Devcontainers cleanup

.devcontainer/Dockerfile

@@ -1,4 +1,69 @@
-FROM ghcr.io/nextflow-io/training:latest
+FROM mcr.microsoft.com/devcontainers/universal:linux
 
-ENV NXF_VER=24.10.0
+# Install util tools.
+# software-properties-common is needed to add ppa support for Apptainer installation
+RUN apt-get update --quiet && \
+    export DEBIAN_FRONTEND=noninteractive && \
+    apt-get install --quiet --yes \
+        apt-transport-https \
+        apt-utils \
+        sudo \
+        git \
+        less \
+        wget \
+        curl \
+        tree \
+        graphviz \
+        software-properties-common && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Apptainer (Singularity)
+RUN add-apt-repository -y ppa:apptainer/ppa && \
+    apt-get update --quiet && \
+    apt install -y apptainer && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Seqera Platform "Tower Agent"
+RUN curl -fSL https://github.com/seqeralabs/tower-agent/releases/latest/download/tw-agent-linux-x86_64 > tw-agent && \
+    chmod +x tw-agent && \
+    mv tw-agent /usr/local/bin/tw-agent
+
+# Set up directories
+RUN mkdir -p /workspaces/.nextflow && \
+    mkdir -p /workspaces/training/
+
+# Uncomment if we need to pin the Nextflow version
 ENV NXF_EDGE=0
+ENV NXF_VER=24.10.0
+ENV NXF_HOME=/workspaces/.nextflow
+
+# Install nextflow, nf-core, Mamba, and pytest-workflow
+RUN conda config --remove channels defaults && \
+    conda config --add channels bioconda && \
+    conda config --add channels conda-forge && \
+    conda config --set channel_priority strict && \
+    conda update --quiet --yes --all && \
+    conda install --quiet --yes --name base \
+        mamba \
+        nextflow \
+        nf-core \
+        nf-test \
+        black \
+        prettier \
+        pre-commit \
+        linkify-it-py \
+        pytest-workflow && \
+    conda clean --all --force-pkgs-dirs --yes
+
+# Cleanup
+RUN printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc
+
+# Update Nextflow
+RUN nextflow self-update && nextflow -version
+
+RUN unset JAVA_TOOL_OPTIONS
+
+# RUN export PS1='\t -> '
+RUN export PS1='\[\e[3;36m\]${PWD/*//} ->\[\e[0m\] '

.devcontainer/devcontainer.json

@@ -1,18 +1,21 @@
 {
-    "name": "nfcore",
-    "build": {
-        "dockerfile": "Dockerfile",
-        "context": ".."
-    },
-    "remoteUser": "gitpod",
+    "name": "nextflow-training",
+
+    // Comment this and uncomment "build" if testing Dockerfile
+    // "image": "ghcr.io/nextflow-io/training:latest",
+
+    // Comment this and uncomment "image" before release
+    "build": { "dockerfile": "Dockerfile", "context": ".." },
+
     "features": {
-        "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
+        "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {
+            "version": "latest"
+        },
+        "ghcr.io/devcontainers/features/common-utils:2": { "version": "latest" }
     },
-    "workspaceFolder": "/workspaces/training/",
-    "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
     "remoteEnv": {
         "NXF_HOME": "/workspaces/.nextflow",
-        "HOST_PROJECT_PATH": "${localWorkspaceFolder}"
+        "HOST_PROJECT_PATH": "/workspaces/training/"
     },
     // Configure tool-specific properties.
     "customizations": {
@@ -26,17 +29,11 @@
             "extensions": [
                 "ms-python.python",
                 "ms-python.vscode-pylance",
-                "nf-core.nf-core-extensionpack",
-                "nextflow.nextflow",
-                "codezombiech.gitignore"
+                "nf-core.nf-core-extensionpack", // nf-core recommended extensions
+                "nextflow.nextflow", // Nextflow VS Code extension
+                "codezombiech.gitignore", // Language support for .gitignore files
+                "cssho.vscode-svgviewer" // SVG viewer
             ]
         }
-    },
-    "portsAttributes": {
-        "3000": {
-            "label": "Application",
-            "onAutoForward": "openPreview"
-        }
-    },
-    "postCreateCommand": "mkdir -p /workspace && ln -s /workspaces /workspace/gitpod"
+    }
 }

.github/workflows/docker.yml

@@ -1,8 +1,8 @@
-# Build and push the Docker image for GitPod
+# Build and push the Docker image for GitHub Codespaces
 # - Only pushes if push or release
 # - Builds without push for PRs to check the Dockerfile
 
-name: Build GitPod Docker image
+name: Build dev Docker image
 
 on:
   pull_request:
@@ -14,7 +14,7 @@ on:
 jobs:
   push_to_registry:
     if: github.repository == 'nextflow-io/training'
-    name: Build + Push Gitpod Docker image
+    name: Build + Push dev Docker image
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
@@ -31,14 +31,14 @@ jobs:
         uses: docker/build-push-action@v5
         if: github.event_name != 'release'
         with:
-          file: .github/gitpod.Dockerfile
+          file: .devcontainer/Dockerfile
           push: ${{ github.event_name == 'push' }}
           tags: ghcr.io/nextflow-io/training:latest
 
       - name: Push release image
         uses: docker/build-push-action@v5
         if: github.event_name == 'release'
         with:
-          file: .github/gitpod.Dockerfile
+          file: .devcontainer/Dockerfile
           push: true
           tags: ghcr.io/nextflow-io/training:${{ github.event.release.tag_name }}