nf-core
Add documentation about using different devcontainers for codespaces
Following from the tools issue https://github.com/nf-core/tools/issues/2158 we will need to add documentation specifying that we have two devcontainer.json to use in GitHub codespaces. One for working on nf-core/tools and a different one for working in pipelines.
It would be great to have information on devcontainers in the docs on VS Code, such as links to any existing devcontainer.json files.
Where should one pull an up-to-date nf-core Docker container? nf-core/base hasn't been updated in 2 years.
If I use nextflow/nextflow:23.10.0 for the devcontainer image, I then can't install any features (e.g., mamba or docker-in-docker) due to the error: ./utils.sh: line 43: apt-get: command not found, which is due to centos rhel fedora used for the nextflow/nextflow:23.10.0 image.
Hi @nick-youngblut. What devcontainer are you trying to use? The Docker container for nf-core/tools is nfcore/tools, but in our devcontainer.json files we use nfcore/gitpod which has nf-core/tools and nextflow installed.
I ended up just using an Ubuntu:22.04 and installing Nextflow via micromamba. I'd be happy to share my devcontainer.json (and associated postCreateCommand script), if you'd like.