🔧 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