merge to main pre transfer

[nickp60]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/funcprofiler branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[vinisalazar]

I also couldn't figure out this failing check... apparently HUMANN modules are pulling Singularity images during runtime?

[miraep8]

This may be helpful. Could try bumping your pipeline version of nextflow to >= 25.04 and see if that resolves it? But they also seem fine with one ignoring it.

[vinisalazar]

Thanks @miraep8 that is very helpful. Will have a go at debugging this later today.

[miraep8]

Just tried a very simple test to see if explicitly listing the containers in the humann module helps the test find them when its running the download. Will fix linting in a sec hold on.

[miraep8]

I have one or two more things to try (locally first)🤔 If it doesn't work I will revert to the last commit before I started messing about.

[nickp60]

Its pulling in the null container cause its expecting either a HUMANN3_* or HUMANN4_* prefix to the process name; not sure why this wasn't raising an issue during local testing

[miraep8]

Just to bring you up to speed too Vini etc - the download test is now passing 🎉 (Nick and I spent some time trying to debug it and in the end he had the idea of trying some dummy processes that don't get added to the manifest, but do show up under nextflow inspect - so do have their containers downloaded). Its a bit hacky - but it should allow the pipeline to download properly.

Nick is off next week, I was going to spend some time trying to debug the remaining tests next week! Feel free to jump in if you have time/inclination though of course. Then when we get this merged/Nick comes back from vacation then we make the first release? 😄

[vinisalazar]

Hi @miraep8, thank you and Nick for this great effort! Yes – also had the week off (as in, had to work on other stuff 😂) last week but tomorrow I can jump back on this.

[vinisalazar]

any idea of what is happening with the other failing check? I inspected some of the logs and was intrigued that each one was pointing to a different error