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Hi! I am experiencing an issue where some multiqc ...
# nf-test
s
Hi! I am experiencing an issue where some multiqc files inclued in the snapshot are disappearing in GHactions. This also happens when I run nf-test on an HPC. I am wondering what if you have seen anything similar before. This is an example of where this happens: github.com/genomic-medicine-sweden/metaval/…/87561844896
m
which MultiQC version?
but yeah, I have seen this before
s
1.35
How did you handle this issue?
m
I think it's an issue with a missing lib, let me see if I can find info about it
s
Thank you! I have also read that one might have: 
export_plots: false
in 
assets/multiqc_config.yml
m
that could be it too
Are you running on bianca, or another secure cluster?
s
I usually run on dardel but for the PR I posted I ran locally and the issue is on GHaction.
m
What is your system locally?
s
mac
m
with docker I assume
s
yes!
m
You have this config file https://github.com/genomic-medicine-sweden/metaval/blob/dev/conf/containers_docker_arm64.config That should allow for using a different container for MultiQC, have you tried it out?
s
I did not! Thank you, I will try it out!
You mean to use the 1.34, right?
m
No, I meant for the 1.35
s
Right! Will try it out!
Maybe I wasn’t clear. When I generate the snapshots locally using docker, all of the multiqc files are there but when I update the snapshots in github, it is that the multiqc files are missing.
m
facepalm
sorry, I mis-understood
So yeah, I have seen the reverse issue that you have
s
No worries 🙂
m
this is running on which runners?
s
m
what happens if you generate the snapshot in a github codepace
s
I am testing now and I will get back to you
👍🏻 1
No issue if I generate the snapshot in guthub codespace
m
ok, so definitively something is wrong with GHA itself
m
you mean "no issue" as in they are the same as when you generate them locally?
s
Or wait!
When I generate them locally in github codespace the multiqc files disappear
m
oh
🫠
s
I meant no issues as the tests were passing 😄 but some multiqc files are missing both locally and on gh actions
shakefist 1
m
what system are you running to have the files, arm (=apple silicon) or x86?
s
x86
m
can you try on your machine with conda?
s
sure!
Copy code
Caused by:
    Failed to create Conda environment
      command: conda env create --prefix /Users/xxxxx/metaval/.nf-test/tests/e9812bb1572a7a3bbcba73a2f8198e85/work/conda/env-4e7a2806bf21778d59d5eb71300de9f9 --file /Users/xxxxxx/metaval/modules/nf-core/untar/environment.yml
      status : 1
      message:
        Collecting package metadata (repodata.json): ...working... done
        Solving environment: ...working... failed

        ResolvePackageNotFound:
          - conda-forge::sed=4.8
It seems that there is an issue with the untar module
Not sure why 😕
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