nf-core · JulianFlesch · May 14, 2025 · May 14, 2025 · May 14, 2025 · May 14, 2025
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,9 +1,12 @@
 {
     "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",
+
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {}
+    },
+
+    "remoteUser": "vscode",
 
     // Configure tool-specific properties.
     "customizations": {

diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+printf "export PS1='\\[\\e[3;36m\\]\${PWD#/workspaces/} ->\\[\\e[0m\\] '\n" >> $HOME/.bashrc
+export PS1='\[\e[3;36m\]${PWD#/workspaces/} ->\[\e[0m\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Install nf-core tools in editable mode
+python -m pip install -r requirements-dev.txt -e . --no-cache-dir
+
+# Install pre-commit hooks
+pre-commit install --install-hooks
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
@@ -28,11 +28,11 @@ jobs:
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev
 
-      - name: Build nfcore/gitpod:dev docker image
-        run: docker build --no-cache . --file nf_core/gitpod/gitpod.Dockerfile -t nfcore/gitpod:dev
+      - name: Build nfcore/devcontainer:dev docker image
+        run: docker build --no-cache . --file nf_core/devcontainer/devcontainer.Dockerfile -t nfcore/devcontainer:dev
 
       - 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
+          docker push nfcore/devcontainer:dev
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -28,15 +28,15 @@ jobs:
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
 
-      - name: Build nfcore/gitpod:latest docker image
-        run: docker build --no-cache . --file nf_core/gitpod/gitpod.Dockerfile -t nfcore/gitpod:latest
+      - name: Build nfcore/devcontainer:latest docker image
+        run: docker build --no-cache . --file nf_core/devcontainer/devcontainer.Dockerfile -t nfcore/devcontainer:latest
 
       - name: Push Docker images to DockerHub (release)
         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 push nfcore/devcontainer:latest
+          docker tag nfcore/devcontainer:latest nfcore/devcontainer:${{ github.event.release.tag_name }}
+          docker push nfcore/devcontainer:${{ github.event.release.tag_name }}
diff --git a/.gitpod.yml b/.gitpod.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@
 
 - Add conda cache dir ([#3610](https://github.com/nf-core/tools/pull/3610))
 - Fixes a bug with the test-datasets subcommand [#3617](https://github.com/nf-core/tools/issues/3617)
+- Stop using Gitpod in favor of devcontainer for codespaces ([#3569](https://github.com/nf-core/tools/pull/3569))
 
 ## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02]
 

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -0,0 +1,21 @@
+# Test build locally before making a PR (from project root directory)
+#   docker build . -t devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
+
+# Uses mcr.microsoft.com/devcontainers/base:ubuntu
+FROM ghcr.io/nextflow-io/training:latest
+
+# Change user to vscode
+USER vscode
+
+# Add the nf-core source files to the image
+COPY --chown=vscode:vscode . /usr/src/nf_core
+WORKDIR /usr/src/nf_core
+
+# Change ownership of conda and nextflow bin
+RUN sudo chown -R vscode:vscode /usr/local/bin/ && \
+    sudo chown -R vscode:vscode /opt/conda
+
+# Install apptainer via conda
+RUN conda install --quiet --yes --update-all --name base \
+    conda-forge::apptainer>=1.4.1 && \
+    conda clean --all --force-pkgs-dirs --yes
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
@@ -1,8 +1,11 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
+    "remoteUser": "vscode",
+
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {}
+    },
 
     // Configure tool-specific properties.
     "customizations": {

diff --git a/nf_core/pipeline-template/.devcontainer/setup.sh b/nf_core/pipeline-template/.devcontainer/setup.sh
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+printf "export PS1='\\[\\e[3;36m\\]\${PWD#/workspaces/} ->\\[\\e[0m\\] '\n" >> $HOME/.bashrc
+export PS1='\[\e[3;36m\]${PWD#/workspaces/} ->\[\e[0m\] '
+
+# Update Nextflow
+nextflow self-update
diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml