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Hi, I'm not sure this is the right place where to ...
# multiqc
m
Hi, I'm not sure this is the right place where to ask this but I'm having an issue on mac that I discovered by setting up nf-test in my pipeline: when I run it locally on my mac, in the results/multiqc folder I only find:
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multiqc
├── multiqc_data
└── multiqc_report.html
while on github it also has the plots folder:
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multiqc
├── multiqc_data
├── multiqc_plots
└── multiqc_report.html
can anyone please help me in finding why and how/where change the settings on my mac in order to align it with the github settings? Now to make the CI tests succeed I had to run nf-test on gitpod to generate a working snap
p
The plots dir is only created if you set export_plots to true (config file or CLI)
Do you have a ~/.multiqc_config file or similar that might be setting it to false locally or anything weird? 🤔
You can check the verbose multiqc_data/multiqc.log file - at the start it prints the configs that it's found
m
That's the mac issue @Júlia Mir and you were talking about, right?
j
yes I think it's the same issue, I saw this message in the logs
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Static plot export uses Kaleido - a tool that is unstable under conflicting architectures, so MultiQC will not save static PNG/PDF/SVG plots to disk. If you still need those, please use a container with a compatible architecture.
m
Hi, apologize for coming back after a while (and my probably #C043FMKUNLB) ... I have a similar message as Júlia in the multiqc.log:
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WARNING: Detected a Rosetta process, implying that MultiQC is running inside an x86_64 container, but hosted by Apple Silicon.

Static plot export uses Kaleido - a tool that is unstable under conflicting architectures, so MultiQC will not save static PNG/PDF/SVG plots to disk. If you still need those, please use a container with a compatible architecture. The official Dockerhub image multiqc/multiqc:latest is available for both platforms, and can be pulled with:

docker pull multiqc/multiqc:latest
...as a shortcut I also tried to set 
export_plots: false
in assets/multiqc_config.yml but if I do so there is a failing test in nf-core pipelines lint:
p
The log message is just a warning, not an error
It's just telling you that it's automatically setting 
export_plots: false
for you
m
Hi Phil thanks, I would like to solve it so that I can run nf-test locally with the same results of what I have on github to avoid the need of checking on gitpod before any PR. How should I tell the pipeline to use the correct container in order to align with export_plots: true?
...as a shortcut in the meanwhile I tried to set 
export_plots: false
in the pipeline assets/multiqc_config.yml (so that also in github they will not be created) but this is not allowed by nf-core pipelines lint:
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[✗] 1 Pipeline Test Failed ────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                             │
│ multiqc_config: assets/multiqc_config.yml does not contain 'export_plots: true'.
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