RNAVAR nf-core pipeline: error on multiqc module

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1

Hello!

I’m trying to run the [rna-var]() pipeline on mouse RNAseq data.

However, I am getting the following error affecting the multiqc module:

.command.sh: line 11:    42 Illegal instruction     (core dumped) multiqc --force --config multiqc_config.yml .

I am launching the pipeline with this command:

NXF_VER=25.04.6 nextflow run nf-core/rnavar \
        --input samplesheet_rnavar.csv \
        --outdir PROCESSING_rnavar \
        --genome GRCm38 \
        --skip_baserecalibration \
        -profile apptainer

I am using this configuration:

process.executor = 'slurm'
executor.queueSize = 5
process.memory = '64 GB'
process.cpus = 8
apptainer.enabled = true

Does anyone know if I can change any configuration or solve anything?

Thanks!

2

I’m guessing you’re trying to run this on an ARM mac using docker?

I suggest updating the multiqc module. There was a known issue with v1.30, which should be fixed if you use the latest image.

Xref 1.29 AMD docker container breaks on M4 ARM architecture with hardware virtualization · Issue #3238 · MultiQC/MultiQC · GitHub

3

Hi!

Thanks for answering!

No, I am using apptainer in an HPC with an x86_64 architecture and Intel processors.

I am calling directly the rnavar pipeline from github repo and I see that is using v1.29. I don’t know if I am able to use another version of this module along the pipeline. Or maybe I should download it and make the changes manually and locally.

4

Can you try again by running the dev version? Just add -r dev to the command

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5

Hi @matthdsm,

Using the dev version solved the issue! Do you think I should report that to their github?

Thanks for your help!

6

No need, this fix is already in dev and will integrated in the next release

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