Merge pull request #513 from nextflow-io/devcontainers-cleanup

Devcontainers cleanup

Author: kenibrewer

.devcontainer/Dockerfile

@@ -1,4 +1,71 @@
-FROM ghcr.io/nextflow-io/training:latest
+FROM mcr.microsoft.com/devcontainers/universal:linux
 
-ENV NXF_VER=24.10.0
+USER root
+
+# 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=24.10.4
+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

@@ -1,20 +1,23 @@
 {
-    "name": "nfcore",
-    "build": {
-        "dockerfile": "Dockerfile",
-        "context": ".."
-    },
-    "remoteUser": "gitpod",
+    "name": "nextflow-training",
+
+    // Update this to pin the release tag before release
+    "image": "ghcr.io/nextflow-io/training:latest",
+    // Uncomment this and comment "image" when testing Dockerfile changes
+    // "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"
+        }
     },
     "workspaceFolder": "/workspaces/training",
     "workspaceMount": "source=${localWorkspaceFolder},target=/workspaces/training,type=bind", // Used for local devcontainers, ignored in Codespaces.
     "remoteEnv": {
         "NXF_HOME": "/workspaces/.nextflow",
-        "HOST_PROJECT_PATH": "/workspaces/training" //Codespaces and local devcontainers will both work with this.
+        "HOST_PROJECT_PATH": "/workspaces/training" // Codespaces and local devcontainers will both work with this.
     },
-    "postCreateCommand": "if [ -z \"$CODESPACES\" ]; then echo \"Local Development\"; else echo \"Codespaces Development\"; fi",
+    "postCreateCommand": "nextflow -version; if [ -z \"$CODESPACES\" ]; then echo \"Devcontainers Development\"; else echo \"Codespaces Development\";  fi",
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
@@ -27,17 +30,12 @@
             "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"
+    "remoteUser": "root"
 }

.github/gitpod.Dockerfile

@@ -1,22 +1,37 @@
-# 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: Docker image
 
 on:
-  pull_request:
-  push:
-    branches: [master]
-  release:
-    types: [published]
+  pull_request: # Build, don't push
+  push: { branches: [master] } # Build + push ('latest' tag)
+  release: { types: [published] } # Build + push (release tag)
+  workflow_dispatch: # Build + push (custom tag)
+    inputs:
+      tag_name:
+        description: "Docker image tag name"
+        type: string
+        required: true
 
 jobs:
-  push_to_registry:
-    if: github.repository == 'nextflow-io/training'
-    name: Build + Push Gitpod Docker image
+  build_push:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
     steps:
+      - name: Set tag variable
+        run: |
+          if [[ '${{ github.event_name }}' == 'release' ]]; then
+            echo "IMAGE_TAG=${{ github.event.release.tag_name }}" >> $GITHUB_ENV
+          elif [[ '${{ github.event_name }}' == 'workflow_dispatch' ]]; then
+            echo "IMAGE_TAG=${{ inputs.tag_name }}" >> $GITHUB_ENV
+          else
+            echo "IMAGE_TAG=latest" >> $GITHUB_ENV
+          fi
+
       - name: Check out the repo
         uses: actions/checkout@v4
 
@@ -27,18 +42,14 @@ jobs:
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Build / push latest image
-        uses: docker/build-push-action@v5
-        if: github.event_name != 'release'
-        with:
-          file: .github/gitpod.Dockerfile
-          push: ${{ github.event_name == 'push' }}
-          tags: ghcr.io/nextflow-io/training:latest
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
 
-      - name: Push release image
-        uses: docker/build-push-action@v5
-        if: github.event_name == 'release'
+      - name: Build / push image
+        uses: docker/build-push-action@v6
         with:
-          file: .github/gitpod.Dockerfile
-          push: true
-          tags: ghcr.io/nextflow-io/training:${{ github.event.release.tag_name }}
+          file: .devcontainer/Dockerfile
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ghcr.io/${{ github.repository }}:${{ env.IMAGE_TAG }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/docker.yml

@@ -1,6 +1,6 @@
 # Build and push the Docker image for building the site (mkdocs material)
 
-name: Build mkdocs docker image
+name: MkDocs image
 
 on:
   pull_request:

.github/workflows/mkdocs-docker.yml

@@ -9,7 +9,7 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.4"
         },
         "timestamp": "2025-02-19T11:57:20.215132756"
     }