Context on why the current

zlib-ng

feedstock is problematic: https://github.com/conda-forge/zlib-ng-feedstock/issues/10#issuecomment-2910925797

I expect linting and tests to fail, but here are some fixes: • https://github.com/nf-core/rnadnavar/pull/53 • https://github.com/nf-core/variantcatalogue/pull/24

Another bad package name low hanging fruit in a pipeline if someone could fix: • openms::openms : ['036_proteomicslfq.yaml'] - that should read bioconda::openms that's the only thing missing for that proteomicslfq pipeline.

@Edmund’s PR to run nf-test CI tests on ARM in nf-core/modules has just been merged 🎉 https://github.com/nf-core/modules/pull/7747

@David Lecomber did you request more nodes in the Stockholm region on AWS?

Hi Phil - yep! The weather has finally changed in Blighty so am trying to get the tensorflow recipe pushed.. it can use the core count to compile, still takes 30 mins.. but a 2 hour turnaround was getting painful!

Hope all's well with you

Should have sepp/busco/pplacer in the next two weeks, just waiting on maintainers of some ocaml packages to merge

@moritz has left the channel

Hi all. What’s the general availability and performance of nf-core pipelines on pure ARM-based platforms? Does a Docker image for a tool successfully built with arm64 also guarantee its run? What will be the trade-off for speed / performance if it’s not an ARM native tool? @Phil Ewels

Hi everyone, I'm trying to pick up some efforts for making oncoanalyser ARM-compatible. I've rebuilt all of ours tools etc but bwa-mem2 and star are giving me some trouble. I'm using wave as the container engine on a GCP ARM-based VM and I've triggered new builds for the versions of bwa-mem2 and STAR that I'm interested in (for ARM-compatibility) and pointing to those (with my local docker images as well) but when looking at the logs, I do see that some other image is being used and that leads to error 127 with the different commands (bwa-mem2 and sambamba) not being found. Anybody ever encountered this ? Much appreciative of any help, thanks ! 🙏 (cc @Edmund)

the relevant lines in the logs

Nov-21 14:38:02.626 [Actor Thread 29] DEBUG io.seqera.wave.plugin.WaveClient - Wave request: <https://wave.seqera.io/v1alpha2/container>; attempt=1 - request: SubmitContainerTokenRequest(towerAccessToken:null, towerRefreshToken:null, towerWorkspaceId:null, towerEndpoint:<https://api.cloud.seqera.io>, containerImage:null, containerFile:null, containerConfig:ContainerConfig(), containerPlatform:linux/amd64, buildRepository:null, cacheRepository:null, timestamp:2025-11-21T14:38:02.625687646Z, fingerprint:1d905f8f5302b15998193d055620a793, freeze:true, format:null, dryRun:false, workflowId:null, containerIncludes:null, packages:PackagesSpec{type=CONDA, envFile='bmFtZTogYndhLW1lbTJfbWVtCmNoYW5uZWxzOgogIC0gY29uZGEtZm9yZ2UKICAtIGJpb2NvbmRhCiAgLSBkZWZhdWx0cwpkZXBlbmRlbmNpZXM6CiAgLSBiaW9jb25kYTo6YndhLW1lbTI9Mi4zCiAgLSBiaW9jb25kYTo6c2FtdG9vbHM9MS4yMQogIC0gYmlvY29uZGE6OnNhbWJhbWJhPTEuMC4xCg==', packages=null, condaOpts=CondaOpts(mambaImage=mambaorg/micromamba:1.5.10-noble; basePackages=conda-forge::procps-ng, commands=null), channels=null}, nameStrategy:null, mirror:false, scanMode:null, scanLevels:null, buildCompression:null)
Nov-21 14:38:02.788 [Actor Thread 29] DEBUG io.seqera.wave.plugin.WaveClient - Wave response: statusCode=200; body={"requestId":"89dc7815b08b","targetImage":"<http://community.wave.seqera.io/library/bwa-mem2_mem:fc55cd0b3dc437f2|community.wave.seqera.io/library/bwa-mem2_mem:fc55cd0b3dc437f2>","containerImage":"<http://community.wave.seqera.io/library/bwa-mem2_mem:fc55cd0b3dc437f2|community.wave.seqera.io/library/bwa-mem2_mem:fc55cd0b3dc437f2>","buildId":"bd-fc55cd0b3dc437f2_1","cached":true,"freeze":true,"mirror":false,"scanId":"sc-9c70054be5dfe71d_1"}
Nov-21 14:38:02.810 [Task submitter] DEBUG io.seqera.wave.plugin.WaveClient - Wave container status response: statusCode=200; body={"id":"89dc7815b08b","status":"DONE","buildId":"bd-fc55cd0b3dc437f2_1","scanId":"sc-9c70054be5dfe71d_1","succeeded":true,"creationTime":"2025-11-20T16:22:34.907767940Z","duration":71.493156506}
Nov-21 14:38:02.816 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-21 14:38:02.816 [Task submitter] INFO  nextflow.Session - [6e/8b3c57] Submitted process > NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (subject_a_subject_a.tumor)
Nov-21 14:38:02.836 [Task submitter] DEBUG io.seqera.wave.plugin.WaveClient - Wave container status response: statusCode=200; body={"id":"89dc7815b08b","status":"DONE","buildId":"bd-fc55cd0b3dc437f2_1","scanId":"sc-9c70054be5dfe71d_1","succeeded":true,"creationTime":"2025-11-20T16:22:34.907767940Z","duration":71.493156506}
Nov-21 14:38:02.861 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (subject_a_subject_a.tumor); status: COMPLETED; exit: 127; error: -; workDir: /home/rhassaine/arm_test_profile/work/6e/8b3c57caf3d145217dd68ecc909d89]
Nov-21 14:38:02.861 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Nov-21 14:38:02.869 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (subject_a_subject_a.tumor); work-dir=/home/rhassaine/arm_test_profile/work/6e/8b3c57caf3d145217dd68ecc909d89
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (subject_a_subject_a.tumor)` terminated with an error exit status (127)
Nov-21 14:38:02.882 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (subject_a_subject_a.tumor)'

Caused by:
  Process `NFCORE_ONCOANALYSER:WGTS:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (subject_a_subject_a.tumor)` terminated with an error exit status (127)

While I supplied this container in my config

process {
    withName: /.*BWAMEM2_ALIGN.*/ {
        container = '<http://community.wave.seqera.io/library/bwa-mem2:2.3--1177f3b3893cb1f6|community.wave.seqera.io/library/bwa-mem2:2.3--1177f3b3893cb1f6>'
    }
}

(cc @Stephen Watts @Oliver Hofmann @Roman Valls Guimera)

@Rayan Hassaïne Here’s a trail of commits and what I did back in April to make it all work: https://github.com/umccr/oncoanalyser-arm64/commits/pipeline_v6.0_aarch64/

howdy folks - whatever happened here looks like it tried to load an amd64 container instead of arm64 / aarch64:

containerImage:null, containerFile:null, containerConfig:ContainerConfig(), containerPlatform:linux/amd64, buildRepository:null, cacheRepository:null,

that wouldn't end well running on aarch64. This looks like some form of nf-core or pipeline problem - can someone more familiar with this help?

do we have more pipelines that should have arm CI runs? https://github.com/nf-core/rnaseq/pull/1641

Hi all, Is there anybody who knows what they’re doing willing to look at this bioconda PR? https://github.com/bioconda/bioconda-recipes/pull/61329 The code should be arm64 compatible, but I’m probably still missing something in the recipe.

After promising it for months, I finally got around to drafting a blog post about our work here 🙂 • https://deploy-preview-3710--nf-core-main-site.netlify.app/blog/2026/arm-pipelines • https://github.com/nf-core/website/pull/3710 Please take a look and review on github / drop comments here! 🙂

ARM64 support - Looking to help a researcher run the rnaseq pipeline on a Nvidia DGX Spark (128GB RAM) as 👍 Was able to run the test pipeline on DGX Spark consuming more than 16GB (M3 Pro) on my laptop

nextflow run nf-core/rnaseq -r 3.22.2 -profile docker,arm64,test --outdir training/results_test

Note: I decided not to try on Mac Studio M4 Max (128 GB RAM), because my experience with getting Metal to use GPU on my M3 Pro laptop was pitiful. (related to my AI/ML aspirations)

hmm, https://github.com/eWaterCycle/setup-apptainer doesn't support arm64 yet... is it worth to add it in a fork, so we can test the pipeilnes also on signularity on arm?

Hello, hello I am trying to run the seqinspector pipeline form the `add_long_reads` branch and having trouble with

toulligqc

. First I got a permission error (

ValueError: sort array is read-only

), but then I updated to the newest version of the toulligqc module, and got the following error:

-[nf-core/seqinspector] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_SEQINSPECTOR:SEQINSPECTOR:TOULLIGQC (Undetermined_05)'

Caused by:
  Process `NFCORE_SEQINSPECTOR:SEQINSPECTOR:TOULLIGQC (Undetermined_05)` terminated with an error exit status (1)


Command executed:

  toulligqc \
      --fastq Undetermined_S0_L001_R1_001.fastq.gz \
      --output-directory Undetermined_05 \

Command exit status:
  1

Command output:
  ToulligQC version 2.7.1
  * Initialize extractors
  * Start Toulligqc info extractor
  * End of Toulligqc info extractor (done in 0m0.00s)
  * Start fastq extractor

Command error:
  Unable to find image '<http://community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80|community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80>' locally
  f883b71bc5c8ba80: Pulling from library/toulligqc_huggingface_hub_matplotlib_numpy_pruned
  6e59cb05818e: Already exists
  dec6b097362e: Already exists
  5f20d5c36a06: Already exists
  4f4fb700ef54: Already exists
  5a47b42d3e8c: Already exists
  ad4a1cea1cef: Already exists
  c0287eaf45ee: Already exists
  4f4fb700ef54: Already exists
  b8a1a9b42924: Already exists
  57d1d9429ba0: Already exists
  a444aa1775d5: Already exists
  b9afb7fce560: Already exists
  a1bf15c61759: Pulling fs layer
  b13abb49f40a: Pulling fs layer
  a1bf15c61759: Verifying Checksum
  a1bf15c61759: Download complete
  a1bf15c61759: Pull complete
  b13abb49f40a: Verifying Checksum
  b13abb49f40a: Download complete
  b13abb49f40a: Pull complete
  Digest: sha256:7c72ded818ef3386a9baeb06e1770640d8fc536dbc513af39458f65849fd6cdb
  Status: Downloaded newer image for <http://community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80|community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80>
  Traceback (most recent call last):
    File "/opt/conda/bin/toulligqc", line 10, in <module>
      sys.exit(main())
               ^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/toulligqc/toulligqc.py", line 426, in main
      extractor.init()
    File "/opt/conda/lib/python3.11/site-packages/toulligqc/fastq_extractor.py", line 60, in init
      self.dataframe_1d = self._load_fastq_data()
                          ^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/toulligqc/fastq_extractor.py", line 253, in _load_fastq_data
  ToulligQC version 2.7.1
  * Initialize extractors
  * Start Toulligqc info extractor
  * End of Toulligqc info extractor (done in 0m0.00s)
  * Start fastq extractor
      run_info = self.check_fastq()
                 ^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.11/site-packages/toulligqc/fastq_extractor.py", line 360, in check_fastq
      metadata = dict(x.split("=") for x in first_line.split(" ")[1:])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  ValueError: dictionary update sequence element #0 has length 1; 2 is required

Work dir:
  /Users/franziska.franziska/workspace/seqinspector/work/28/b92f680318c3de080e707650ae0766

Container:
  <http://community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80|community.wave.seqera.io/library/toulligqc_huggingface_hub_matplotlib_numpy_pruned:f883b71bc5c8ba80>

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

My command was:

nextflow run <http://main.nf|main.nf> -profile docker,arm64,test --input ../../Desktop/seqinspector_input/test_data/samplesheet.csv --outdir /Users/franziska.franziska/Desktop/seqinspector_outdir_test/ --fastq_screen_references ../../Desktop/seqinspector_input/fastq_screen_refs_base.csv --fasta /Users/franziska.franziska/Desktop/seqinspector_input/sars_cov2_genome/ncbi_dataset\(1\)/ncbi_dataset/data/genomic.fna --tools toulligqc

@Maxime Garcia was able to run it on his linux computer without issues, but I am on a Mac, so I assume some problems due to the different structure

(the issue persists without giving a fasta file or fastq_screen_references)

I also tried to run it with the newest container on Seqera containers:

docker run -i --cpu-shares 2048 --memory 8192m --platform linux/amd64 -v /Users/franziska.franziska/workspace/seqinspector:/Users/franziska.franziska/workspace/seqinspector -u $(id -u):$(id -g) <http://community.wave.seqera.io/library/toulligqc:2.8.4--2e474221a8568dff|community.wave.seqera.io/library/toulligqc:2.8.4--2e474221a8568dff> toulligqc --fastq Undetermined_S0_L001_R1_001.fastq.gz --output-directory Undetermined_05

and get yet another error that seems to be linked to the mac chip issue:

qemu: uncaught target signal 11 (Segmentation fault) - core dumped

@Mahesh Binzer-Panchal

How about we make an issue on https://github.com/GenomiqueENS/toulligQC and ask them if they managed to run it on MacOS?

Hi, I've tried to add support for arm64 for glimpse software but it is using AVX2 and this seems to cause a few issue. Has anyone encounter such problem before ?

Hello everyone, I’m testing the centrifuger module locally on an Apple Silicon (arm64) machine., When running: i get : - with

nf-test test modules

... --> i get segmentation fault error 139, while - with

nf-core modules test

--> i get specified "rosetta error, couldnt find free space to alocate memory"... From what I understand, this is likely due to Docker using linux/amd64 containers.. Shall i try to rely on Github CI or is other way recommended way to work with AMR-based system??? Thank you for your time

Looking impressive https://github.com/google/deepvariant/pull/1085

Hello everyone, hope you’ve been enjoying Hackathon so far :) I have a known issue I’ve been dealing with for a while and figured I’d ask if anyone has a solution. When I run a pipeline, it sometimes gives me:

Command error:
  WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

From searching in Slack, it seems this is due to running on macOS (ARM64) in combination with Docker. When I rerun the same command locally, it might run successfully, or it might fail with the same error. in Codespaces runs successfully every time. Command:

nextflow run . -profile test,docker --outdir results