Hi, I've been trying for a bit to fix

UNIVERSC

module. After some debugging I finally manage to make it work on github runner but for that I need to use oras:// protocol for singularity (OOM error during convertion if I use the same container). But doing so, the linting now fails. What would be the best way to deal with this issue ?

why oras?

Because I need to pull the sif image without the OCI conversion that comes from using directly quay.io url.

and the one from galaxy is not working?

Unfortunately the tool is using cellranger and isn't available through bioconda.

Oh I see

If I do

container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
        '<https://quay.io/nf-core/universc:1.2.5.1-sif>' :
        '<http://quay.io/nf-core/universc:1.2.5.1|quay.io/nf-core/universc:1.2.5.1>' }"

I get

While checking container encryption: could not open image /path/quay.io-nf-core-universc-1.2.5.1-sif.img: image format not recognized

While the following works

container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
        '<oras://quay.io/nf-core/universc:1.2.5.1-sif>' :
        '<http://quay.io/nf-core/universc:1.2.5.1|quay.io/nf-core/universc:1.2.5.1>' }"

Can we host sif on quay.io?

I tried and it works 😅

but nextflow or singularity seems to have an issue with it

Just if you use https:// instead of oras://

singularity run <https://quay.io/nf-core/universc:1.2.5.1-sif>

give

image format not recognized

while

singularity run <oras://quay.io/nf-core/universc:1.2.5.1-sif>

works

☝️ this works in any non-ancient apptainer/singularity. There also seems to be 10 or so modules having

oras://

URLS already (for what that is worth).