A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

hello i get this error :
```─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮
│                ╷                              ╷                              │
│ Module name    │ File path                    │ Test message                 │
│╶───────────────┼──────────────────────────────┼─────────────────────────────╴│
│ numorph/3dunet │ modules/nf-core/numorph/3du… │ singularity_tag: Unable to   │
│                │                              │ resolve singularity          │
│                │                              │ container                    │
│                ╵                              ╵                              │
╰──────────────────────────────────────────────────────────────────────────────╯```
PR: <https://github.com/nf-core/modules/pull/12130>
i specify the container like this :      `container "<http://quay.io/nf-core/numorph-3dunet:1.0.9|quay.io/nf-core/numorph-3dunet:1.0.9>"`
all other tests pass. Not sure what I need to do to resolve this :sweat_smile: (from nf-core 4.0.3dev)

Did you add it to the skip list for singularity in skip-nf-test.json?

still get the error after adding it to skip nf-test singularity, na i did something wrong, sorry

i added it, but nf-test singularity still runs :face_with_peeking_eye:

okay, that's a bug then. will try to fix it. sorry

okidoki no worries :slightly_smiling_face: thank you for looking into it :pray:

Singularity should still work for cases like this, it just pulls and converts the docker image

we have the automatic singularity images for biocontainers and seqera containers, but not for things on <http://quay.io|quay.io> or elsewhere

It is also happening in <https://github.com/nf-core/modules/pull/11859/changes|github.com/nf-core/modules/pull/11859/changes>

will it work all the time or do we have some edge cases? otherwise I might drop this lint test completely instead of just having it skipped here <https://github.com/nf-core/tools/pull/4358>

I'm not sure what you mean.
If the image is from biocontainers or seqera containers we should be able to grab a singularity image easily

but currently we don't host converted docker containers from <http://quay.io|quay.io> or elsewhere

I mean the case that it converts the docker image.

as far as I know singularity can always convert docker images, given enough disk space and time.
Pulling the image directly is quicker, which is why we do it when possible

we want to catch the case where the singularity image is missing when it should be provided

ah, yes, so basically just searching for quay,io/biocontainers in the docker image name. t

updated the linting check accordingly <https://github.com/nf-core/tools/pull/4358>