"Local" nf-core modules without singularity container builds cause issues

[pontus]

It seems there's been a number of nf-core modules that have been patched locally in nf-core, relating to specific container builds. I'm not sure why these have been made, but they seem to lack singularity builds which makes offline use harder, causes needless rebuild wait and an overall suboptimal experience.

These specific builds don't seem to have been fed-back to nf-core/modules, so I'm not sure if there's a plan for them.

The ones I've seen are

modules/nf-core/bedtools/genomecov/main.nf
modules/nf-core/cat/fastq/main.nf
modules/nf-core/sortmerna/main.nf
modules/nf-core/star/align/main.nf
modules/nf-core/star/genomegenerate/main.nf

[pinin4fjords]

IIRC this is a product of Seqera Containers usage. @maxulysse was of the opinion that everything should be in quay.io, so mirrored SC containers there, leaving Singularity conversion to happen dynamically.

[edmundmiller]

Hey @maxulysse could you document why #1441 was necessary at the time? Just for reference in this conversation.

Is it just because it made it easier to mirror everything if it was all in quay.io?

Because nextflow inspect should make pulling all of the containers(at least docker) easy and make mirroring simple. See #1515

[maxulysse]

So for me, there is 2 components here:

• mirroring to quay.io
• removing links to direct download singularity containers.

The mirroring to quay.io was done because it was preferable to have a single registry to simplify local mirroring.
But hopefully we will be solving that with nextflow inspect.
I dropped the direct link to allow download of singularity container because it wasn't supported by nf-core/tools download, hence without that direct link, it was forcing a conversion.

[pontus]

Ok. If https://nf-co.re/blog/2024/seqera-containers-part-2 is something that's actually happening I guess this isn't worth caring about.

[pinin4fjords]

At a minimum, in the short term, I think we've agreed to revert the patches here which underly most of these issues.

[pontus]

Just for us to remember, giving issues today at least https://nfcore.slack.com/archives/CE8SSJV3N/p1745008545954919.

[pinin4fjords]

Sorry, this has been on my radar for a while, I'll try to get to it this week.

[pinin4fjords]

I believe this is covered by #1558, should be addressed in next release, closing for now