeting! Can you react to this message if you are planning to come¿

Hello team! Tomorrow we have the viralrecon regular meeting! Can you react to this message if you are planning to come¿

message has been deleted

Hello team! Tomorrow we have the viralrecon regular meeting! Can you react to this message if you are planning to come¿

message has been deleted

Might be of interest to the viralrecon team, France has their own HIV DRM algorithm: hivfrenchresistance.org

Hi team! As requested by some members, we will have a meeting tomorrow too!

Soo tomorrow 17 September, at 15 CEST we will be meeting in workadventure to have a development meeting. We will have another one next week too!

message has been deleted

Hello team! Tomorrow we have the viralrecon regular meeting! Can you react to this message if you are planning to come¿

message has been deleted

Hello viralrecon team! Next week I'll be on vacation so if you need a meeting tomorrow, react to this message please!

We will have a meeting at 15 CEST today for those of you that need help or to clarify doubts with the pipeline development!

message has been deleted

depictio Depictio dashboard for viralrecon: 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 discussed an earlier version with @Sarai, but the project has evolved a lot since and I am now sharing it more widely, so I would like the view of other viralrecon users and developers too. ✨ 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 viralrecon: per-sample QC, coverage per window and per amplicon, every variant call with its effect and allele frequency, and Pangolin lineages with Nextclade clades, 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? 👉 Dashboards: Illumina run and Nanopore run (no account needed) 💬 Comment on the dashboard (Google sign-in) or in the GitHub discussion dedicated to viralrecon. ⭐ A star on the repo is welcome if you find it useful. Thanks! 🙏 🎤 I am also presenting it today at the Nextflow Summit (virtual agenda) if you're interested in the project.

Hello viralrecon team! As I've been on vacation last week, if you need a meeting tomorrow to discuss your doubts or PRs, please react to this message!

Hello viralrecon team! Our next meeting is tomorrow at 15:00 CEST. @Thomas Weber will be presenting the changes in #C0AFS06G9HR for viralrecon! React to this message if you’re planning to join, so we have an idea of who’ll be there. 😊

Hey team, I am updating the freya version at the moment in modules and will open a PR to viralrecon shortly. Do you have an ETA for the next release already? reason I am asking is, that the current freya version is causing various failures for us, and I'd like to determine if we should work from a git commit hash for a while that has the freya bump or can wait for a proper release

@Lili Andersson-Li @Anna Norén I can meet you both tomorrow, as I don't have meetings. On Thursday and Friday is impossible for me as I'll be teaching in a training. Let me know a time that suits you.

I opened a PR to fix the conflicts with the template update and explained a little bit the snap changes: github.com/nf-core/viralrecon/pull/624 Can I have a review please??

@Lili Andersson-Li @CJ Jossart I merged the latest template update PR. Just your you to remember to update your own PRs

Adding a new variant caller lofreq (marking indels) to

viralrecon

is ready for review: github.com/nf-core/viralrecon/pull/629

Hello team! Tomorrow we have the viralrecon regular meeting at 15 CET! Can you react to this message if you are planning to come??