Hi there! I have two quick question: 1. Is there currently a way to call ASV/OTUs for full length 16S amplicons from Nanopore sequencing (SUP Basecalled with latest chemistry)? 2. For epa-ng phylognetic placement is there maybe a resource with some reference trees I could use out of the box (eg a tree and msa from the SILVA DB)? Thanks!

Hello! We are interested in processing sequences from the 515FY/926R PCR primer pair for both 18S and 16S amplicons. This requires a splitting step during the pipeline (if not, the 18S reads are lost as they do not overlap). Is this possible to do in ampliseq? Here is a pipeline describing it, and here is the paper. Thank you!

I'm preparing the pipeline for a new release of the SBDI-GTDB database, based on GTDB R11-RS232. In doing this, I also made sure the pipeline can run phylogenetic placement (using code also available standalone in #C04NLA7QHH9) to the GTDB reference trees optimized for 16S sequences (just speficify `--dada_ref_taxonomy sbdi-gtdb --run_pplace`; phylogenetic placement unfortunately requires quite a lot of memory, ca. 100 GiB). To investigate how phylogenetic placement performs compared to the standard DADA2 methods

assignTaxonomy

and

addSpecies

, see attached html. In short, phylogenetic placement gives a more specific assignment than the sequence composition and sequence identity-based methods in DADA2. Hopefully, this will be available soon in the next stable release of Ampliseq. (PR coming soon, @Daniel Straub.)

PR for the ☝️ database addition: https://github.com/nf-core/ampliseq/pull/1009

Hello! I've sequenced samples with the IDT xGen 16S Amplicon Panel v2 and was trying to analyze our results with the ampliseq multiregion option, but I keep getting empty files after dada2 (too few reads after trimming), so SIDLE starts running with no input. As input I used the primers as provided by the manufacturer one for each region, although some of these have degenerate primers (in which case I only used the pair that has the most matches in SILVA) It seems this (or similar) questions have been posted before, but no conclusion was reached, any idea on how we could proceed? or is this pipeline incompatible with this kind of samples?

✅ ampliseq/test_full completed successfully! 🎉 Run Name marvelous_albattani Duration 2h 7m 41s Status ✅ Success Tasks Completed: 208, Failed: 26 Jun 15, 2026 at 5:01 PM

✅ ampliseq/test_full completed successfully! 🎉 Run Name adoring_mendel Duration 1h 50m 1s Status ✅ Success Tasks Completed: 208, Failed: 4 Jun 17, 2026 at 9:17 AM

✅ ampliseq/test_full completed successfully! 🎉 Run Name romantic_ritchie Duration 1h 50m Status ✅ Success Tasks Completed: 208, Failed: 4 Jun 17, 2026 at 1:11 PM

Does anyone have an opinion on buildt-in benchmarking? First step in https://github.com/nf-core/ampliseq/pull/1021

Hello all, I have a small question to put. In the CLI for ampliseq, putting samplesheet.csv is a mandate then why haven't you mentioned it in the "required" key? I see the --input parameter being added in the nextflow_schema.config for other pipelines like taxprofiler and so on but not for this one. I have attached the schema.json for ampliseq below:

Hello, Will the pipeline remove the primer sequences and anything that comes before (F primer) or after them (R primer), like adaptor sequences? The pipeline clearly states that only the primer sequence should be included in the code. Do I need to remove adaptor sequences prior to launching the pipeline? Thank you!

Dear #CEA7TBJGJ people, I am currently updating #C024915L4KB for a coming release. I have done https://github.com/nf-core/fetchngs/pull/383 to replace the old https://github.com/nf-core/fetchngs/pull/324 / https://github.com/nf-core/fetchngs/pull/361 Am I missing anything?

Are the log fold changes reported in the ancom-bc analysis 10-based or 2-based ?

We did considerable work at ampliseq and are aiming to relese 3.0.0 in the next weeks. I made a new metro map, with substantial simplifications, but otherwise it seems too crowded. Comments would be great!

We are about to remove --input_folder (i.e.only samplesheet input remains), if anyone wants to object, now is the time. github.com/nf-core/ampliseq/issues/1110

Not sure if this is already being fixed in ampliseq 3.0.0, but I think there may be an issue with the update to nf-schema 3.0.0, resulting in errors like

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/ampliseq>, projectDir:
...
 -- Did you mean 'paramsSummaryLog' instead?

 -- Check script '/usersoftware/collab004/.nextflow/nf-core/ampliseq/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf' at line: 76 or see '.nextflow.log' file for more details

I saw this link posted over in the nf-schema channel: nextflow-io.github.io/nf-schema/latest/3_0_0_migration_guide#… If this is as simple as locking the specification to 3.0.0 I'm happy to make a PR with the suggested changes, let me know!

❌ ampliseq/test_full failed 😿 Run Name curious_hodgkin Duration 869ms Status ❌ Failed Error Message

Script compilation error
- file : /.nextflow/assets/.repos/nf-core/ampliseq/clones/d8fa986434964f2b1048ae4fc643197e76e22452/main.nf
- cause: Unexpected input: '{' @ line 76, column 8.
   params {
          ^

1 error

NOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced.

Command Line

nextflow run '<https://github.com/nf-core/ampliseq>' -name curious_hodgkin -params-file '<https://api.cloud.seqera.io/ephemeral/IyqFIrFKOMkRJGcdJ9xSww.json>' -with-tower -r dev -profile test_full,aws_scratch

Oct 8, 2026 at 10:32 AM

Hello! In my QIIME2 input folder, I do not have a file called taxa-bar-plots. Is this normal? If it is not normal, how can I fix it? I think I am missing some plots from my output. Thanks!

❌ ampliseq/test_full failed 😿 Run Name stoic_bohr Duration 1s Status ❌ Failed Error Message

Script compilation error
- file : /.nextflow/assets/.repos/nf-core/ampliseq/clones/f48d928128fc92a6aedb3289db17ff41b6949b80/main.nf
- cause: Unexpected input: '{' @ line 76, column 8.
   params {
          ^

1 error

NOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced.

Command Line

nextflow run '<https://github.com/nf-core/ampliseq>' -name stoic_bohr -params-file '<https://api.cloud.seqera.io/ephemeral/DaZ5MymOYNMw6C9OkLp8-A.json>' -with-tower -r dev -profile test_full,aws_scratch

Oct 8, 2026 at 4:54 PM

Release 3.0.0 is out, please note the breaking changes! 🎉

❌ ampliseq/test_full failed 😿 Run Name goofy_kowalevski Duration 758ms Status ❌ Failed Error Message

Script compilation error
- file : /.nextflow/assets/.repos/nf-core/ampliseq/clones/992e6df34065067185b5e34665b5861b6827981d/main.nf
- cause: Unexpected input: '{' @ line 76, column 8.
   params {
          ^

1 error

NOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced.

Command Line

nextflow run '<https://github.com/nf-core/ampliseq>' -name goofy_kowalevski -params-file '<https://api.cloud.seqera.io/ephemeral/xgC_C1fHiYh-S5vrwCekEA.json>' -with-tower -r 992e6df34065067185b5e34665b5861b6827981d -profile test_full,aws_scratch

Oct 9, 2026 at 12:48 PM

depictio Depictio dashboard for ampliseq: 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 @Daniel Straub, but the project has evolved a lot since and I am now sharing it more widely, so I would like the view of other ampliseq users and developers too. I'm myself an ampliseq user and contributed a few times, in the context of TREC data analysis. ✨ 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 ampliseq: taxonomic composition per group and per sample, alpha diversity with rarefaction curves, ordination, ANCOM-BC differential abundance and the phylogenetic tree, 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: ampliseq dashboard (no account needed) 💬 Comment on the dashboard (Google sign-in) or in the GitHub discussion dedicated to ampliseq. 🎤 I am also presenting it today at the Nextflow Summit (virtual agenda) if you're interested in the project ⭐ A star on the repo is welcome if you find it useful. Thanks! 🙏

When nf-co.re/daamicrobiome hits maybe we can make sure that ampliseq provides compatible output.

❌ ampliseq/test_full failed 😿 Run Name gloomy_moriondo Duration 26.8s Status ❌ Failed Error Message

Unknown error

Command Line

nextflow run '<https://github.com/nf-core/ampliseq>' -name gloomy_moriondo -params-file '<https://api.cloud.seqera.io/ephemeral/0zWJj62GlWChCl5QRTSxEg.json>' -with-tower -r 992e6df34065067185b5e34665b5861b6827981d -profile test_full,aws_scratch

Oct 19, 2026 at 11:36 AM

❌ ampliseq/test_full failed 😿 Run Name gloomy_moriondo_2 Duration 30.2s Status ❌ Failed Error Message

Unknown error

Command Line

nextflow run '<https://github.com/nf-core/ampliseq>' -name gloomy_moriondo_2 -params-file '<https://api.cloud.seqera.io/ephemeral/GNOyJC-ZqLqQA-F589omuA.json>' -with-tower -r 992e6df34065067185b5e34665b5861b6827981d -profile test_full,aws_scratch -resume 4056c2c6-6acf-4335-96fd-5010f1a03560

Oct 19, 2026 at 11:44 AM

✅ ampliseq/test_full completed successfully! 🎉 Run Name friendly_picasso Duration 2h 8m 39s Status ✅ Success Tasks Completed: 219, Failed: 1 Oct 19, 2026 at 1:59 PM

❌ ampliseq/test_full failed 😿 Run Name spontaneous_bose Duration 811ms Status ❌ Failed Error Message

Script compilation error
- file : /.nextflow/assets/.repos/nf-core/ampliseq/clones/591c3322a015feef7304c2110eea925d6c5b9f98/main.nf
- cause: Unexpected input: '{' @ line 76, column 8.
   params {
          ^

1 error

NOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced.

Command Line

nextflow run '<https://github.com/nf-core/ampliseq>' -name spontaneous_bose -params-file '<https://api.cloud.seqera.io/ephemeral/HTE3H8F_1sMf42Mk8KECYA.json>' -with-tower -r dev -profile test_full,aws_scratch

Oct 21, 2026 at 12:43 PM

✅ ampliseq/test_full completed successfully! 🎉 Run Name adoring_montalcini Duration 1h 47m 21s Status ✅ Success Tasks Completed: 219, Failed: 1 Oct 26, 2026 at 9:39 AM

✅ ampliseq/test_full completed successfully! 🎉 Run Name nice_monod Duration 2h 9m 51s Status ✅ Success Tasks Completed: 219, Failed: 1 Oct 28, 2026 at 12:20 PM

✅ ampliseq/test_full completed successfully! 🎉 Run Name serene_mestorf Duration 1h 52m 41s Status ✅ Success Tasks Completed: 219, Failed: 1 Oct 28, 2026 at 5:15 PM