For when you are back Sofia, I've commited the changes left over from my previous review for you, leaving you with just the last couple of nf-test fixes

(and resolved a merge conflict)

Otherwise I don't see anything else for now so I'll catch up on some other things 🙂

Hi, I recently ran the pipeline to analyse faecal mouse samples. I was just wondering why Host-Read Removal is optional if it is supposed to improve performance and reduce false positive read assignment. In which cases or studies are you not supposed to know the host? Many thanks for your answer!

Goodmorning! I will be at workadventure until 10 today

I will try and join for 30m in 10m

If there is anything I can help with?

i am joining also

I'm on kid duty today, so I can't join

Goodmorning, I will be in workadventure in ten mins

I am in the workadventure

Hey all, when looking at centrifuge's github, realized it has been superseded by centrifuger github.com/mourisl/centrifuger. Is updating centrifuge to centrifuger or adding centrifuger as a seperate option for taxonomic profiling in the works/planned?

Hey, quick question. I need the final number of reads of the analysis ready fastqs, although I did not output the reads themselves, so I can't verify this. Is this the same as the "reads_unmapped" column in the multiqc_samtools_stats.txt file in the output?

or "result reads" in bbduk.txt? (all from the multiqc/data output)

I made a change to

krakenuniq

which may affect how taxprofiler is passing args to it. Specifically the

--preload-size

coming in via

ext.args

should be checked and moved to

ext.args2

if used anywhere. github.com/nf-core/modules/pull/12912

Goodmorning! I will be at workadventure at 9.15

goodmorning, also joining

Goodmorning, I will be at workadventure at 9.15.

And from Salzberg lab, so generally should be petty good

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Goodmorning, I am at a conference today and will not join the dev meeting.

❌ taxprofiler/test_full failed 😿 Run Name dreamy_roentgen Duration 33.1s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/taxprofiler>, projectDir: /.nextflow/assets/.repos/nf-core/taxprofiler/clones/3b8595987edec10bd4aff0d9dcecfb93c850871e, commitId: 3b8595987edec10bd4aff0d9dcecfb93c850871e, revision: dev, startTime: 2026-10-08T08:24:40.927710738Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/taxprofiler>' -name dreamy_roentgen -params-file '<https://api.cloud.seqera.io/ephemeral/i0jj1FESutbRYIoUj-pZJg.json>' -with-tower -r dev -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.6, build:12646, timestamp:09-07-2026 18:49 UTC, preview:nextflow.NextflowMeta$Preview@6c6fdf5d, enable:nextflow.NextflowMeta$Features@187c8f96, strictModeEnabled:true, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/taxprofiler/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/taxprofiler>' -name dreamy_roentgen -params-file '<https://api.cloud.seqera.io/ephemeral/i0jj1FESutbRYIoUj-pZJg.json>' -with-tower -r dev -profile test_full

Oct 8, 2026 at 8:25 AM

depictio Depictio dashboard for taxprofiler: 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 taxprofiler 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 taxprofiler: sequencing depth (Nonpareil), the community each classifier reports, diversity, agreement between classifiers and the genome identity of sylph matches, 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: taxprofiler dashboard (no account needed) 💬 Comment on the dashboard (Google sign-in) or in the GitHub discussion dedicated to taxprofiler. ⭐ A star on the repo is welcome if you find it useful. Thanks! 🙏 🎤 I was speaking about Depictio at the Nextflow Summit (session page), and the recording will be available in the coming weeks.

Goodmorning! I will be at workadventure at 09.15 today

Hello, all! I'm diving back into the world of shotgun metagenomics and utilizing taxprofiler. I'm interested in doing some downstream analysis to get statistical information on the alpha and beta diversity of each sample as well as my sample groups as defined by metadata. I had previously employed a method similar to the one reported here birgitrijvers.github.io/qiime2-diversity-tutorial. In that tutorial, they import the Kraken2 or Bracken tables into QIIME2 to make use of the diversity tools and visualizations it produces. I know some folks are working on tools like Depictio to produce interactive dashboards from the data, so I'll look into that as well. But in the meantime, I'm curious if the link I've shared sounds like a good plan for translating the output from taxprofiler into stats and visualizations, specifically those related to diversity? Thanks for any insight y'all can share! 🙂

@Sofia Stamouli @Haris Spyridis After the next nf-core tools patch release, I'm planning to do a release of createtaxdb - are there any other taxprofiler level changes I should be aware of? Otherwise, @Haris Spyridis I've rereviewd the strict-syntax PR (with suggestions for improvements - although not-blocking); and ping me once sourmash is ready 🙂

This PR has been created by stev004 as it seems that there have been missing files in the

deacon_filter

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