Merge pull request #3835 from JulianFlesch/fix/template-devcontainer

Author: mashehu

CHANGELOG.md

@@ -1,5 +1,11 @@
 # nf-core/tools: Changelog
 
+## [v3.4.1 - Ducol Dingo Patch 1](https://github.com/nf-core/tools/releases/tag/3.4.0) - [2025-10-10]
+
+### Template
+
+- Fix devcontainer configuration for pipeline template [3835](https://github.com/nf-core/tools/pull/3835)
+
 ## [v3.4.0 - Ducol Dingo](https://github.com/nf-core/tools/releases/tag/3.4.0) - [2025-10-10]
 
 **Highlights**

nf_core/pipeline-template/.devcontainer/devcontainer.json

@@ -5,7 +5,16 @@
     "remoteUser": "root",
     "privileged": true,
 
-    // Mount full current path to make mounting into docker-outside-of-docker work
-    "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
-    "workspaceFolder": "${localWorkspaceFolder}"
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
+    }
 }

nf_core/pipeline-template/.devcontainer/setup.sh

@@ -1,4 +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 {{ name }} devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "3.4.0"
+version = "3.4.1"
 
 with open("README.md") as f:
     readme = f.read()