Are we ok to remove

.gitpod.yml

config files from the pipeline template / core repos now? 🤔

YES

not on the website… https://nf-co.re/docs/tutorials/gitpod/overview

Not yet

We should do it together with the migration to devcontainers in my opinion. The container needs to be corrected in particular

Yup, fair point 👍🏻

Where's the Dockerfile?

There isn't one 😁

Then it's likely missing what we're using like apptainer and docker

Nope, docker is here, apptainer is here

OK. I'll have to look over it later. I've a bunch of meetings from 13.00

The one part we haven't fully resolved is getting it to work well both locally and on codespaces. @Jonathan Manning has been working on that and I owe him a review on this PR to resolve that.

> Definitely keen to hear what others think though. Especially if anyone can figure out how to resolve local + codespaces into a single devcontainer setup, something that we haven't quite been able to manage yet. After a few separate rabit-hole attempts I convinced myself this wasn't possible due to mostly to the docker-outside-docker. You have to make the local paths valid both on the main container and any Nexflow workers, and than involves using variables specific to the local devcontainers setup. Happy for a smarty-pants to prove me wrong though, or maybe we do docker-in-docker (I don't remember the case against that)

perhaps this is not relevant on this thread but during the hackathon I’ve noticed Docker not working on code spaces while working fine on gitpod. have the feeling (also using solely code spaces in class) it’s still not very stable. just my own feeling? the consequence has been I couldn’t test all profiles on github while I could on gitpod

Could you elaborate? We had problems with Codespaces builds failing on some earlier versions but I hadn't heard of any problems since the 2.1.4 release..

sure sorry. the issue is with pipeline template v.3.2.0. (or any update to codespaces, can’t say). when I load a codespace from an nf-core pipeline repo created with nf-core tools v.3.2.0, I can’t run an nf-test with

--profile docker

because the docker daemon is not working. checking

docker ps

gives the message

Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?

Didn’t have an easy fix. I suppose it’s got to do with the docker in docker thingy, but I haven’t experienced this before. In order to answer your message I’ve double checked with the

.devcontainer

used in the nf-core modules repo, and it’s different from the one shipped with the pipeline template, in particular the modules one has these features:

"features": {
        "<http://ghcr.io/devcontainers/features/github-cli:1.0.11|ghcr.io/devcontainers/features/github-cli:1.0.11>": {
            "digest": "sha256:464564228ccdd6028f01f8a62a3cfbaf76e9ba7953b29ac0e53ba2c262604312"
        },
        "<http://ghcr.io/devcontainers/features/docker-in-docker:2.9.2|ghcr.io/devcontainers/features/docker-in-docker:2.9.2>": {
            "digest": "sha256:9074d8eaf4585ab1498c81a8762078992725614fc7a9cfafe799aa22717a6bbf"
        }
    }

and when spinning up a codespace with this one, the docker daemon works. I’ve tested it by adding these to the

devcontainer.json

in the nf-core pipeline’s fork, and the docker daemon works. so it might be perhaps be an easy fix to the next template release? and/or inform pipeline developers in the meanwhile. this is only important to run nf-tests when developing local modules or local workflows in a pipeline I suppose, but it prevents from testing them with docker. I’d be quite in favour of running all conda, docker, singularity before making a pull request, even if it’s local modules. I didn’t notice this difference in the

devcontainer.json

definition until now, so during the hackathon I’ve developed in gitpod where the problem doesn’t appear. hence my message here.

ohhh you're not talking about the training.nextflow.io codespaces devcontainer, you're talking about launching a codespaces from the pipeline devcontainers config?

Something else to consider for the Devcontainer documentation: https://nfcore.slack.com/archives/CE5LG7WMB/p1743781922533119