nf-core · JulianFlesch · Sep 3, 2025 · May 14, 2025 · May 14, 2025 · May 14, 2025
diff --git a/.devcontainer/build-devcontainer/Dockerfile b/.devcontainer/build-devcontainer/Dockerfile
@@ -0,0 +1,38 @@
+# devcontainers/miniconda image based on debian (bookworm)
+# see tags and images: https://mcr.microsoft.com/en-us/artifact/mar/devcontainers/miniconda/tags
+FROM "mcr.microsoft.com/devcontainers/miniconda@sha256:8e262a2664fab1d53054738d3633338558a2078ce66d3abde55c130f0d5da94f" AS build
+
+# copy this repo at current revision
+COPY . /root/nfcore-tools/
+
+# Explicitly reinstall python 3.13 via conda
+# install local nf-core tools version, and precommit hooks
+RUN cd /root/nfcore-tools/ && \
+    conda install -y python=3.13 && \
+    pip install --no-cache-dir --upgrade pip setuptools wheel pre-commit && \
+    pip install -r requirements.txt --no-cache-dir -e . && \
+    pre-commit install --install-hooks && \
+    rm -rf /root/.cache/pip
+
+# Install nextflow and nf-test via conda and run conda clean
+RUN conda install -c bioconda -y nextflow nf-test && \
+    conda clean -afy
+
+# Install dependencies for apptainer build and apptainer and run apt clean
+RUN apt-get update --quiet && \
+    apt-get install -y curl rpm2cpio cpio && \
+    curl -s https://raw.githubusercontent.com/apptainer/apptainer/main/tools/install-unprivileged.sh | bash -s - /usr/local/apptainer && \
+    echo "PATH=/usr/local/apptainer/bin:$PATH" >> $HOME/.bashrc && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Final stage to copy only the required files after installation
+FROM "mcr.microsoft.com/devcontainers/base:debian@sha256:ce2e9e611939e611b737362c045bb6d3449bb3efb84898525d724aace1737b90" AS final
+
+# Copy only the conda environment and site-packages from build stage
+COPY --from=build /opt/conda /opt/conda
+COPY --from=build /root/nfcore-tools/nf_core /root/nfcore-tools/nf_core
+
+# Copy aptainer install from build stage
+COPY --from=build /usr/local/apptainer /usr/local/apptainer
+COPY --from=build /root/.bashrc /root/.bashrc
diff --git a/.devcontainer/build-devcontainer/devcontainer.json b/.devcontainer/build-devcontainer/devcontainer.json
@@ -0,0 +1,40 @@
+{
+    "name": "nfcore-devcontainer-build",
+
+    // installs python3.13, nf-core tools from current workspace, nextflow, nf-test,
+    // and apptainer based on mcr.microsoft.com/devcontainers/miniconda image
+    "build": {
+        "dockerfile": "./Dockerfile",
+        "context": "../.."
+    },
+
+    "features": {
+        "ghcr.io/devcontainers/features/docker-outside-of-docker:1.6.3": {}
+    },
+
+    "remoteEnv": {
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "remoteUser": "root",
+    "privileged": true,
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": [
+                "charliermarsh.ruff",
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "nf-core.nf-core-extensionpack"
+            ]
+        }
+    }
+}
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,21 +1,14 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python"
-            },
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "remoteUser": "root",
+    "privileged": true
 }
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the nf-core devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
@@ -17,22 +17,45 @@ jobs:
     # Only run for the nf-core repo, for releases and merged PRs
     if: ${{ github.repository == 'nf-core/tools' }}
     env:
-      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
-      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+      TARGET_PLATFORM: "linux/amd64,linux/arm64"
     strategy:
       fail-fast: false
     steps:
       - name: Check out code
         uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
-      - name: Build nfcore/tools:dev docker image
-        run: docker build --no-cache . -t nfcore/tools:dev
+      - name: Set up QEMU for multi-architecture build
+        uses: docker/setup-qemu-action@29109295f81e9208d7d86ff1c6c12d2833863392 # v3
 
-      - name: Build nfcore/gitpod:dev docker image
-        run: docker build --no-cache . --file nf_core/gitpod/gitpod.Dockerfile -t nfcore/gitpod:dev
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435 # v3
 
-      - name: Push Docker images to DockerHub (dev)
-        run: |
-          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push nfcore/tools:dev
-          docker push nfcore/gitpod:dev
+      - name: Log in to Docker Hub
+        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772 # v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASS }}
+
+      # Retry building tools image once after a delay because of
+      # irregularly occuring 403 http errors when installing nf-test
+      - name: Build nfcore/tools image (dev)
+        uses: nick-fields/retry@ce71cc2ab81d554ebbe88c79ab5975992d79ba08 # v3
+        with:
+          timeout_minutes: 20
+          max_attempts: 2
+          retry_wait_seconds: 60
+          command: |
+            docker buildx build \
+            --platform ${{ env.TARGET_PLATFORM }} \
+            -t nfcore/tools:dev \
+            --push --no-cache .
+
+      - name: Build and push nfcore/devcontainer:dev image (dev)
+        uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3
+        with:
+          configFile: .devcontainer/build-devcontainer/devcontainer.json
+          imageName: nfcore/devcontainer
+          imageTag: dev
+          platform: ${{ env.TARGET_PLATFORM }}
+          push: always
+          noCache: true
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -1,6 +1,6 @@
 name: nf-core Docker push (release)
 # This builds the docker image and pushes it to DockerHub
-# Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
+# Runs on nf-core repo releases
 on:
   release:
     types: [published]
@@ -17,26 +17,39 @@ jobs:
     # Only run for the nf-core repo, for releases and merged PRs
     if: ${{ github.repository == 'nf-core/tools' }}
     env:
-      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
-      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+      TARGET_PLATFORM: "linux/amd64,linux/arm64"
     strategy:
       fail-fast: false
     steps:
       - name: Check out code
         uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
-      - name: Build nfcore/tools:latest docker image
-        run: docker build --no-cache . -t nfcore/tools:latest
+      - name: Set up QEMU for multi-architecture build
+        uses: docker/setup-qemu-action@29109295f81e9208d7d86ff1c6c12d2833863392 # v3
 
-      - name: Build nfcore/gitpod:latest docker image
-        run: docker build --no-cache . --file nf_core/gitpod/gitpod.Dockerfile -t nfcore/gitpod:latest
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@e468171a9de216ec08956ac3ada2f0791b6bd435 # v3
 
-      - name: Push Docker images to DockerHub (release)
+      - name: Log in to Docker Hub
+        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772 # v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASS }}
+
+      - name: Build and push nfcore/tools docker image (latest)
         run: |
-          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push nfcore/tools:latest
-          docker tag nfcore/tools:latest nfcore/tools:${{ github.event.release.tag_name }}
-          docker push nfcore/tools:${{ github.event.release.tag_name }}
-          docker push nfcore/gitpod:latest
-          docker tag nfcore/gitpod:latest nfcore/gitpod:${{ github.event.release.tag_name }}
-          docker push nfcore/gitpod:${{ github.event.release.tag_name }}
+          docker buildx build \
+           --platform ${{ env.TARGET_PLATFORM }} \
+           -t nfcore/tools:${{ github.event.release.tag_name }} \
+           -t nfcore/tools:latest \
+           --push --no-cache .
+
+      - name: Build nfcore/devcontainer:latest devcontainer image
+        uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3
+        with:
+          configFile: .devcontainer/build-devcontainer/devcontainer.json
+          imageName: nfcore/devcontainer
+          imageTag: ${{ github.event.release.tag_name }},latest
+          platform: ${{ env.TARGET_PLATFORM }}
+          push: always
+          noCache: true
diff --git a/.gitpod.yml b/.gitpod.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@
 
 - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674))
 - Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681))
+- Stop using Gitpod in favor of devcontainer for codespaces ([#3569](https://github.com/nf-core/tools/pull/3569))
 - Update dependency textual to v5 ([#3699](https://github.com/nf-core/tools/pull/3699))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.7 ([#3697](https://github.com/nf-core/tools/pull/3697))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.17.1 ([#3698](https://github.com/nf-core/tools/pull/3698))

diff --git a/Dockerfile b/Dockerfile
@@ -32,7 +32,7 @@ RUN curl -s https://get.nextflow.io | bash \
     && mv nextflow /usr/local/bin \
     && chmod a+rx /usr/local/bin/nextflow
 # Install nf-test
-RUN curl -fsSL https://code.askimed.com/install/nf-test | bash \
+RUN curl -fsSL https://get.nf-test.com | bash \
     && mv nf-test /usr/local/bin \
     && chmod a+rx /usr/local/bin/nf-test
 

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
diff --git a/nf_core/pipeline-template/.devcontainer/devcontainer.json b/nf_core/pipeline-template/.devcontainer/devcontainer.json
@@ -1,20 +1,11 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python"
-            },
+    "remoteUser": "root",
+    "privileged": true,
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+    // Mount full current path to make mounting into docker-outside-of-docker work
+    "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
+    "workspaceFolder": "${localWorkspaceFolder}"
 }
diff --git a/nf_core/pipeline-template/.devcontainer/setup.sh b/nf_core/pipeline-template/.devcontainer/setup.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+# Update welcome message
+echo "Welcome to the {{ name }} devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml