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

nf-core

<https://github.com/nf-core/tools/issues/2357|About 2.5 years ago I asked> about getting the `apptainer` to download the singularity images rather than docker, and since then we still need to use the `singularity` profile instead.
Is it time to finally bulk update all the modules to fix this?
Also, why exactly do we have `task.ext.singularity_pull_docker_container` , when would someone want to use the docker (which has quite a large overhead of conversion) instead of singularity?

About <https://nf-co.re/blog/2024/seqera-containers-part-2|1 year ago> we laid out a plan for bulk updates to all containers - including properly dealing with apptainer. It's slow, but there is progress... <https://github.com/orgs/nf-core/projects/90>

Your issue is being tracked on that project board actually

Help always welcome! <@UV41DBFAT> is driving this project with me loosely in the background, but there's plenty to do.

I honestly can't really remember the `singularity_pull_docker_container` thing any more :thinking_face: It's been there for ages, I'm pretty sure that there was a reason for it. Not sure what it was now though..

Yeah, I know the plan was a year ago, see the thread. Where basically we go "oh, it'll be fixed soon"

It looks like the original reason was because <@UEB97FBN3> had a proxy issue: <https://nfcore.slack.com/archives/CJRH30T6V/p1602679889186600>

I have a feeling this isn't really required now we have much better tools for downloading containers

I can't see any example of anyone telling anyone to use it in a config, nor do we mention it on the website at all.
I think this could be safely removed :wink:

It would be nice to get rid of it :thinking_face:

Curious what <!subteam^S08LAB76NBU> thinks

if it is not useful, I also agree to remove it

Yeah I've never heard anyone actually using that

This is my suggestion:
```    container workflow.containerEngine in ['singularity', 'apptainer'] ?
        '<https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f3f7e07c7f261ec7fd86168d8a273624cc0aace8e28eb20e37ddfb2f8f9c75b/data>' :
        '<http://community.wave.seqera.io/library/fgbio:3.0.0--c1b70e1869d6fa49|community.wave.seqera.io/library/fgbio:3.0.0--c1b70e1869d6fa49>'```
(note you can see in <https://github.com/nf-core/modules/actions/runs/19238789294/job/54996011969#step:6:909|this CI run> that it is indeed pulling the singularity image correctly)

Also note that we don't need the `"${`  and `}"` surrounding it

(although I don't know what version of nextflow that might have changed)

Hmm, that is a 25.10.0 change with the strict syntax