This might not be exactly an nf-core question but it's somewhat related. I noticed that modules using Wave containers (community.wave.seqera.io) seems to fail when using Singularity with

ext.singularity_pull_docker_container = true

It looks like the

PATH

environment variable is supposed to be updated by

shell-hook.sh

which is called in the

ENTRYPOINT

section in the Dockerfile, but

singularity exec

doesn't invoke the

ENTRYPOINT

section which is translated to

%runscript

when converting from OCI image to SIF. The native Singularity images don't have this issue because the

shell-hook.sh

script is invoked in the

%environment

section. While this is not a critical issue, it would be nice to be consistent with where and when we update the environment variables and to allow users to run OCI-converted Wave containers with Singularity.

If you could please open an issue there with a minimal repo / more details that would be great, yes please 👍🏻

Makes sense and yes it only happens when using Singularity with Docker images (and specifically Docker images where the environment variables are updated with the ENTRYPOINT instruction instead of ENV)

@Junxuan Gao, can I ask why you are using

singularity_pull_docker_container

? Because I have been suggesting to remove this from the template, as I didn't see a use-case for it.

@Simon Pearce When we deploy our pipeline, we pre-cache all the images used by the pipeline into a shared cache directory to avoid the per-user blob cache that is used by singularity by default. We then point the Singularity cache dir for the pipeline to the shared cache. We use the Docker images instead of the native Singularity images on Wave because the native Singularity images don't have unique names (just

data

if you try to run

singularity pull

with

--disable-cache

)

The nf-core CLI has

nf-core pipeline download

for exactly this task

Thanks I will take a look

Please let us know if that is suitable for you, because I'm still keen to remove that

singularity_pull_docker_container

option if possible

That being said I think the issue I brought up regarding Wave using different directives for Docker vs Singularity is still worth looking into.

Yup, good to fix that either way - thank you 🙏🏻

@Junxuan Gao, did you fix your issue? I'm still keen to remove

singularity_pull_docker_container

in a future update