🔧 update image and bioconda container for VueGen to latest version

[enryH]

Update VueGen to the latest version.

[famosab]

Please request to join the github org in slack :) under #github-invitations, you can join slack here https://nf-co.re/join

[famosab]

Maybe you can add something that renders the versions.yml file to the nf-test file because it seems to me that the versions are not correctly rendered in the snap :)

I think you can find it in other modules but you will need to adjust the .nf.test file and add

path(process.out.versions[0]).yaml

[enryH]

I saw that the main.nf did not correctly implement getting the version, so I changed it to

python -c "import vuegen; print(vuegen.__version__)"

Is the other change something different?

[famosab]

Is the other change something different?

Its helpful for a reviewer to not only see the version md5sum but how its actually printed in the end. So I would like to see that :) Its just one line added to the nf.test file.

[enryH]

Ok. I get it know. So when specifying in main.nf.test for a test under snapshot

...
            assertAll(
                { assert process.success },
                {
                    assert snapshot([
                        versions: path(process.out.versions[0]).yaml,
                    ]).match()
                }
            )

then the snapshot displays the file content of a yaml file in a structured way:

        "content": [
            {
                "versions": {
                    "VUEGEN": {
                        "vuegen": "0.5.1"
                    }
                }
            }
        ],

[famosab]

Can we get this container moved to the nf-core quay.io please?

[enryH]

Do I need special permission? are there instructions for moving it?

[mashehu]

a core member (like me) needs to do it. could you prepare it according to step 2 here please https://nf-co.re/docs/checklists/community_governance/core_team#making-custom-docker-containers-for-modules

[enryH]

ok. We have a Dockerfile and I will add it to the module here, see: Multiomics-Analytics-Group/nf-vuegen#1

[enryH]

I see that most core modules 'only' have a conda environment file. Would you then auto-build the docker container (I like wave, but so far i think one has to either use wave or docker, and cannot 'just' use wave for modules which do not have their own docker images)

[mashehu]

if you have everything in a conda env file, you can just use seqera containers to build docker and singularity images: https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers

[enryH]

done.

[enryH]

I do not get the errors on the CI (actions). Locally it worked, but codespace nf-test fails both for singularity and conda.

[mashehu]

looks like a problem with quarto. you should be able to test singularity in github codespaces

[enryH]

So I see issues on singularity with deno.

 /opt/conda/bin/quarto: line 197: /opt/conda/bin/tools/x86_64/deno: No such file or directory
    [2025-10-24 10:02:23,660] vuegen: ERROR - Error running 'Vuegen Test' html report: Command '['quarto', 'render', 'quarto_report/quarto_report.qmd']' returned non-zero exit status 127.

Quick search reveals @mahesh-panchal ran into the same issue using quarto. Will try to follow his approach:

https://github.com/mahesh-panchal/quarto-docker-singularity-problem

[enryH]

Ok. No I see the OsError you suspected @mashehu:

  error: Uncaught (in promise) Error: Read-only file system (os error 30): mkdir '/home/runner/.cache/quarto'
      Deno.mkdirSync(dir, { recursive: true });
           ^
      at Object.mkdirSync (ext:deno_fs/30_fs.js:192:3)
      at ensureDirSync (file:///opt/conda/bin/quarto.js:1881:10)
      at quartoDir (file:///opt/conda/bin/quarto.js:36030:3)
      at quartoCacheDir (file:///opt/conda/bin/quarto.js:36022:10)
      at file:///opt/conda/bin/quarto.js:38736:23

I will try to work on it in a GitHub workspace to track down the apptainer issue:

https://apptainer.org/docs/user/main/cli/apptainer_cache.html

[mahesh-panchal]

I suggest adding these lines too:

modules/modules/nf-core/quartonotebook/main.nf

Lines 56 to 59 in 0c47e41

	# Set environment variables needed for Quarto rendering
	export XDG_CACHE_HOME="./.xdg_cache_home"
	export XDG_DATA_HOME="./.xdg_data_home"

[enryH]

ok. Thanks @mahesh-panchal. This fixed this error. Now I just need to see how to set the latex path correctly:

Rendering PDF
running lualatex - 1

No TeX installation was detected.

Please run 'quarto install tinytex' to install TinyTex.
If you prefer, you may install TexLive or another TeX distribution.

[mahesh-panchal]

I think you would need to add it to your container/ env description, but since you're using quarto, then could you use typst (https://quarto.org/docs/output-formats/typst.html) instead of TeX to generate the pdf?