Is there an issue with the MULTIQC reporting and PROKKA for the BACASS pipeline? I ran a pipeline with 13 samples and got 13 annotated assemblies, but in the MULTIQC report I only get an annotation report for one of the assemblies (and I don’t even know which one)

Hi bacass fans I’m working on the #C07S9BW2STT porting - and looking over the packages that need to be ported to run on Arm platforms. The ‘dfast’ package is required in the pipeline - but that uses metagene_annotator. Metagene_annotator is very old (perhaps 2012 is last releae) and the source code is not available. Is this important - or can it even be removed, can anyone swap in an alternative? Or is anyone in touch with the original developers ( in nic.ac.jp)?

is nanopolish removable from bacass? this is seen as something that shouldn’t be used now - I’ve been chatting with Nanopore on that.

Hello bacass team! I am running missing aws megatests at the moment. Bacass keeps failing with

# Time used to run KMA for species identifation: 2.259 s
  Cant open file: [Errno 2] No such file or directory: '20190108_kmerfinder_stable_dirs/bacteria.tax'

https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/DUjD8zksXbtKC Could you please take a look?

Hi Team, I have WGS data for Streptococcus pneumoniae sequenced using the Oxford Nanopore SQK-RBK114.96 kit on a PromethION flowcell. I'm looking for recommendations or a workflow to extract the following from my dataset: • Species confirmation/identification • MLST (MultiLocus Sequence Typing) • Serotyping • AMR (Antimicrobial Resistance) gene detection • Virulence factor gene detection Given that it's long-read Nanopore data with moderate coverage, what tools or pipelines would you recommend?

Hi everybody, thanks for a great pipeline. I have a question, when I'm using the conda profile. Our Institute restricted the usage of the default channel when using conda. I therefore get the error message:

UnavailableInvalidChannel: HTTP 403 FORBIDDEN for channel pkgs/main <<https://repo.anaconda.com/pkgs/main>>

The channel is not accessible or is invalid.

How can I restrict the conda create command to use only the conda-forge and bioconda channel in the nextflow pipeline with a local congif file? I tried to add a local config file

conda {

channels = ['conda-forge', 'bioconda']

strictChannels = true

}

but for some reason it still looks for the default channel

Hi everyone, I'm trying to run bacass using bakta. I've downloaded version 5.1 of the bakta database from https://zenodo.org/records/10522951. I've untarred the database to a folder called

db

I'm running version 2.4.0 of the pipeline (though the dev version gives the same error) on the following system:

Nextflow version: 24.10.5 build 5935
Java version: openjdk 17.0.6 2023-01-17 LTS
Operating system: Rocky Linux, VERSION="8.8 (Green Obsidian)",ID_LIKE="rhel centos fedora")
Bash version: version 5.1.16(1)-release (x86_64-pc-linux-gnu)
Apptainer: V1.3.3
Executor: slurm or direct

Hardware HPC -- submitting pipeline from <http://tower.nf|tower.nf>
Tower Agent version 0.5.0 (build d758993)

Which gives this error:

predict rRNAs...
    found: 0
predict ncRNAs...
    found: 0
predict ncRNA regions...
    found: 0
predict CRISPR arrays...
    found: 1
predict & annotate CDSs...
    predicted: 116
    discarded spurious: 2
    revised translational exceptions: 0
    detected IPSs: 5
    found PSCs: 30
    found PSCCs: 27
    lookup annotations...
    conduct expert systems...
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/bakta/main.py", line 275, in main
    expert_amr_found = exp_amr.search(cdss, cds_aa_path)
  File "/usr/local/lib/python3.10/site-packages/bakta/expert/amrfinder.py", line 47, in search
    raise Exception(f"amrfinder error! error code: {proc.returncode}. Please, try 'amrfinder_update --force_update --database {amrfinderplus_db_path}' to update AMRFinderPlus's internal database.")
Exception: amrfinder error! error code: 1. Please, try 'amrfinder_update --force_update --database /mnt/scratch/projects/biol-tf-2018/nextflow/Data/bakta_db/2024.01.19_ver5.1/db/amrfinderplus-db' to update AMRFinderPlus's internal database.

Any thoughts on how to resolve this? Thanks.

Is it possible to make an update to the pipeline without htis channel? I have downloaded the repository and removed all the

-default

rows from all files inside the module folder, if you can use it.

@Alex Peltzer @Daniel Straub @Daniel_VM i added the option to use a protein fasta file for prokka if the user wants to use custom annotation: https://github.com/nf-core/bacass/pull/239

I was wondering if there is a way to force bacassto use a newer version of spades.py. When running unicycler separately, it show much better results when I used spades.py version 4.1 (or 4.2). But bacass always try v. 4.0. How or where can I force it to use a newer version? In my nextflow.config file I already use this to force a newer unicycler version, But I don't find any reference to spades.py in the whole repository/script.

withName:UNICYCLER {

container = '<https://depot.galaxyproject.org/singularity/unicycler:0.5.1--py312hdcc493e_4>'

//		container = '<https://depot.galaxyproject.org/singularity/spades:4.1.0--haf24da9_0>' # this throws an error

}

any help would be appreciated.

Hi @Daniel_VM, I was thinking about making the newly introduced nf-test tests more reliable. The problem is, I exclude more and more files that appear unstable in their content (i.e. varying md5sum) and have to be excluded in

tests/.nftignore

. Possibly it would be better to use a positive list instead of a negative list? Would you have some key files in mind that are possibly stable?

I'm having some trouble when tyring to download the latest version of the KmerFinder database

(base) ruben@FCP10492:~/Nextflow/nfcore_bacass/database$ KmerFinder_DB=$(pwd)
(base) ruben@FCP10492:~/Nextflow/nfcore_bacass/database$ cd kmerfinder_db/
(base) ruben@FCP10492:~/Nextflow/nfcore_bacass/database/kmerfinder_db$ bash INSTALL.sh $KmerFinder_DB bacteria latest

Downloading database(s) for bacteria
curl: /home/ruben/miniconda3/lib/libcurl.so.4: no version information available (required by curl)
Input date tag is not valid. There is no database available for this date. Please check the ftp site <ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/> for valid updates tags of the databases.
--2025-12-03 12:43:20--  <ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria*>
           => '/home/ruben/Nextflow/nfcore_bacass/database/.listing'
Resolving ftp.cbs.dtu.dk (ftp.cbs.dtu.dk)... 130.225.74.194
Connecting to ftp.cbs.dtu.dk (ftp.cbs.dtu.dk)|130.225.74.194|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /public/CGE/databases/KmerFinder/version/latest ... 
No such directory 'public/CGE/databases/KmerFinder/version/latest'.

--2025-12-03 12:43:21--  <ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/config>
           => '/home/ruben/Nextflow/nfcore_bacass/database/config'
Resolving ftp.cbs.dtu.dk (ftp.cbs.dtu.dk)... 130.225.74.194
Connecting to ftp.cbs.dtu.dk (ftp.cbs.dtu.dk)|130.225.74.194|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /public/CGE/databases/KmerFinder/version/latest ... 
No such directory 'public/CGE/databases/KmerFinder/version/latest'.

tar (child): /home/ruben/Nextflow/nfcore_bacass/database/bacteria.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
rm: cannot remove '/home/ruben/Nextflow/nfcore_bacass/database/*.tar.gz': No such file or directory

It seems there is no file called latest and when i try to check which one is the latest version (by number) i cannot connect to their ftp sever because it requires me to have password For now i'm using the version from Zenodo, but i would like to get the latest posible. So if anyone could provide me with the actual latest number I woudl appreciate it.

Hi. I have ONT reads (50x depth) and Illumina reads (30x) from WGS of a bacterial strain for genome assembly. I see that nf-core has two assembly pipelines: bacass and genomeassembler. Both has the hybrid option: assembly from long reads + polishing by short reads. Which one is better for my purpose, or they are kind of equivalent for this use case?

Hello! I am regenerating some of the aws megatest results at the moment. Bacass 2.5.0 fails for me with

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Assembly type not provided.
  Please specify the '--assembly_type' parameter to perform the assembly.
  Accepted: short, long, hybrid.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4JxnUjPL5BOSxa/v2/logs

I propose to change default settings in https://github.com/nf-core/bacass/issues/271, opinions welcome.

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Hi Channel!! Here is the url to the workadventure in bacass Room 3 for the nf-core hackathon: https://app.hackathon.nf-co.re/_/global/app.hackathon.nf-co.re/maps/default/map.json (Edited:) Workadventure ROOM 2 for bacass

Hackathon 2026 – March 📍 InSite (Madrid-Spain) // Online Day 1 11/03/2026 - Schedule -- All times in CET (GMT+1) 0900–1000 — Welcome and introduction to the pipelines 1000–1030 — Task distribution 1030–1130 — Hands-on: implementation and development 1130–1200 — Coffee break 1200–1400 — Hands-on: implementation and development 1400–1500 — Lunch 1500–1630 — Hands-on: implementation and development 1630–1700 — Wrap-up 1700–1800 — Games and networking

PR closing

Create a meta.yml file for each local module #199

https://github.com/nf-core/bacass/pull/281

Is the new version output format not compatible with the current pipeline's version collection of bacass?

Hello!! For people joining the nf-core hackathon who want to work on the bacass project, you can join us online via: WorkAdventure ROOM 2: https://app.hackathon.nf-co.re/_/global/app.hackathon.nf-co.re/maps/default/map.json Here is the schedule for Day 2 - 12/03/2025 All times in CET (GMT+1)

9:00 – 9:30
 Task review and questions
9:30 – 11:30
 Hands-on: Implementation and development
11:30 – 12:00
 Coffee break
12:00 – 14:00
 Hands-on: Implementation and development
14:00 – 15:00
 Lunch
15:00 – 16:30
 Hands-on: Implementation and development
16:30 – 17:00
 Wrap-up

PR adding new dataset of heterogeneus long + short + hybrid to test "auto" in assembly_type: https://github.com/nf-core/test-datasets/pull/1912

Hello! I’ve created a metro map for Bacass. Could you give me some feedback? Is it easy to follow? Is there anything you would improve? I still need to add the version tag, so it will be 2.6.0 (next release)

Hello everyone, I am developing a Nextflow pipeline that processes data from raw FASTQ files through to downstream analysis for both whole genome sequencing (isolate data) and shotgun metagenomics. For publication and reproducibility, I am looking for publicly available test datasets (preferably small to moderate size) that include: • Paired-end WGS isolate data • Shotgun metagenomic sequencing data The organism is not critical, but the data should be well-documented and suitable for benchmarking a full pipeline. I would appreciate any recommendations for reliable sources (e.g., specific studies, accession numbers, or curated benchmark datasets). Many thanks in advance.

Hi all!! 🚀 bacass v2.6.0 is out Main highlights: • Multiple assemblers can now run in parallel (

--assembler

supports lists) and are compared via QUAST • All assemblers are enabled by default • New short-read assembler: MEGAHIT • New long-read workflows: Autocycler + Flye + Raven • Added RASUSA for long-read downsampling • New metromap visualization Give it a try 🙂 https://github.com/nf-core/bacass/tree/2.6.0

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❌ bacass/test_full failed 😿 Run Name admiring_babbage Duration 4m 28s Status ❌ Failed Error Message

Unknown error

Command Line

nextflow run '<https://github.com/nf-core/bacass>' -name admiring_babbage -params-file '<https://api.cloud.seqera.io/ephemeral/CI5899nu1rJwr9QKGOyS2Q.json>' -with-tower -r dev -profile test_full

Oct 30, 2026 at 8:11 AM

✅ bacass/test_full completed successfully! 🎉 Run Name reverent_moriondo Duration 34m 47s Status ✅ Success Tasks Completed: 29 Oct 30, 2026 at 11:27 AM

✅ bacass/test_full completed successfully! 🎉 Run Name trusting_hugle Duration 29m 56s Status ✅ Success Tasks Completed: 29 Nov 3, 2026 at 7:08 PM

nf-core/bacass v2.7.0 is out! 🎉 Major changes: •

--assembly_type

now defaults to auto, detecting the available read types per sample and running compatible assemblers automatically. • Added optional

--assembly_type_label

to distinguish automatically routed outputs with -short, -long, or -hybrid. • MultiQC now provides custom, per-sample and multi-assembler assembly summary tables, including BUSCO results. • Restored Medaka and Nanopolish polishing for hybrid assemblies while respecting

--skip_polish

. • Improved genome-size handling in samplesheets, supporting raw bases and

k, m, or g

units. • Reorganised output directories and updated core tools including Canu, Medaka, and NanoPlot. Release 👉🏽 github.com/nf-core/bacass/…/2.7.0