dev -> main for 3.4.1

CHANGELOG.md

@@ -1,5 +1,13 @@
 # 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))
+- Fix Jinja2 template formatting in nextflow.config ([#3836](https://github.com/nf-core/tools/pull/3836))
+- Add codespaces badge to template README ([#3824](https://github.com/nf-core/tools/pull/3824))
+
 ## [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

nf_core/pipeline-template/README.md

@@ -13,6 +13,7 @@
 
 {% endif -%}
 {% if github_badges -%}
+{% if codespaces %}[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/{{ name }}){% endif %}
 [![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/nf-test.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/{{ name }}/actions/workflows/linting.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/linting.yml){% endif -%}
 {% if is_nfcore -%}[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/{{ short_name }}/results){% endif -%}

nf_core/pipeline-template/nextflow.config

@@ -53,8 +53,8 @@ params {
     {%- if test_config %}
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+    {%- if nf_core_configs %}
 
-    {%- if nf_core_configs -%}
     // Config options
     config_profile_name        = null
     config_profile_description = null

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()