downgrade multiqc version to accommodate ARM

[tobsecret]

On my ARM laptop the multiqc module fails with an error that appears to be CPU specific. My specs:

Chip: Apple M4 Max
OS: 15.5 (24F74) 

Invocation:

nextflow run main.nf -profile docker,arm,test

Error:

Command error:
  .command.sh: line 11:    33 Illegal instruction     multiqc --force .

Downgrading from 1.29 to 1.28 fixes the issue.

This can be easily verified:

.test.command.sh

#!/usr/bin/bash
multiqc .

docker run --rm -it --platform=linux/amd64 -u $(id -u):$(id -g) -v "$PWD":/data -w /data quay.io/biocontainers/multiqc:1.29--pyhdfd78af_0 bash .test.command.sh
# .test.command.sh: line 2:     7 Illegal instruction     multiqc .
docker run --rm -it --platform=linux/amd64 -u $(id -u):$(id -g) -v "$PWD":/data -w /data quay.io/biocontainers/multiqc:1.28--pyhdfd78af_0 bash .test.command.sh

#/// MultiQC 🔍 v1.28
#
#     version_check | MultiQC Version v1.29 now available!
#       file_search | Search path: /data
#         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 10/10  
#           multiqc | No analysis results found. Cleaning up…

PR checklist

• [x] This comment contains a description of changes (with reason).
• [x] Use BioConda and BioContainers if possible to fulfill software requirements.

[SPPearce]

@ewels

[mashehu]

and cc @edmundmiller

[tobsecret]

linking https://github.com/MultiQC/MultiQC/issues/3238 here as well where I did some more testing regarding the varieties of images. In summary: this is broken in all of the 1.29 AMD images I tested, both on docker (multiqc/multiqc) and on quay (biocontainers/multiqc). The 1.29 ARM image works fine.

Not including all of that detail here because this PR is only concerned with making sure the latest version of the nf-core module is usable on ARM architectures.

[ewels]

Sounds like we may be able to patch this in MultiQC quite easily.. 'cc @vladsavelyev

[tobsecret]

This can be closed once https://github.com/MultiQC/MultiQC/pull/3240 has been incorporated into a patch.

[SPPearce]

@tobsecret , multiqc has now been updated to v1.30, hopefully that solves your issue.

[tobsecret]

Looks like @matthdsm has tried running the 1.30 container but has found the issue persists. I no longer have the relevant hardware and can thus not verify if it does or not.

On Thu, Jul 10, 2025, 11:55 AM Simon Pearce @.***> wrote:

SPPearce left a comment (nf-core/modules#8717) https://github.com/nf-core/modules/pull/8717#issuecomment-3056673028

@tobsecret https://github.com/tobsecret , multiqc has now been updated to v1.30, hopefully that solves your issue.

— Reply to this email directly, view it on GitHub https://github.com/nf-core/modules/pull/8717#issuecomment-3056673028, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACOTRBZIHCUGCYRBEEOJHTL3HY2CFAVCNFSM6AAAAACADSKBLSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTANJWGY3TGMBSHA . You are receiving this because you were mentioned.Message ID: @.***>

[mashehu]

@matthdsm is this still relevant?

[matthdsm]

Nope! All good!

---

Van: Matthias Hörtenhuber @.> Verzonden: Wednesday, October 1, 2025 11:14:51 AM Aan: nf-core/modules @.> CC: Matthias De Smet @.>; Mention @.> Onderwerp: Re: [nf-core/modules] downgrade multiqc version to accommodate ARM (PR #8717)

[https://avatars.githubusercontent.com/u/6169021?s=20&v=4]mashehu left a comment (nf-core/modules#8717)https://github.com/nf-core/modules/pull/8717#issuecomment-3355441300

@matthdsmhttps://github.com/matthdsm is this still relevant?

— Reply to this email directly, view it on GitHubhttps://github.com/nf-core/modules/pull/8717#issuecomment-3355441300, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AC2NHEC4H7W7SBE2BUP7U433VOLQXAVCNFSM6AAAAACADSKBLSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTGNJVGQ2DCMZQGA. You are receiving this because you were mentioned.Message ID: @.***>