nf-core download has wrong name for singularity converted containers

[maxulysse]

Description of the bug

nf-core download sarek produces
nf-core-gatk-4.4.0.0.img

nextflow run nf-core/sarek produces
quay.io-nf-core-gatk-4.4.0.0.img

Command used and terminal output

No response

System information

No response

[MatthiasZepper]

In a way, this is a feature and not a bug. In PRs #2336 and #2403 we implemented a dynamic registry resolution that allows to provide multiple, also custom or private, registries to pull containers from. The corresponding issue was #2311.

Hence, it is that the resulting container name need to be agnostic to the registry from which it was pulled. I assumed this feature request was part of a larger coordinated effort by Seqera and that Nextflow would receive corresponding updates to its container resolution to ensure container images are always found.

So far I can't recall ever having had issues with that and assumed this was due to Nextflow's versatile resolution, but maybe it also always worked, because we just happen to maintain a completely cluttered $NXF_SINGULARITY_CACHEDIR with hundreds of container images, so chances are that the respective image will be present in any case.

[adamrtalbot]

We can reproduce this problem with this repo which just contains the module in question: https://github.com/adamrtalbot/nf-experiments/tree/nf-core-download-fails

nf-core download adamrtalbot/nf-experiments -r nf-core-download-fails -s singularity -l quay.io --force

Downloaded image: nf-core-gatk-4.4.0.0.img

nextflow run  adamrtalbot/nf-experiments -r nf-core-download-fails

Image that is ran: quay.io-nf-core-gatk-4.4.0.0.img

When we run nf-core download for different modules, it generally downloads the Singularity version which includes the full URI. For a quick solution, we might need to stick on the registry to match nextflow run to match the names up although I think a better solution would be to change the Nextflow behaviour.

[adamrtalbot]

A quick workaround might be trying:

singularity.registry = ''

Which works on my mini test case.

[asp8200]

I believe I ran into the same problem some time ago:

https://nfcore.slack.com/archives/CGFUX04HZ/p1701112794985919

[MatthiasZepper]

I have written a fix. Not polished, but should work. Tests and reviews (later next week) welcome.

[MatthiasZepper]

Should be fixed with the nf-core tools release 2.13.1 today! 👌🎉

(I would still appreciate seeing an update to Nextflow as well at some point)