Deprecate devcontainer.json

[kenibrewer]

Given that gitpod classic is going away beginning of March and the new gitpod also supports the devcontainer.json specification, we should probably start a project to migrate fully over to devcontainer.json

We should also migrate any links and references we use to "Open in Gitpod" over to "Open in Codespaces" as new gitpod will have no free tier at all while Codespaces will be maintaining its free tier allowance.

Here's a list of suggested tasks:

• Rename nf_core/gitpod/gitpod.Dockerfile to nf_core/devcontainer/devcontainer.Dockerfile
• Switch base image in devcontainer.Dockerfile from gitpod base to codespaces base (or maybe Seqera containers base)
• Delete nf_core/pipeline-template/.gitpod.yml
• Change the docker image that we publish via CI from nfcore/gitpod to nfcore/devcontainer`
• Remove "remoteUser": "gitpod", from devcontainer.json.

[mahesh-panchal]

I guess you don't mean deprecate, but update the devcontainer.json.

I agree with the list of suggested tasks.

Another thing that I've been wanting to do is really trim down the container if possible. This would definitely be a good time to change base too. I was wondering if having a Pixi toml to install packages on container spin up would be useful instead of installing with Conda in the image.

We would probably also need a blog post too describing the change from Gitpod Classic to using Devcontainers and it working with Gitpod Flex if desired.