I updated a module where the most recent version o...
# linting
f
I updated a module where the most recent version of the tool is only available via pip and needs some more dependencies installed to work via the pip installation. To use the most recent version of the tool I created wave containers that combine all tools necessary for the use and the tool itself. When I lint the module I get:
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╭─ [!] 2 Module Test Warnings ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                    ╷                                           ╷                                                                                                                                                                                                    │
│ Module name        │ File path                                 │ Test message                                                                                                                                                                                       │
│╶───────────────────┼───────────────────────────────────────────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ crabs/insilicopcr  │ modules/nf-core/crabs/insilicopcr/main.nf │ Unable to connect to container registry, code:  404, url: <https://community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:04f6c0370c0226c5>                                            │
│ crabs/insilicopcr  │ modules/nf-core/crabs/insilicopcr/main.nf │ Container versions do not match                                                                                                                                                                    │
│                    ╵                                           ╵                                                                                                                                                                                                    │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
When I check, the container is available. Does anyone know what is going on here?
p
I don't think it should have a
https://
prefix - did you add that?
Is it singularity or docker?
f
No I did not add that. I think its the docker container that is mentioned.
p
Where did you get the URL from?
f
From the web interface, this is how it looks in the module:
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        '<oras://community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:0cd5cb1e549e5033>':
        '<http://community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:04f6c0370c0226c5|community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:04f6c0370c0226c5>' }"
p
ok werid, then I'm not sure as that looks fine
f
Both of those are warnings so I was just curious why the container would not be found even though I can pull it locally and also the web interface says the build was successful
p
Can maybe repost to #CJRH30T6V as I know others have done it
I guess it's something weird / outdated in #CE5LG7WMB, but not certain
We're about to replace all of this infrastructure anyway
👍 1
f
Yeah I am probably going to leave it as is for now.
m
Why are the checksums different ?
0cd5cb1e549e5033
vs
04f6c0370c0226c5'
p
Singularity vs Docker - they are separate builds
Seqera Containers does native Singularity builds, so the recipe file is different (Singularity recipe instead of Dockerfile) = different checksum
👌 1
m
ty