From 5703505ca1a7ec727aac4b1b01a8d4bc74fcbbba Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 15 Oct 2025 14:56:16 +0200
Subject: [PATCH 1/6] Fix: Add updated devcontainer config for template

---
 .../.devcontainer/devcontainer.json               | 15 ++++++++++++---
 nf_core/pipeline-template/.devcontainer/setup.sh  |  9 +++++++++
 2 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/.devcontainer/devcontainer.json b/nf_core/pipeline-template/.devcontainer/devcontainer.json
index 1ae1f300d3..97c8c97fe3 100644
--- a/nf_core/pipeline-template/.devcontainer/devcontainer.json
+++ b/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"
+    }
 }
diff --git a/nf_core/pipeline-template/.devcontainer/setup.sh b/nf_core/pipeline-template/.devcontainer/setup.sh
index c14b6de433..e954806a2c 100644
--- a/nf_core/pipeline-template/.devcontainer/setup.sh
+++ b/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

From 6a34d0d2a350e65f2e833b9c2aa7a33e0b5d8331 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 15 Oct 2025 15:06:19 +0200
Subject: [PATCH 2/6] Add changelog entry

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5e2d853958..2f03f16cc7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # nf-core/tools: Changelog
 
+## [v3.4.1 - Ducol Dingo](https://github.com/nf-core/tools/releases/tag/3.4.0) - [2025-10-10]
+
+### Template
+
+- Fix devcontainer configuration for pipeline template
+
 ## [v3.4.0 - Ducol Dingo](https://github.com/nf-core/tools/releases/tag/3.4.0) - [2025-10-10]
 
 **Highlights**

From 8fbe06285647b7c83c2a3c3d0e108bfe572d8e24 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 15 Oct 2025 15:08:00 +0200
Subject: [PATCH 3/6] Change setup.sh script to be executable

---
 nf_core/pipeline-template/.devcontainer/setup.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 nf_core/pipeline-template/.devcontainer/setup.sh

diff --git a/nf_core/pipeline-template/.devcontainer/setup.sh b/nf_core/pipeline-template/.devcontainer/setup.sh
old mode 100644
new mode 100755

From 3d78b4b5fa65a38a8998d46b1cf9e035f7f6abbb Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 15 Oct 2025 15:09:38 +0200
Subject: [PATCH 4/6] Bump version

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 1f1afc90f1..bb5f81090b 100644
--- a/setup.py
+++ b/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()

From bb19c8b6c4dd8ae9c440fef31ac64c7877d48f15 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 15 Oct 2025 15:15:11 +0200
Subject: [PATCH 5/6] Add Path version to semantic version name

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2f03f16cc7..4c889016fe 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # nf-core/tools: Changelog
 
-## [v3.4.1 - Ducol Dingo](https://github.com/nf-core/tools/releases/tag/3.4.0) - [2025-10-10]
+## [v3.4.1 - Ducol Dingo Patch 1](https://github.com/nf-core/tools/releases/tag/3.4.0) - [2025-10-10]
 
 ### Template
 

From 4ff5df7fb78d4754c48c20b276e7360306a67788 Mon Sep 17 00:00:00 2001
From: JulianFlesch <julianflesch@googlemail.com>
Date: Wed, 15 Oct 2025 16:01:13 +0200
Subject: [PATCH 6/6] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4c889016fe..e7059b6a07 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@
 
 ### Template
 
-- Fix devcontainer configuration for pipeline 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]