From 80b018200748f972dadca1ae0d0b91944db0e87c Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 14 May 2025 11:00:29 +0200
Subject: [PATCH 01/79] Renaming Dockerfile and location. Changing to building
 the Dockerfile locally for now

---
 .devcontainer/devcontainer.json                               | 4 +++-
 .../devcontainer.Dockerfile}                                  | 0
 2 files changed, 3 insertions(+), 1 deletion(-)
 rename nf_core/{gitpod/gitpod.Dockerfile => devcontainer/devcontainer.Dockerfile} (100%)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index fa1bfca649..1cd8533a74 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,6 +1,8 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
+    "build": {
+        "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile"
+    },
     "postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
     "remoteUser": "gitpod",
     "runArgs": ["--privileged"],
diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
similarity index 100%
rename from nf_core/gitpod/gitpod.Dockerfile
rename to nf_core/devcontainer/devcontainer.Dockerfile

From 7a8cebdd2d7e133531165816d66e1b86ce48f7b3 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 14 May 2025 13:53:27 +0200
Subject: [PATCH 02/79] change Container user. Change base Image for
 devcontainer

---
 .devcontainer/devcontainer.json              |  2 +-
 nf_core/devcontainer/devcontainer.Dockerfile | 10 ++++++----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 1cd8533a74..dd2ac8128e 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -4,7 +4,7 @@
         "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile"
     },
     "postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
-    "remoteUser": "gitpod",
+    "remoteUser": "nfcore-user",
     "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 2af42974f6..52ab69373b 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -2,7 +2,7 @@
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-FROM gitpod/workspace-base@sha256:7f35e401405c38ebc1185dfc3d6c066f73a524e8b86641453ea4690cc5c24fb6
+FROM mcr.microsoft.com/devcontainers/python:0-3.11-bullseye
 
 USER root
 
@@ -32,15 +32,17 @@ RUN apt-get update --quiet && \
 # Set PATH for Conda
 ENV PATH="/opt/conda/bin:$PATH"
 
+# Set our Username
+ENV CONTAINER_USER="nfcore-user"
+
 # Add the nf-core source files to the image
 COPY . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
 # Change ownership for gitpod
-RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
+RUN chown -R ${CONTAINER_USER}:${CONTAINER_USER} /opt/conda /usr/src/nf_core
+USER ${CONTAINER_USER}
 
-# Change user to gitpod
-USER gitpod
 # Install nextflow, nf-core, nf-test, and other useful tools
 RUN conda config --add channels bioconda && \
     conda config --add channels conda-forge && \

From 5fd706a4489e297cc1515f6b5818f88cd00fb156 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 14 May 2025 14:32:33 +0200
Subject: [PATCH 03/79] Remove installation of apptainer via apt-get because of
 404 from ppa

---
 nf_core/devcontainer/devcontainer.Dockerfile | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 52ab69373b..d46709046f 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -20,9 +20,6 @@ RUN apt-get update --quiet && \
     tree \
     graphviz \
     software-properties-common && \
-    add-apt-repository -y ppa:apptainer/ppa && \
-    apt-get update --quiet && \
-    apt-get install --quiet --yes apptainer && \
     wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
     bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
     rm Miniforge3-Linux-x86_64.sh && \

From 0d6e6a541a82750e7b29102c54d0c7da9d1556fb Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 14 May 2025 14:49:28 +0200
Subject: [PATCH 04/79] Create unprivileged user

---
 .devcontainer/devcontainer.json              | 2 +-
 nf_core/devcontainer/devcontainer.Dockerfile | 9 +++------
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index dd2ac8128e..75395f60c3 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -4,7 +4,7 @@
         "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile"
     },
     "postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
-    "remoteUser": "nfcore-user",
+    "remoteUser": "nemo",
     "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index d46709046f..e8caa3976c 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -29,16 +29,13 @@ RUN apt-get update --quiet && \
 # Set PATH for Conda
 ENV PATH="/opt/conda/bin:$PATH"
 
-# Set our Username
-ENV CONTAINER_USER="nfcore-user"
-
 # Add the nf-core source files to the image
 COPY . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
-# Change ownership for gitpod
-RUN chown -R ${CONTAINER_USER}:${CONTAINER_USER} /opt/conda /usr/src/nf_core
-USER ${CONTAINER_USER}
+RUN useradd -mU nemo
+RUN chown -R nemo:nemo /opt/conda /usr/src/nf_core
+USER nemo
 
 # Install nextflow, nf-core, nf-test, and other useful tools
 RUN conda config --add channels bioconda && \

From be2996e68e37559118616f0e6cd9188da1017b7c Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 14 May 2025 14:53:10 +0200
Subject: [PATCH 05/79] Change git workflow for container creation and use the
 correct container.

---
 .devcontainer/devcontainer.json              |  4 +---
 .github/workflows/push_dockerhub_dev.yml     |  6 +++---
 .github/workflows/push_dockerhub_release.yml | 10 +++++-----
 3 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 75395f60c3..08feb329c6 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,8 +1,6 @@
 {
     "name": "nfcore",
-    "build": {
-        "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile"
-    },
+    "image": "nfcore/tools-devcontainer",
     "postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
     "remoteUser": "nemo",
     "runArgs": ["--privileged"],
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 6409335ac7..25a5d192b1 100644
--- 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/tools-devcontainer:dev docker image
+        run: docker build --no-cache . --file nf_core/devcontainer/devcontainer.Dockerfile -t nfcore/tools-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/tools-devcontainer:dev
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
index d29b03b687..e3fdbfb8d1 100644
--- a/.github/workflows/push_dockerhub_release.yml
+++ b/.github/workflows/push_dockerhub_release.yml
@@ -28,8 +28,8 @@ 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/tools-devcontainer:latest docker image
+        run: docker build --no-cache . --file nf_core/devcontainer/devcontainer.Dockerfile -t nfcore/tools-devcontainer:latest
 
       - name: Push Docker images to DockerHub (release)
         run: |
@@ -37,6 +37,6 @@ jobs:
           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/tools-devcontainer:latest
+          docker tag nfcore/tools-devcontainer:latest nfcore/tools-devcontainer:${{ github.event.release.tag_name }}
+          docker push nfcore/tools-devcontainer:${{ github.event.release.tag_name }}

From 53dd172dbeb7ea76521034f3527dcf925e21b4a6 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 14 May 2025 14:56:57 +0200
Subject: [PATCH 06/79] Update instruction to build locally for testing

---
 nf_core/devcontainer/devcontainer.Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index e8caa3976c..06bad66594 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -1,5 +1,5 @@
-# Test build locally before making a PR
-#   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
+# Test build locally before making a PR (from project root directory)
+#   docker build . -t tools-devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
 FROM mcr.microsoft.com/devcontainers/python:0-3.11-bullseye

From dd6ddc3e53393220db29a2027aeb2c97f71f1007 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 14 May 2025 13:02:19 +0000
Subject: [PATCH 07/79] [automated] Update CHANGELOG.md

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 60afb1faab..6c01ffdcf1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -77,6 +77,7 @@
 - chore(deps): update python:3.12-slim docker digest to bae1a06 ([#3558](https://github.com/nf-core/tools/pull/3558))
 - Update CI to test template pipelines with nf-test ([#3559](https://github.com/nf-core/tools/pull/3559))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.9 ([#3563](https://github.com/nf-core/tools/pull/3563))
+- [DRAFT] Issues/3466 gitpod ([#3569](https://github.com/nf-core/tools/pull/3569))
 
 ## [v3.2.1 - Pewter Pangolin Patch](https://github.com/nf-core/tools/releases/tag/3.2.1) - [2025-04-29]
 

From 464d3bdd9ded9ae7da1053f35c19d46886cbc851 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 14 May 2025 15:44:21 +0200
Subject: [PATCH 08/79] More descriptive changelog entry

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6c01ffdcf1..aede081f1d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -77,7 +77,7 @@
 - chore(deps): update python:3.12-slim docker digest to bae1a06 ([#3558](https://github.com/nf-core/tools/pull/3558))
 - Update CI to test template pipelines with nf-test ([#3559](https://github.com/nf-core/tools/pull/3559))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.9 ([#3563](https://github.com/nf-core/tools/pull/3563))
-- [DRAFT] Issues/3466 gitpod ([#3569](https://github.com/nf-core/tools/pull/3569))
+- Stop using Gitpod in favor of devcontainer for codespaces ([#3569](https://github.com/nf-core/tools/pull/3569))
 
 ## [v3.2.1 - Pewter Pangolin Patch](https://github.com/nf-core/tools/releases/tag/3.2.1) - [2025-04-29]
 

From 2ee5fc1d76850395e336d08b931cc02e38081a86 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 11:18:39 +0200
Subject: [PATCH 09/79] Change base Image

---
 nf_core/devcontainer/devcontainer.Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 06bad66594..8749dced3e 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -2,7 +2,8 @@
 #   docker build . -t tools-devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-FROM mcr.microsoft.com/devcontainers/python:0-3.11-bullseye
+#FROM mcr.microsoft.com/devcontainers/python:0-3.11-bullseye
+FROM gitpod/workspace-base:2025-05-14-07-50-25
 
 USER root
 

From 776b2c8468caa324fb5af0f9394b2778d521942c Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 11:26:37 +0200
Subject: [PATCH 10/79] Change back to using gitpod user

---
 nf_core/devcontainer/devcontainer.Dockerfile | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 8749dced3e..20a77332e6 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -21,6 +21,9 @@ RUN apt-get update --quiet && \
     tree \
     graphviz \
     software-properties-common && \
+    add-apt-repository -y ppa:apptainer/ppa && \
+    apt-get update --quiet && \
+    apt-get install --quiet --yes apptainer && \
     wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
     bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
     rm Miniforge3-Linux-x86_64.sh && \
@@ -34,9 +37,8 @@ ENV PATH="/opt/conda/bin:$PATH"
 COPY . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
-RUN useradd -mU nemo
-RUN chown -R nemo:nemo /opt/conda /usr/src/nf_core
-USER nemo
+RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
+USER gitpod
 
 # Install nextflow, nf-core, nf-test, and other useful tools
 RUN conda config --add channels bioconda && \

From a5c66443309b7eabe620702c332b8566da3a8407 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 11:53:47 +0200
Subject: [PATCH 11/79] Remove comment

---
 nf_core/devcontainer/devcontainer.Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 20a77332e6..894ebb23f5 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -2,7 +2,6 @@
 #   docker build . -t tools-devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-#FROM mcr.microsoft.com/devcontainers/python:0-3.11-bullseye
 FROM gitpod/workspace-base:2025-05-14-07-50-25
 
 USER root

From c77a469d7bd0ffa737200f51d6e31bca17db908b Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 11:54:40 +0200
Subject: [PATCH 12/79] WIP: build container locally instead of pulling. Change
 to gitpod user. Update postCreateCommand to match context

---
 .devcontainer/devcontainer.json | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 08feb329c6..406b5dac23 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,8 +1,12 @@
 {
     "name": "nfcore",
-    "image": "nfcore/tools-devcontainer",
-    "postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
-    "remoteUser": "nemo",
+    // "image": "nfcore/tools-devcontainer",
+    "build": {
+        "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile",
+        "context": ".."
+    },
+    "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
+    "remoteUser": "gitpod",
     "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.

From 36e5f7a1b6b7e19c745e7aa00d9702ecb8b09fd3 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 12:01:05 +0200
Subject: [PATCH 13/79] Rename pushed container to nf-core/devcontainer

---
 .devcontainer/devcontainer.json              |  2 +-
 .github/workflows/push_dockerhub_dev.yml     |  6 +++---
 .github/workflows/push_dockerhub_release.yml | 10 +++++-----
 nf_core/devcontainer/devcontainer.Dockerfile |  2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 406b5dac23..9be21800d6 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,6 +1,6 @@
 {
     "name": "nfcore",
-    // "image": "nfcore/tools-devcontainer",
+    // "image": "nfcore/devcontainer",
     "build": {
         "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile",
         "context": ".."
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 25a5d192b1..92cabb06e5 100644
--- 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/tools-devcontainer:dev docker image
-        run: docker build --no-cache . --file nf_core/devcontainer/devcontainer.Dockerfile -t nfcore/tools-devcontainer: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/tools-devcontainer:dev
+          docker push nfcore/devcontainer:dev
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
index e3fdbfb8d1..895fa37669 100644
--- a/.github/workflows/push_dockerhub_release.yml
+++ b/.github/workflows/push_dockerhub_release.yml
@@ -28,8 +28,8 @@ jobs:
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
 
-      - name: Build nfcore/tools-devcontainer:latest docker image
-        run: docker build --no-cache . --file nf_core/devcontainer/devcontainer.Dockerfile -t nfcore/tools-devcontainer: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: |
@@ -37,6 +37,6 @@ jobs:
           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/tools-devcontainer:latest
-          docker tag nfcore/tools-devcontainer:latest nfcore/tools-devcontainer:${{ github.event.release.tag_name }}
-          docker push nfcore/tools-devcontainer:${{ 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/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 894ebb23f5..ef0276436c 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -1,5 +1,5 @@
 # Test build locally before making a PR (from project root directory)
-#   docker build . -t tools-devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
+#   docker build . -t devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
 FROM gitpod/workspace-base:2025-05-14-07-50-25

From 4f8a2c07c88d2067af807125b16d612732e9e9b1 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 12:04:22 +0200
Subject: [PATCH 14/79] Remove gitpod.yml from template

---
 nf_core/pipeline-template/.gitpod.yml | 10 ----------
 1 file changed, 10 deletions(-)
 delete mode 100644 nf_core/pipeline-template/.gitpod.yml

diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml
deleted file mode 100644
index c6a2e40b87..0000000000
--- a/nf_core/pipeline-template/.gitpod.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-image: nfcore/gitpod:latest
-tasks:
-  - name: Update Nextflow and setup pre-commit
-    command: |
-      pre-commit install --install-hooks
-      nextflow self-update {%- if code_linters %}
-
-vscode:
-  extensions:
-    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack{% endif %}

From c225114a7eb87ed812958ad94c67602a106339da Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 12:05:21 +0200
Subject: [PATCH 15/79] Remove .gitpod.yml

---
 .gitpod.yml | 12 ------------
 1 file changed, 12 deletions(-)
 delete mode 100644 .gitpod.yml

diff --git a/.gitpod.yml b/.gitpod.yml
deleted file mode 100644
index d5948695bf..0000000000
--- a/.gitpod.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-image: nfcore/gitpod:dev
-tasks:
-  - name: install current state of nf-core/tools and setup pre-commit
-    command: |
-      python -m pip install -e .
-      python -m pip install -r requirements-dev.txt
-      pre-commit install --install-hooks
-      nextflow self-update
-
-vscode:
-  extensions:
-    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack

From f5256571177fcb2a0cac87df00a4cef7b5d1c5ae Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 12:18:03 +0200
Subject: [PATCH 16/79] Remove local container building

---
 .devcontainer/devcontainer.json | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 9be21800d6..44740d710d 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,10 +1,6 @@
 {
     "name": "nfcore",
-    // "image": "nfcore/devcontainer",
-    "build": {
-        "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile",
-        "context": ".."
-    },
+    "image": "nfcore/devcontainer",
     "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
     "remoteUser": "gitpod",
     "runArgs": ["--privileged"],

From e0e6d97e747e73fb7410b19d4fe99ffc3f03ac5e Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 12:27:06 +0200
Subject: [PATCH 17/79] Change base image tag

---
 nf_core/devcontainer/devcontainer.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index ef0276436c..0b08de836d 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -2,7 +2,7 @@
 #   docker build . -t devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-FROM gitpod/workspace-base:2025-05-14-07-50-25
+FROM gitpod/workspace-base@sha256:7f35e401405c38ebc1185dfc3d6c066f73a524e8b86641453ea4690cc5c24fb6
 
 USER root
 

From 923d99d04d93fb8a86c8053ebf76ccd353ded117 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 12:28:47 +0200
Subject: [PATCH 18/79] re-add comments

---
 nf_core/devcontainer/devcontainer.Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 0b08de836d..a0d7779e28 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -36,7 +36,10 @@ ENV PATH="/opt/conda/bin:$PATH"
 COPY . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
+# Change ownership for gitpod
 RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
+
+# Change user to gitpod
 USER gitpod
 
 # Install nextflow, nf-core, nf-test, and other useful tools

From b5e748728939dd70e6eaf2e3903c8900a093a5e7 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 12:48:33 +0200
Subject: [PATCH 19/79] Add latest tag explicitly

---
 .devcontainer/devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 44740d710d..7484e1a24a 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,6 +1,6 @@
 {
     "name": "nfcore",
-    "image": "nfcore/devcontainer",
+    "image": "nfcore/devcontainer:latest",
     "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
     "remoteUser": "gitpod",
     "runArgs": ["--privileged"],

From 8785edba934aded957e062626fc35885b3f5ec71 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 17:59:43 +0200
Subject: [PATCH 20/79] Test seqera container base image

---
 nf_core/devcontainer/seqeracontainer.Dockerfile | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 nf_core/devcontainer/seqeracontainer.Dockerfile

diff --git a/nf_core/devcontainer/seqeracontainer.Dockerfile b/nf_core/devcontainer/seqeracontainer.Dockerfile
new file mode 100644
index 0000000000..6fc73960a0
--- /dev/null
+++ b/nf_core/devcontainer/seqeracontainer.Dockerfile
@@ -0,0 +1,15 @@
+FROM community.wave.seqera.io/library/nextflow_nf-test_apptainer_curl_pruned:eeb39fa4eeaed3f3
+
+RUN curl -sSL https://get.docker.com/ | sh
+
+# Add the nf-core source files to the image
+COPY . /usr/src/nf_core
+WORKDIR /usr/src/nf_core
+
+# Update Nextflow and Install nf-core
+RUN python -m pip install . --no-cache-dir
+
+# Setup pdiff for nf-test diffs
+ENV NFT_DIFF="pdiff"
+ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
+ENV JAVA_TOOL_OPTIONS=

From cccb21c21d6319071784d363d1469603e5c49c4f Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 18:08:54 +0200
Subject: [PATCH 21/79] update comments. todo

---
 nf_core/devcontainer/seqeracontainer.Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nf_core/devcontainer/seqeracontainer.Dockerfile b/nf_core/devcontainer/seqeracontainer.Dockerfile
index 6fc73960a0..930a660af1 100644
--- a/nf_core/devcontainer/seqeracontainer.Dockerfile
+++ b/nf_core/devcontainer/seqeracontainer.Dockerfile
@@ -1,5 +1,8 @@
 FROM community.wave.seqera.io/library/nextflow_nf-test_apptainer_curl_pruned:eeb39fa4eeaed3f3
 
+# TODO: Create unprivileged user? -> root used by default in seqera images
+
+# Install docker (Note: requires mounting /var/run/docker.sock)
 RUN curl -sSL https://get.docker.com/ | sh
 
 # Add the nf-core source files to the image

From 774b4cd9940feb5dfb870ada0c53cbc734497a42 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 18:11:02 +0200
Subject: [PATCH 22/79] Rename to reflect base image

---
 .../{devcontainer.Dockerfile => devcontainer_gitpod.Dockerfile}   | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename nf_core/devcontainer/{devcontainer.Dockerfile => devcontainer_gitpod.Dockerfile} (100%)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer_gitpod.Dockerfile
similarity index 100%
rename from nf_core/devcontainer/devcontainer.Dockerfile
rename to nf_core/devcontainer/devcontainer_gitpod.Dockerfile

From 0091a34eab0b4ac68155ee99f3ecf361da3adc8f Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 19:37:29 +0200
Subject: [PATCH 23/79] WIP: devcontainer with docker-in-docker feature

---
 .devcontainer/devcontainer.json              | 20 +++++-
 nf_core/devcontainer/devcontainer.Dockerfile | 65 ++++++++++++++++++++
 2 files changed, 82 insertions(+), 3 deletions(-)
 create mode 100644 nf_core/devcontainer/devcontainer.Dockerfile

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 7484e1a24a..656062ed8c 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,9 +1,23 @@
 {
     "name": "nfcore",
     "image": "nfcore/devcontainer:latest",
-    "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    //"build": {
+    //    "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile",
+    //    "context": "..",
+    //}
+    //"image":  "mcr.microsoft.com/devcontainers/python:3.11",
+
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {
+            "version": "latest",
+            "enableNonRootDocker": "true",
+            "moby": "true"
+        }
+    },
+
+    //"postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
+    //"remoteUser": "gitpod",
+    //"runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {
diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
new file mode 100644
index 0000000000..a8633a3998
--- /dev/null
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -0,0 +1,65 @@
+# Test build locally before making a PR (from project root directory)
+#   docker build . -t devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
+
+# See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
+FROM mcr.microsoft.com/devcontainers/python:3.11
+
+USER root
+
+# Install util tools.
+# software-properties-common is needed to add ppa support for Apptainer installation
+RUN apt-get update --quiet && \
+    apt-get install --quiet --yes --no-install-recommends \
+    apt-transport-https \
+    apt-utils \
+    sudo \
+    git \
+    less \
+    wget \
+    curl \
+    tree \
+    graphviz \
+    software-properties-common && \
+    wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
+    bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
+    rm Miniforge3-Linux-x86_64.sh && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Set PATH for Conda
+ENV PATH="/opt/conda/bin:$PATH"
+
+# Add the nf-core source files to the image
+COPY . /usr/src/nf_core
+WORKDIR /usr/src/nf_core
+
+# Change ownership for gitpod
+#RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
+
+# Change user to gitpod
+#USER gitpod
+
+# Install nextflow, nf-core, nf-test, and other useful tools
+RUN conda config --add channels bioconda && \
+    conda config --add channels conda-forge && \
+    conda config --set channel_priority strict && \
+    conda install --quiet --yes --update-all --name base \
+    apptainer \
+    nextflow \
+    nf-test \
+    prettier \
+    pre-commit \
+    ruff \
+    mypy \
+    openjdk \
+    pytest-workflow && \
+    conda clean --all --force-pkgs-dirs --yes
+
+# Update Nextflow and Install nf-core
+RUN nextflow self-update && \
+    python -m pip install . --no-cache-dir
+
+# Setup pdiff for nf-test diffs
+ENV NFT_DIFF="pdiff"
+ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
+ENV JAVA_TOOL_OPTIONS=

From 875d66135de3a6b48113ab3a386a1d201c1fae09 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 20 May 2025 20:38:24 +0200
Subject: [PATCH 24/79] Add seqera url as comment

---
 nf_core/devcontainer/seqeracontainer.Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/devcontainer/seqeracontainer.Dockerfile b/nf_core/devcontainer/seqeracontainer.Dockerfile
index 930a660af1..5546a17e9f 100644
--- a/nf_core/devcontainer/seqeracontainer.Dockerfile
+++ b/nf_core/devcontainer/seqeracontainer.Dockerfile
@@ -1,3 +1,4 @@
+# Seqera Container Url: https://wave.seqera.io/view/builds/bd-eeb39fa4eeaed3f3_1
 FROM community.wave.seqera.io/library/nextflow_nf-test_apptainer_curl_pruned:eeb39fa4eeaed3f3
 
 # TODO: Create unprivileged user? -> root used by default in seqera images

From 6a2c92d7e060efd23aacedf83d57349e60e6e753 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 10:00:27 +0200
Subject: [PATCH 25/79] Overwrite base image entrypoint. Add non-privileged
 user.

---
 nf_core/devcontainer/devcontainer.Dockerfile | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index a8633a3998..ba5a6126a0 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -34,10 +34,13 @@ COPY . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
 # Change ownership for gitpod
-#RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
+RUN useradd -m -s /bin/bash nfc-user  && \
+    chown -R nfc-user:nfc-user /opt/conda /usr/src/nf_core && \
+    groupadd docker && \
+    usermod -aG docker nfc-user
 
 # Change user to gitpod
-#USER gitpod
+USER nfc-user
 
 # Install nextflow, nf-core, nf-test, and other useful tools
 RUN conda config --add channels bioconda && \
@@ -63,3 +66,5 @@ RUN nextflow self-update && \
 ENV NFT_DIFF="pdiff"
 ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
 ENV JAVA_TOOL_OPTIONS=
+
+ENTRYPOINT [ "/bin/sh -c" ]

From 77a83575a296bb956a2a47e92e1c4ae483153203 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 10:00:49 +0200
Subject: [PATCH 26/79] Clean up

---
 .devcontainer/devcontainer.json | 16 +++-------------
 1 file changed, 3 insertions(+), 13 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 656062ed8c..a79644c35e 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,23 +1,13 @@
 {
     "name": "nfcore",
     "image": "nfcore/devcontainer:latest",
-    //"build": {
-    //    "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile",
-    //    "context": "..",
-    //}
-    //"image":  "mcr.microsoft.com/devcontainers/python:3.11",
 
     "features": {
-        "ghcr.io/devcontainers/features/docker-in-docker:2": {
-            "version": "latest",
-            "enableNonRootDocker": "true",
-            "moby": "true"
-        }
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {}
     },
 
-    //"postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
-    //"remoteUser": "gitpod",
-    //"runArgs": ["--privileged"],
+    "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
+    "remoteUser": "nfc-user",
 
     // Configure tool-specific properties.
     "customizations": {

From 0aa49b372bdcc1dc3faaf2f7c093485a518309dd Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 10:06:27 +0200
Subject: [PATCH 27/79] Make user privileged when running container

---
 .devcontainer/devcontainer.json              | 1 +
 nf_core/devcontainer/devcontainer.Dockerfile | 2 --
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index a79644c35e..fd2ee4f0b9 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -8,6 +8,7 @@
 
     "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
     "remoteUser": "nfc-user",
+    "privileged": true,
 
     // Configure tool-specific properties.
     "customizations": {
diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index ba5a6126a0..7fad08ae98 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -66,5 +66,3 @@ RUN nextflow self-update && \
 ENV NFT_DIFF="pdiff"
 ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
 ENV JAVA_TOOL_OPTIONS=
-
-ENTRYPOINT [ "/bin/sh -c" ]

From e9fa6dfb19f9e877292a4f3030c9e22ea187d868 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 10:27:44 +0200
Subject: [PATCH 28/79] Change to non-root user 'vscode' from base image. Try
 running without privileged

---
 .devcontainer/devcontainer.json              | 4 ++--
 nf_core/devcontainer/devcontainer.Dockerfile | 7 ++-----
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index fd2ee4f0b9..de45c4b858 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -7,8 +7,8 @@
     },
 
     "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
-    "remoteUser": "nfc-user",
-    "privileged": true,
+    "remoteUser": "vscode",
+    //"privileged": true,
 
     // Configure tool-specific properties.
     "customizations": {
diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 7fad08ae98..8b1210e2fb 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -34,13 +34,10 @@ COPY . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
 # Change ownership for gitpod
-RUN useradd -m -s /bin/bash nfc-user  && \
-    chown -R nfc-user:nfc-user /opt/conda /usr/src/nf_core && \
-    groupadd docker && \
-    usermod -aG docker nfc-user
+RUN chown -R vscode:vscode /opt/conda /usr/src/nf_core
 
 # Change user to gitpod
-USER nfc-user
+USER vscode
 
 # Install nextflow, nf-core, nf-test, and other useful tools
 RUN conda config --add channels bioconda && \

From 552b0ff6e9f25deb8e2f755848a88af91ead1a9f Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 10:38:51 +0200
Subject: [PATCH 29/79] Run privileged

---
 .devcontainer/devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index de45c4b858..c3b123fd91 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -8,7 +8,7 @@
 
     "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
     "remoteUser": "vscode",
-    //"privileged": true,
+    "privileged": true,
 
     // Configure tool-specific properties.
     "customizations": {

From dd021d0dacf3f6baff07428aa536c9030eab9366 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 11:05:28 +0200
Subject: [PATCH 30/79] Change nf-core install to have dev dependencies and
 --editable set

---
 nf_core/devcontainer/devcontainer.Dockerfile | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 8b1210e2fb..62737373df 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -57,9 +57,4 @@ RUN conda config --add channels bioconda && \
 
 # Update Nextflow and Install nf-core
 RUN nextflow self-update && \
-    python -m pip install . --no-cache-dir
-
-# Setup pdiff for nf-test diffs
-ENV NFT_DIFF="pdiff"
-ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
-ENV JAVA_TOOL_OPTIONS=
+    python -m pip install -r requirements-dev.txt -e . --no-cache-dir

From 64e86d54c6e4d7bf56c01be3a106bc0e3c84b295 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 11:06:26 +0200
Subject: [PATCH 31/79] Install pre-commit hooks in image

---
 nf_core/devcontainer/devcontainer.Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 62737373df..05bb8b5160 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -57,4 +57,5 @@ RUN conda config --add channels bioconda && \
 
 # Update Nextflow and Install nf-core
 RUN nextflow self-update && \
-    python -m pip install -r requirements-dev.txt -e . --no-cache-dir
+    python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
+    pre-commit --install-hooks

From 9eda307bab17959607f0e7db05a5b6e551afc3f6 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 11:07:36 +0200
Subject: [PATCH 32/79] =?UTF-8?q?Remove=C2=A0redundant=20post-create=20ins?=
 =?UTF-8?q?tallation=20of=20nf-core=20and=20pre-commit=20hooks?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 nf_core/devcontainer/devcontainer.Dockerfile | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 05bb8b5160..c26c728581 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -47,12 +47,6 @@ RUN conda config --add channels bioconda && \
     apptainer \
     nextflow \
     nf-test \
-    prettier \
-    pre-commit \
-    ruff \
-    mypy \
-    openjdk \
-    pytest-workflow && \
     conda clean --all --force-pkgs-dirs --yes
 
 # Update Nextflow and Install nf-core

From d0fea24243dae68155e2f39a9f44fb0f0172ddd0 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 12:22:46 +0200
Subject: [PATCH 33/79] Remove postCreateCommand. Remove Privileged

---
 .devcontainer/devcontainer.json | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index c3b123fd91..ac18733f70 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -6,9 +6,7 @@
         "ghcr.io/devcontainers/features/docker-in-docker:2": {}
     },
 
-    "postCreateCommand": "python -m pip install --upgrade -r requirements-dev.txt -e . && pre-commit install --install-hooks",
     "remoteUser": "vscode",
-    "privileged": true,
 
     // Configure tool-specific properties.
     "customizations": {

From d9749522aa32c6feb48a7b3534451945408b4679 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 12:31:59 +0200
Subject: [PATCH 34/79] Fix pre-commit install cmd

---
 nf_core/devcontainer/devcontainer.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index c26c728581..7661afc814 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -52,4 +52,4 @@ RUN conda config --add channels bioconda && \
 # Update Nextflow and Install nf-core
 RUN nextflow self-update && \
     python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
-    pre-commit --install-hooks
+    pre-commit install --install-hooks

From 3216521a611f384dad42840d0a166b26bc3c21f7 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 12:32:20 +0200
Subject: [PATCH 35/79] Remove more redundant conda packages

---
 nf_core/devcontainer/devcontainer.Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 7661afc814..3233cb2db5 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -45,8 +45,7 @@ RUN conda config --add channels bioconda && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --update-all --name base \
     apptainer \
-    nextflow \
-    nf-test \
+    nextflow && \
     conda clean --all --force-pkgs-dirs --yes
 
 # Update Nextflow and Install nf-core

From e400076c152d71a12d6650c0c208ab48c36f1a7d Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 12:38:09 +0200
Subject: [PATCH 36/79] Chown nf-core dir when copying. Chown conda folder only
 when using conda

---
 nf_core/devcontainer/devcontainer.Dockerfile | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 3233cb2db5..7ea5dba3df 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -30,17 +30,15 @@ RUN apt-get update --quiet && \
 ENV PATH="/opt/conda/bin:$PATH"
 
 # Add the nf-core source files to the image
-COPY . /usr/src/nf_core
+COPY --chown=vscode:vscode . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
-# Change ownership for gitpod
-RUN chown -R vscode:vscode /opt/conda /usr/src/nf_core
-
 # Change user to gitpod
 USER vscode
 
 # Install nextflow, nf-core, nf-test, and other useful tools
-RUN conda config --add channels bioconda && \
+RUN chown -R vscode:vscode /opt/conda && \
+    conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --update-all --name base \

From 7e1aba21cb770075cb5f003fceddc23ade8a13e7 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 12:39:21 +0200
Subject: [PATCH 37/79] Remove unneeded dependencies and those already in base
 image

---
 nf_core/devcontainer/devcontainer.Dockerfile | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 7ea5dba3df..f8b2a95011 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -7,19 +7,11 @@ FROM mcr.microsoft.com/devcontainers/python:3.11
 USER root
 
 # Install util tools.
-# software-properties-common is needed to add ppa support for Apptainer installation
 RUN apt-get update --quiet && \
     apt-get install --quiet --yes --no-install-recommends \
     apt-transport-https \
     apt-utils \
-    sudo \
-    git \
-    less \
-    wget \
-    curl \
-    tree \
     graphviz \
-    software-properties-common && \
     wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
     bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
     rm Miniforge3-Linux-x86_64.sh && \

From 14a3e9572a50b9dfe6e5d605454f10930006d9fa Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 12:41:49 +0200
Subject: [PATCH 38/79] Fix command end

---
 nf_core/devcontainer/devcontainer.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index f8b2a95011..52115804bb 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -11,7 +11,7 @@ RUN apt-get update --quiet && \
     apt-get install --quiet --yes --no-install-recommends \
     apt-transport-https \
     apt-utils \
-    graphviz \
+    graphviz && \
     wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
     bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
     rm Miniforge3-Linux-x86_64.sh && \

From 6d284fb6f1f8883830352cee8496a13d612b56e2 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 12:56:17 +0200
Subject: [PATCH 39/79] WIP: Comment out section adding lots of size to the
 image

---
 nf_core/devcontainer/devcontainer.Dockerfile | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 52115804bb..27ef17bd6e 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -39,6 +39,7 @@ RUN chown -R vscode:vscode /opt/conda && \
     conda clean --all --force-pkgs-dirs --yes
 
 # Update Nextflow and Install nf-core
-RUN nextflow self-update && \
-    python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
-    pre-commit install --install-hooks
+# TODO: This adds 900MB to the image
+# RUN nextflow self-update && \
+#     python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
+#     pre-commit install --install-hooks

From 5d8503bf28b434827a2cd2fa817c1f75517b7f61 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 12:57:06 +0200
Subject: [PATCH 40/79] Use vscode user everywhere

---
 nf_core/devcontainer/devcontainer.Dockerfile | 21 ++++++++++----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 27ef17bd6e..1f8b86f3c3 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -4,19 +4,21 @@
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
 FROM mcr.microsoft.com/devcontainers/python:3.11
 
-USER root
+# Change user to vscode
+USER vscode
+WORKDIR /home/vscode
 
 # Install util tools.
-RUN apt-get update --quiet && \
-    apt-get install --quiet --yes --no-install-recommends \
+RUN sudo apt-get update --quiet && \
+    sudo apt-get install --quiet --yes --no-install-recommends \
     apt-transport-https \
     apt-utils \
     graphviz && \
     wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
-    bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
+    sudo bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
     rm Miniforge3-Linux-x86_64.sh && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
+    sudo apt-get clean && \
+    sudo rm -rf /var/lib/apt/lists/*
 
 # Set PATH for Conda
 ENV PATH="/opt/conda/bin:$PATH"
@@ -25,11 +27,8 @@ ENV PATH="/opt/conda/bin:$PATH"
 COPY --chown=vscode:vscode . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
-# Change user to gitpod
-USER vscode
-
-# Install nextflow, nf-core, nf-test, and other useful tools
-RUN chown -R vscode:vscode /opt/conda && \
+# Install nextflow and apptainer via conda
+RUN sudo chown -R vscode:vscode /opt/conda && \
     conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \

From 08d29fc956ecdf1eb2b371c7d880fb4cf22376f5 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 13:11:28 +0200
Subject: [PATCH 41/79] Re-introduce nextflow update, nf-core dev, and commit
 hooks install

---
 nf_core/devcontainer/devcontainer.Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 1f8b86f3c3..ea0115b2d1 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -39,6 +39,6 @@ RUN sudo chown -R vscode:vscode /opt/conda && \
 
 # Update Nextflow and Install nf-core
 # TODO: This adds 900MB to the image
-# RUN nextflow self-update && \
-#     python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
-#     pre-commit install --install-hooks
+RUN nextflow self-update && \
+    python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
+    pre-commit install --install-hooks

From c5dd2d240939eb218a142142987afd5d13f39bd8 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Tue, 27 May 2025 13:25:39 +0200
Subject: [PATCH 42/79] Use nextflow/training base image to share nextflow,
 conda installation

---
 nf_core/devcontainer/devcontainer.Dockerfile | 32 +++-----------------
 1 file changed, 5 insertions(+), 27 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index ea0115b2d1..474e2b222e 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -1,27 +1,11 @@
 # Test build locally before making a PR (from project root directory)
 #   docker build . -t devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
 
-# See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-FROM mcr.microsoft.com/devcontainers/python:3.11
+# Uses mcr.microsoft.com/devcontainers/base:ubuntu
+FROM ghcr.io/nextflow-io/training:latest
 
 # Change user to vscode
 USER vscode
-WORKDIR /home/vscode
-
-# Install util tools.
-RUN sudo apt-get update --quiet && \
-    sudo apt-get install --quiet --yes --no-install-recommends \
-    apt-transport-https \
-    apt-utils \
-    graphviz && \
-    wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
-    sudo bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
-    rm Miniforge3-Linux-x86_64.sh && \
-    sudo apt-get clean && \
-    sudo rm -rf /var/lib/apt/lists/*
-
-# Set PATH for Conda
-ENV PATH="/opt/conda/bin:$PATH"
 
 # Add the nf-core source files to the image
 COPY --chown=vscode:vscode . /usr/src/nf_core
@@ -29,16 +13,10 @@ WORKDIR /usr/src/nf_core
 
 # Install nextflow and apptainer via conda
 RUN sudo chown -R vscode:vscode /opt/conda && \
-    conda config --add channels bioconda && \
-    conda config --add channels conda-forge && \
-    conda config --set channel_priority strict && \
     conda install --quiet --yes --update-all --name base \
-    apptainer \
-    nextflow && \
+    conda-forge::apptainer>=1.4.1 && \
     conda clean --all --force-pkgs-dirs --yes
 
-# Update Nextflow and Install nf-core
-# TODO: This adds 900MB to the image
-RUN nextflow self-update && \
-    python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
+# Install nf-core with development dependencies and git commit hooks
+RUN python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
     pre-commit install --install-hooks

From 0fa9993d2e186e061ac7c6d16ef0fcaaadce96be Mon Sep 17 00:00:00 2001
From: JulianFlesch <julianflesch@googlemail.com>
Date: Wed, 28 May 2025 09:01:02 +0000
Subject: [PATCH 43/79] Add setup.sh to fix run issues with nf/training img.
 Move latest tools install to setup.sh

---
 .devcontainer/setup.sh                       | 14 ++++++++++++++
 nf_core/devcontainer/devcontainer.Dockerfile |  4 ----
 2 files changed, 14 insertions(+), 4 deletions(-)
 create mode 100644 .devcontainer/setup.sh

diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100644
index 0000000000..1416fd3a7d
--- /dev/null
+++ 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/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 474e2b222e..936d216bcb 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -16,7 +16,3 @@ RUN sudo chown -R vscode:vscode /opt/conda && \
     conda install --quiet --yes --update-all --name base \
     conda-forge::apptainer>=1.4.1 && \
     conda clean --all --force-pkgs-dirs --yes
-
-# Install nf-core with development dependencies and git commit hooks
-RUN python -m pip install -r requirements-dev.txt -e . --no-cache-dir && \
-    pre-commit install --install-hooks

From 2eceaf72df17736ed002d4bcc8a2e66c0b2dd645 Mon Sep 17 00:00:00 2001
From: JulianFlesch <julianflesch@googlemail.com>
Date: Wed, 28 May 2025 09:14:34 +0000
Subject: [PATCH 44/79] change ownership of nextflow installation location

---
 nf_core/devcontainer/devcontainer.Dockerfile | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 936d216bcb..825ac38797 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -7,12 +7,15 @@ FROM ghcr.io/nextflow-io/training:latest
 # Change user to vscode
 USER vscode
 
+# Change the nextflow directory
+RUN chown -R vscode:vscode /usr/local/bin/ && \
+    sudo chown -R vscode:vscode /opt/conda
+
 # Add the nf-core source files to the image
 COPY --chown=vscode:vscode . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
 # Install nextflow and apptainer via conda
-RUN sudo chown -R vscode:vscode /opt/conda && \
-    conda install --quiet --yes --update-all --name base \
+RUN conda install --quiet --yes --update-all --name base \
     conda-forge::apptainer>=1.4.1 && \
     conda clean --all --force-pkgs-dirs --yes

From 4b825df6e849d88160871f430c8967195ef96bd7 Mon Sep 17 00:00:00 2001
From: JulianFlesch <julianflesch@googlemail.com>
Date: Wed, 28 May 2025 09:41:51 +0000
Subject: [PATCH 45/79] Update comment. Change layer order

---
 nf_core/devcontainer/devcontainer.Dockerfile | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 825ac38797..0fe28f921a 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -7,15 +7,15 @@ FROM ghcr.io/nextflow-io/training:latest
 # Change user to vscode
 USER vscode
 
-# Change the nextflow directory
-RUN chown -R vscode:vscode /usr/local/bin/ && \
-    sudo chown -R vscode:vscode /opt/conda
-
 # Add the nf-core source files to the image
 COPY --chown=vscode:vscode . /usr/src/nf_core
 WORKDIR /usr/src/nf_core
 
-# Install nextflow and apptainer via conda
+# 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

From d7854ff88ecbd95520c733dd52fab12aa6fb332b Mon Sep 17 00:00:00 2001
From: JulianFlesch <julianflesch@googlemail.com>
Date: Wed, 28 May 2025 10:15:34 +0000
Subject: [PATCH 46/79] Update template devcontainer

---
 .../pipeline-template/.devcontainer/devcontainer.json    | 9 ++++++---
 nf_core/pipeline-template/.devcontainer/setup.sh         | 8 ++++++++
 2 files changed, 14 insertions(+), 3 deletions(-)
 create mode 100644 nf_core/pipeline-template/.devcontainer/setup.sh

diff --git a/nf_core/pipeline-template/.devcontainer/devcontainer.json b/nf_core/pipeline-template/.devcontainer/devcontainer.json
index b290e09017..d8ef9f325d 100644
--- 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
new file mode 100644
index 0000000000..371f6c7407
--- /dev/null
+++ 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

From 3dff96d6569ac58aacc3f12db98340dba8ed34ba Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Wed, 28 May 2025 12:20:55 +0200
Subject: [PATCH 47/79] Remove testing Dockerfiles

---
 .../devcontainer_gitpod.Dockerfile            | 67 -------------------
 .../devcontainer/seqeracontainer.Dockerfile   | 19 ------
 2 files changed, 86 deletions(-)
 delete mode 100644 nf_core/devcontainer/devcontainer_gitpod.Dockerfile
 delete mode 100644 nf_core/devcontainer/seqeracontainer.Dockerfile

diff --git a/nf_core/devcontainer/devcontainer_gitpod.Dockerfile b/nf_core/devcontainer/devcontainer_gitpod.Dockerfile
deleted file mode 100644
index a0d7779e28..0000000000
--- a/nf_core/devcontainer/devcontainer_gitpod.Dockerfile
+++ /dev/null
@@ -1,67 +0,0 @@
-# Test build locally before making a PR (from project root directory)
-#   docker build . -t devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
-
-# See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-FROM gitpod/workspace-base@sha256:7f35e401405c38ebc1185dfc3d6c066f73a524e8b86641453ea4690cc5c24fb6
-
-USER root
-
-# Install util tools.
-# software-properties-common is needed to add ppa support for Apptainer installation
-RUN apt-get update --quiet && \
-    apt-get install --quiet --yes --no-install-recommends \
-    apt-transport-https \
-    apt-utils \
-    sudo \
-    git \
-    less \
-    wget \
-    curl \
-    tree \
-    graphviz \
-    software-properties-common && \
-    add-apt-repository -y ppa:apptainer/ppa && \
-    apt-get update --quiet && \
-    apt-get install --quiet --yes apptainer && \
-    wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
-    bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
-    rm Miniforge3-Linux-x86_64.sh && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
-# Set PATH for Conda
-ENV PATH="/opt/conda/bin:$PATH"
-
-# Add the nf-core source files to the image
-COPY . /usr/src/nf_core
-WORKDIR /usr/src/nf_core
-
-# Change ownership for gitpod
-RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
-
-# Change user to gitpod
-USER gitpod
-
-# Install nextflow, nf-core, nf-test, and other useful tools
-RUN conda config --add channels bioconda && \
-    conda config --add channels conda-forge && \
-    conda config --set channel_priority strict && \
-    conda install --quiet --yes --update-all --name base \
-    nextflow \
-    nf-test \
-    prettier \
-    pre-commit \
-    ruff \
-    mypy \
-    openjdk \
-    pytest-workflow && \
-    conda clean --all --force-pkgs-dirs --yes
-
-# Update Nextflow and Install nf-core
-RUN nextflow self-update && \
-    python -m pip install . --no-cache-dir
-
-# Setup pdiff for nf-test diffs
-ENV NFT_DIFF="pdiff"
-ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
-ENV JAVA_TOOL_OPTIONS=
diff --git a/nf_core/devcontainer/seqeracontainer.Dockerfile b/nf_core/devcontainer/seqeracontainer.Dockerfile
deleted file mode 100644
index 5546a17e9f..0000000000
--- a/nf_core/devcontainer/seqeracontainer.Dockerfile
+++ /dev/null
@@ -1,19 +0,0 @@
-# Seqera Container Url: https://wave.seqera.io/view/builds/bd-eeb39fa4eeaed3f3_1
-FROM community.wave.seqera.io/library/nextflow_nf-test_apptainer_curl_pruned:eeb39fa4eeaed3f3
-
-# TODO: Create unprivileged user? -> root used by default in seqera images
-
-# Install docker (Note: requires mounting /var/run/docker.sock)
-RUN curl -sSL https://get.docker.com/ | sh
-
-# Add the nf-core source files to the image
-COPY . /usr/src/nf_core
-WORKDIR /usr/src/nf_core
-
-# Update Nextflow and Install nf-core
-RUN python -m pip install . --no-cache-dir
-
-# Setup pdiff for nf-test diffs
-ENV NFT_DIFF="pdiff"
-ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
-ENV JAVA_TOOL_OPTIONS=

From a7b5c484c1e098990b3e418b690536a22245b6df Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Mon, 14 Jul 2025 12:41:12 +0200
Subject: [PATCH 48/79] Fix base image version

---
 nf_core/devcontainer/devcontainer.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 0fe28f921a..5aa2c95cdb 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -2,7 +2,7 @@
 #   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
+FROM ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2FROM
 
 # Change user to vscode
 USER vscode

From 4a556518cd5d08929e9c084e57c279e8e5a103da Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Mon, 14 Jul 2025 12:47:56 +0200
Subject: [PATCH 49/79] Fix sha typo

---
 nf_core/devcontainer/devcontainer.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
index 5aa2c95cdb..458d274dfa 100644
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ b/nf_core/devcontainer/devcontainer.Dockerfile
@@ -2,7 +2,7 @@
 #   docker build . -t devcontainer:local -f nf_core/devcontainer/devcontainer.Dockerfile
 
 # Uses mcr.microsoft.com/devcontainers/base:ubuntu
-FROM ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2FROM
+FROM ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2
 
 # Change user to vscode
 USER vscode

From cd292aa6988bc013272d4dd6f438efc9262a8172 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Mon, 14 Jul 2025 11:43:49 +0000
Subject: [PATCH 50/79] WIP: Build locally for testing image changes

---
 .devcontainer/devcontainer.json | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index ac18733f70..e151c2f3f9 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,6 +1,12 @@
 {
     "name": "nfcore",
-    "image": "nfcore/devcontainer:latest",
+
+    //"image": "nfcore/devcontainer:latest",
+    // ToDo: Build locally for testing
+    "build": {
+        "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile",
+        "context": ".."
+    },
 
     "features": {
         "ghcr.io/devcontainers/features/docker-in-docker:2": {}

From 2f5574631f2be32eeae11c98be363c1fce79af46 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Mon, 14 Jul 2025 18:51:11 +0200
Subject: [PATCH 51/79] Remove container build

---
 .devcontainer/devcontainer.json | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index e151c2f3f9..4305d009e2 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,12 +1,7 @@
 {
     "name": "nfcore",
 
-    //"image": "nfcore/devcontainer:latest",
-    // ToDo: Build locally for testing
-    "build": {
-        "dockerfile": "../nf_core/devcontainer/devcontainer.Dockerfile",
-        "context": ".."
-    },
+    "image": "nfcore/devcontainer:latest",
 
     "features": {
         "ghcr.io/devcontainers/features/docker-in-docker:2": {}

From df3bd4bc126c68377fa9e3c5c573a964eebdaa92 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:10:26 +0200
Subject: [PATCH 52/79] Change to root user

---
 .devcontainer/devcontainer.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 4305d009e2..9a5d300bdb 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -7,7 +7,8 @@
         "ghcr.io/devcontainers/features/docker-in-docker:2": {}
     },
 
-    "remoteUser": "vscode",
+    "remoteUser": "root",
+    "privileged": true,
 
     // Configure tool-specific properties.
     "customizations": {

From 7de59cb86ccce9c0c5021ec26e4794c4150dd356 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:12:05 +0200
Subject: [PATCH 53/79] Add apptainer as local feature

---
 .devcontainer/devcontainer.json                   |  3 ++-
 .../apptainer/devcontainer-feature.json           |  5 +++++
 .devcontainer/local-features/apptainer/install.sh | 15 +++++++++++++++
 3 files changed, 22 insertions(+), 1 deletion(-)
 create mode 100644 .devcontainer/local-features/apptainer/devcontainer-feature.json
 create mode 100755 .devcontainer/local-features/apptainer/install.sh

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 9a5d300bdb..f540078b88 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -4,7 +4,8 @@
     "image": "nfcore/devcontainer:latest",
 
     "features": {
-        "ghcr.io/devcontainers/features/docker-in-docker:2": {}
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {},
+        "./local-features/apptainer": {}
     },
 
     "remoteUser": "root",
diff --git a/.devcontainer/local-features/apptainer/devcontainer-feature.json b/.devcontainer/local-features/apptainer/devcontainer-feature.json
new file mode 100644
index 0000000000..7471c46a98
--- /dev/null
+++ b/.devcontainer/local-features/apptainer/devcontainer-feature.json
@@ -0,0 +1,5 @@
+{
+    "id": "apptainer",
+    "name": "Install Apptainer",
+    "version": "1.0.0"
+}
diff --git a/.devcontainer/local-features/apptainer/install.sh b/.devcontainer/local-features/apptainer/install.sh
new file mode 100755
index 0000000000..030d1c50bc
--- /dev/null
+++ b/.devcontainer/local-features/apptainer/install.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+# Install Apptainer (Singularity)
+
+apt-get update --quiet
+
+# installs add-apt-repository
+apt install --reinstall -y software-properties-common
+
+add-apt-repository -y ppa:apptainer/ppa
+
+apt install -y apptainer
+
+apt-get clean
+rm -rf /var/lib/apt/lists/*

From fb5ca93fbc23d55f89497c46604dc098c8498e26 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:18:03 +0200
Subject: [PATCH 54/79] Use existing tutorial baseimage and instead mount
 current folder.

---
 .devcontainer/devcontainer.json | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index f540078b88..2f24e22c9c 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,13 +1,18 @@
 {
     "name": "nfcore",
 
-    "image": "nfcore/devcontainer:latest",
+    // Uses mcr.microsoft.com/devcontainers/base:ubuntu
+    "image": "ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2",
 
     "features": {
         "ghcr.io/devcontainers/features/docker-in-docker:2": {},
         "./local-features/apptainer": {}
     },
 
+    // Mount full current path to make mounting into docker-from-docker work
+    "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
+    "workspaceFolder": "${localWorkspaceFolder}",
+
     "remoteUser": "root",
     "privileged": true,
 

From 403f3e3f39c90fdff6ea17d85839460c99531560 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:20:14 +0200
Subject: [PATCH 55/79] Remove docker-in-docker feature to avoid interference
 with parent feature docker-outside-of-docker

---
 .devcontainer/devcontainer.json | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 2f24e22c9c..c4f0980f0d 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -5,11 +5,10 @@
     "image": "ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2",
 
     "features": {
-        "ghcr.io/devcontainers/features/docker-in-docker:2": {},
         "./local-features/apptainer": {}
     },
 
-    // Mount full current path to make mounting into docker-from-docker work
+    // Mount full current path to make mounting into docker-outside-of-docker work
     "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
     "workspaceFolder": "${localWorkspaceFolder}",
 

From 24a05c7204e66802c44788bfcd417005d3842c51 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:21:35 +0200
Subject: [PATCH 56/79] Change container prompt to cope with long paths

---
 .devcontainer/setup.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
index 1416fd3a7d..bb10f7f433 100644
--- a/.devcontainer/setup.sh
+++ b/.devcontainer/setup.sh
@@ -1,8 +1,9 @@
 #!/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/} ->\[\e[0m\] '
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 
 # Update Nextflow
 nextflow self-update

From c00b89ae2aece4adb781d403a3cd7ae3a8585010 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:22:05 +0200
Subject: [PATCH 57/79] update welcome message

---
 .devcontainer/setup.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
index bb10f7f433..e1c10414bf 100644
--- a/.devcontainer/setup.sh
+++ b/.devcontainer/setup.sh
@@ -13,3 +13,6 @@ python -m pip install -r requirements-dev.txt -e . --no-cache-dir
 
 # Install pre-commit hooks
 pre-commit install --install-hooks
+
+# Update welcome message
+echo "Welcome to the nf-core/tools devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

From 0398115a04e30c4f5d4cbdf7e0db39402b2c9982 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:25:21 +0200
Subject: [PATCH 58/79] Remove obsolete Dockerfile

---
 nf_core/devcontainer/devcontainer.Dockerfile | 21 --------------------
 1 file changed, 21 deletions(-)
 delete mode 100644 nf_core/devcontainer/devcontainer.Dockerfile

diff --git a/nf_core/devcontainer/devcontainer.Dockerfile b/nf_core/devcontainer/devcontainer.Dockerfile
deleted file mode 100644
index 458d274dfa..0000000000
--- a/nf_core/devcontainer/devcontainer.Dockerfile
+++ /dev/null
@@ -1,21 +0,0 @@
-# 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@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2
-
-# 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

From d99a89660a0d7f2e609eabd7af616593268a64f5 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:28:49 +0200
Subject: [PATCH 59/79] Change template devcontainer to reuse training base
 image, fix docker in container, change to root user

---
 .../.devcontainer/devcontainer.json                | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/nf_core/pipeline-template/.devcontainer/devcontainer.json b/nf_core/pipeline-template/.devcontainer/devcontainer.json
index d8ef9f325d..b426a68425 100644
--- a/nf_core/pipeline-template/.devcontainer/devcontainer.json
+++ b/nf_core/pipeline-template/.devcontainer/devcontainer.json
@@ -1,11 +1,15 @@
 {
     "name": "nfcore",
-    "image": "nfcore/devcontainer:latest",
-    "remoteUser": "vscode",
 
-    "features": {
-        "ghcr.io/devcontainers/features/docker-in-docker:2": {}
-    },
+    // Uses mcr.microsoft.com/devcontainers/base:ubuntu
+    "image": "ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2",
+
+    "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}",
 
     // Configure tool-specific properties.
     "customizations": {

From 65e8cb418ad7857245aa557a5c0010d61d6ef4f1 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:29:36 +0200
Subject: [PATCH 60/79] Custom prompt to cope with long paths. Updates welcome
 message

---
 nf_core/pipeline-template/.devcontainer/setup.sh | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/.devcontainer/setup.sh b/nf_core/pipeline-template/.devcontainer/setup.sh
index 371f6c7407..7833653256 100644
--- a/nf_core/pipeline-template/.devcontainer/setup.sh
+++ b/nf_core/pipeline-template/.devcontainer/setup.sh
@@ -1,8 +1,12 @@
 #!/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/} ->\[\e[0m\] '
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 
 # Update Nextflow
 nextflow self-update
+
+# Update welcome message
+echo "Welcome to the nf-core/tools devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

From 19066ee7a8dc28ceebd84a250314a100e77a484c Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:29:42 +0200
Subject: [PATCH 61/79] Custom prompt to cope with long paths. Updates welcome
 message

---
 nf_core/pipeline-template/.devcontainer/setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.devcontainer/setup.sh b/nf_core/pipeline-template/.devcontainer/setup.sh
index 7833653256..c496948752 100644
--- a/nf_core/pipeline-template/.devcontainer/setup.sh
+++ b/nf_core/pipeline-template/.devcontainer/setup.sh
@@ -9,4 +9,4 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 nextflow self-update
 
 # Update welcome message
-echo "Welcome to the nf-core/tools devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
+echo "Welcome to the nf-core pipeline devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

From d82eac5920eac7f161410a9fb1e3a6fe059caf5a Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:36:10 +0200
Subject: [PATCH 62/79] Add nf-core, pre-commit hook install to setup. Update
 welcome message

---
 nf_core/pipeline-template/.devcontainer/setup.sh | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/nf_core/pipeline-template/.devcontainer/setup.sh b/nf_core/pipeline-template/.devcontainer/setup.sh
index c496948752..bc22cabcf7 100644
--- a/nf_core/pipeline-template/.devcontainer/setup.sh
+++ b/nf_core/pipeline-template/.devcontainer/setup.sh
@@ -8,5 +8,11 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 # Update Nextflow
 nextflow self-update
 
+# Install nf-core tools
+python -m pip install nf-core
+
+# Install pre-commit hooks
+pre-commit install --install-hooks
+
 # Update welcome message
 echo "Welcome to the nf-core pipeline devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

From 685a8d8fbdde343454a71a467835c8e3b845734e Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:36:41 +0200
Subject: [PATCH 63/79] Add local features nf-test, apptainer. (Util fixed in
 parent)

---
 .../.devcontainer/devcontainer.json               |  5 +++++
 .../apptainer/devcontainer-feature.json           |  5 +++++
 .../local-features/apptainer/install.sh           | 15 +++++++++++++++
 .../nf-test/devcontainer-feature.json             |  5 +++++
 .../local-features/nf-test/install.sh             |  7 +++++++
 5 files changed, 37 insertions(+)
 create mode 100644 nf_core/pipeline-template/.devcontainer/local-features/apptainer/devcontainer-feature.json
 create mode 100755 nf_core/pipeline-template/.devcontainer/local-features/apptainer/install.sh
 create mode 100644 nf_core/pipeline-template/.devcontainer/local-features/nf-test/devcontainer-feature.json
 create mode 100755 nf_core/pipeline-template/.devcontainer/local-features/nf-test/install.sh

diff --git a/nf_core/pipeline-template/.devcontainer/devcontainer.json b/nf_core/pipeline-template/.devcontainer/devcontainer.json
index b426a68425..10092ecfcb 100644
--- a/nf_core/pipeline-template/.devcontainer/devcontainer.json
+++ b/nf_core/pipeline-template/.devcontainer/devcontainer.json
@@ -11,6 +11,11 @@
     "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
     "workspaceFolder": "${localWorkspaceFolder}",
 
+    "features": {
+        ".local-features/apptainer": {},
+        ".local-features/nf-test": {}
+    },
+
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
diff --git a/nf_core/pipeline-template/.devcontainer/local-features/apptainer/devcontainer-feature.json b/nf_core/pipeline-template/.devcontainer/local-features/apptainer/devcontainer-feature.json
new file mode 100644
index 0000000000..7471c46a98
--- /dev/null
+++ b/nf_core/pipeline-template/.devcontainer/local-features/apptainer/devcontainer-feature.json
@@ -0,0 +1,5 @@
+{
+    "id": "apptainer",
+    "name": "Install Apptainer",
+    "version": "1.0.0"
+}
diff --git a/nf_core/pipeline-template/.devcontainer/local-features/apptainer/install.sh b/nf_core/pipeline-template/.devcontainer/local-features/apptainer/install.sh
new file mode 100755
index 0000000000..030d1c50bc
--- /dev/null
+++ b/nf_core/pipeline-template/.devcontainer/local-features/apptainer/install.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+# Install Apptainer (Singularity)
+
+apt-get update --quiet
+
+# installs add-apt-repository
+apt install --reinstall -y software-properties-common
+
+add-apt-repository -y ppa:apptainer/ppa
+
+apt install -y apptainer
+
+apt-get clean
+rm -rf /var/lib/apt/lists/*
diff --git a/nf_core/pipeline-template/.devcontainer/local-features/nf-test/devcontainer-feature.json b/nf_core/pipeline-template/.devcontainer/local-features/nf-test/devcontainer-feature.json
new file mode 100644
index 0000000000..f7647ff041
--- /dev/null
+++ b/nf_core/pipeline-template/.devcontainer/local-features/nf-test/devcontainer-feature.json
@@ -0,0 +1,5 @@
+{
+    "id": "nf-test",
+    "name": "Install nf-test",
+    "version": "1.0.0"
+}
diff --git a/nf_core/pipeline-template/.devcontainer/local-features/nf-test/install.sh b/nf_core/pipeline-template/.devcontainer/local-features/nf-test/install.sh
new file mode 100755
index 0000000000..c903aaaf02
--- /dev/null
+++ b/nf_core/pipeline-template/.devcontainer/local-features/nf-test/install.sh
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+# download and install
+wget -qO- https://get.nf-test.com | bash
+
+# move to location on the path
+mv nf-test "$HOME/.local/bin"

From def9bf27fbcba2d768c41b3b840cf9801dd9435f Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Thu, 17 Jul 2025 10:37:50 +0200
Subject: [PATCH 64/79] Add nf-test also to tools devcontainer as local feature

---
 .devcontainer/devcontainer.json                            | 3 ++-
 .../local-features/nf-test/devcontainer-feature.json       | 5 +++++
 .devcontainer/local-features/nf-test/install.sh            | 7 +++++++
 3 files changed, 14 insertions(+), 1 deletion(-)
 create mode 100644 .devcontainer/local-features/nf-test/devcontainer-feature.json
 create mode 100755 .devcontainer/local-features/nf-test/install.sh

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index c4f0980f0d..9c1ab5e886 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -5,7 +5,8 @@
     "image": "ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2",
 
     "features": {
-        "./local-features/apptainer": {}
+        "./local-features/apptainer": {},
+        "./local-features/nf-test": {}
     },
 
     // Mount full current path to make mounting into docker-outside-of-docker work
diff --git a/.devcontainer/local-features/nf-test/devcontainer-feature.json b/.devcontainer/local-features/nf-test/devcontainer-feature.json
new file mode 100644
index 0000000000..f7647ff041
--- /dev/null
+++ b/.devcontainer/local-features/nf-test/devcontainer-feature.json
@@ -0,0 +1,5 @@
+{
+    "id": "nf-test",
+    "name": "Install nf-test",
+    "version": "1.0.0"
+}
diff --git a/.devcontainer/local-features/nf-test/install.sh b/.devcontainer/local-features/nf-test/install.sh
new file mode 100755
index 0000000000..c903aaaf02
--- /dev/null
+++ b/.devcontainer/local-features/nf-test/install.sh
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+# download and install
+wget -qO- https://get.nf-test.com | bash
+
+# move to location on the path
+mv nf-test "$HOME/.local/bin"

From 4918d6cebb4eb5ef637bedfe5b9c92be3540f47b Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 14:55:07 +0200
Subject: [PATCH 65/79] Adapt git workflow to build with devcontainer ci

---
 .github/workflows/push_dockerhub_dev.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 92cabb06e5..cb7fa474d2 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -28,8 +28,14 @@ jobs:
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev
 
-      - name: Build nfcore/devcontainer:dev docker image
-        run: docker build --no-cache . --file nf_core/devcontainer/devcontainer.Dockerfile -t nfcore/devcontainer:dev
+      - name: Build nfcore/devcontainer:dev devcontainer image
+        uses: devcontainers/ci@v0.3
+        with:
+          configFile: .devcontainer/build-devcontainer/devcontainer.json
+          imageName: nfcore/devcontainer
+          imageTag: dev
+          platform: linux/amd64,linux/arm64
+          push: false
 
       - name: Push Docker images to DockerHub (dev)
         run: |

From b1079a587097a9b8a561254767bb6ae05858b298 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 14:55:38 +0200
Subject: [PATCH 66/79] Adds devcontaner config for building.

---
 .../build-devcontainer/devcontainer.json      | 32 +++++++++++++++++++
 .devcontainer/build-devcontainer/setup.sh     | 18 +++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 .devcontainer/build-devcontainer/devcontainer.json
 create mode 100644 .devcontainer/build-devcontainer/setup.sh

diff --git a/.devcontainer/build-devcontainer/devcontainer.json b/.devcontainer/build-devcontainer/devcontainer.json
new file mode 100644
index 0000000000..fb5985fcb0
--- /dev/null
+++ b/.devcontainer/build-devcontainer/devcontainer.json
@@ -0,0 +1,32 @@
+{
+    "name": "nfcore-devcontainer-build",
+
+    // Uses mcr.microsoft.com/devcontainers/base:ubuntu
+    "image": "ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2",
+
+    "features": {
+        "./local-features/apptainer": {},
+        "./local-features/nf-test": {}
+    },
+
+    // Mount full current path to make mounting into docker-outside-of-docker work
+    //"workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
+    //"workspaceFolder": "${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": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}
diff --git a/.devcontainer/build-devcontainer/setup.sh b/.devcontainer/build-devcontainer/setup.sh
new file mode 100644
index 0000000000..e1c10414bf
--- /dev/null
+++ b/.devcontainer/build-devcontainer/setup.sh
@@ -0,0 +1,18 @@
+#!/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 PS1='\[\e[3;36m\]\w ->\[\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
+
+# Update welcome message
+echo "Welcome to the nf-core/tools devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

From 9a9c2669112623b8731ef51b55dccd968d0cc32a Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 14:57:45 +0200
Subject: [PATCH 67/79] Simplified devcontainer config for running. Removes all
 feature installations

---
 .devcontainer/devcontainer.json |  9 +--------
 .devcontainer/setup.sh          | 14 --------------
 2 files changed, 1 insertion(+), 22 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 9c1ab5e886..3214aa7ad2 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,13 +1,6 @@
 {
     "name": "nfcore",
-
-    // Uses mcr.microsoft.com/devcontainers/base:ubuntu
-    "image": "ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2",
-
-    "features": {
-        "./local-features/apptainer": {},
-        "./local-features/nf-test": {}
-    },
+    "image": "nfcore/devcontainer", // ToDo: Add version hash once available
 
     // Mount full current path to make mounting into docker-outside-of-docker work
     "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
index e1c10414bf..5f880cfa47 100644
--- a/.devcontainer/setup.sh
+++ b/.devcontainer/setup.sh
@@ -1,18 +1,4 @@
 #!/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 PS1='\[\e[3;36m\]\w ->\[\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
-
 # Update welcome message
 echo "Welcome to the nf-core/tools devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

From 5622095bb3bfd4e3737e77914dba8a52a95c5541 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 15:00:57 +0200
Subject: [PATCH 68/79] Change workflow for release to build with devcontainer
 ci

---
 .github/workflows/push_dockerhub_release.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
index 895fa37669..0e40395c2f 100644
--- a/.github/workflows/push_dockerhub_release.yml
+++ b/.github/workflows/push_dockerhub_release.yml
@@ -28,8 +28,14 @@ jobs:
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
 
-      - name: Build nfcore/devcontainer:latest docker image
-        run: docker build --no-cache . --file nf_core/devcontainer/devcontainer.Dockerfile -t nfcore/devcontainer:latest
+      - name: Build nfcore/devcontainer:latest devcontainer image
+        uses: devcontainers/ci@v0.3
+        with:
+          configFile: .devcontainer/build-devcontainer/devcontainer.json
+          imageName: nfcore/devcontainer
+          imageTag: latest
+          platform: linux/amd64,linux/arm64
+          push: false
 
       - name: Push Docker images to DockerHub (release)
         run: |

From 491ec957b41cb54bca3b3b2b677679105e2f3036 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 15:03:20 +0200
Subject: [PATCH 69/79] Change to using prebuild image. Remove local feature
 installs. Simplify setup.sh

---
 .../.devcontainer/devcontainer.json                |  9 +--------
 nf_core/pipeline-template/.devcontainer/setup.sh   | 14 --------------
 2 files changed, 1 insertion(+), 22 deletions(-)

diff --git a/nf_core/pipeline-template/.devcontainer/devcontainer.json b/nf_core/pipeline-template/.devcontainer/devcontainer.json
index 10092ecfcb..785d4dfff8 100644
--- a/nf_core/pipeline-template/.devcontainer/devcontainer.json
+++ b/nf_core/pipeline-template/.devcontainer/devcontainer.json
@@ -1,8 +1,6 @@
 {
     "name": "nfcore",
-
-    // Uses mcr.microsoft.com/devcontainers/base:ubuntu
-    "image": "ghcr.io/nextflow-io/training@sha256:97cce091b2c786f8fbd86f470e59d096dff546fe07941cf0e97421b6f95333e2",
+    "image": "nfcore/devcontainer", // ToDo: Add version hash once available
 
     "remoteUser": "root",
     "privileged": true,
@@ -11,11 +9,6 @@
     "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
     "workspaceFolder": "${localWorkspaceFolder}",
 
-    "features": {
-        ".local-features/apptainer": {},
-        ".local-features/nf-test": {}
-    },
-
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
diff --git a/nf_core/pipeline-template/.devcontainer/setup.sh b/nf_core/pipeline-template/.devcontainer/setup.sh
index bc22cabcf7..93c2918036 100644
--- a/nf_core/pipeline-template/.devcontainer/setup.sh
+++ b/nf_core/pipeline-template/.devcontainer/setup.sh
@@ -1,18 +1,4 @@
 #!/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 PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
-
-# Update Nextflow
-nextflow self-update
-
-# Install nf-core tools
-python -m pip install nf-core
-
-# Install pre-commit hooks
-pre-commit install --install-hooks
-
 # Update welcome message
 echo "Welcome to the nf-core pipeline devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

From 2308afcb9c0808615b5b35e6dc59b4e72b85b67d Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 15:10:32 +0200
Subject: [PATCH 70/79] Fix devcontainers/ci version by sha

---
 .github/workflows/push_dockerhub_dev.yml     | 2 +-
 .github/workflows/push_dockerhub_release.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index cb7fa474d2..afe41833bb 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -29,7 +29,7 @@ jobs:
         run: docker build --no-cache . -t nfcore/tools:dev
 
       - name: Build nfcore/devcontainer:dev devcontainer image
-        uses: devcontainers/ci@v0.3
+        uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3
         with:
           configFile: .devcontainer/build-devcontainer/devcontainer.json
           imageName: nfcore/devcontainer
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
index 0e40395c2f..18f2b9f584 100644
--- a/.github/workflows/push_dockerhub_release.yml
+++ b/.github/workflows/push_dockerhub_release.yml
@@ -29,7 +29,7 @@ jobs:
         run: docker build --no-cache . -t nfcore/tools:latest
 
       - name: Build nfcore/devcontainer:latest devcontainer image
-        uses: devcontainers/ci@v0.3
+        uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3
         with:
           configFile: .devcontainer/build-devcontainer/devcontainer.json
           imageName: nfcore/devcontainer

From 355f913c01c23444b1015541a8e2d5f493f6d219 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 15:15:21 +0200
Subject: [PATCH 71/79] Testing: run workflow on personal feature branch
 temporarily

---
 .github/workflows/push_dockerhub_dev.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index afe41833bb..e928e80f27 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -3,7 +3,7 @@ name: nf-core Docker push (dev)
 # Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
 on:
   push:
-    branches: [dev]
+    branches: [dev, issues/3466-gitpod]
 
 # Cancel if a newer run is started
 concurrency:

From e1fcc0994a5adc94715a19998dd9953849bed208 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 15:42:05 +0200
Subject: [PATCH 72/79] Testing: Add workflow_dispatch to run wf manually

---
 .github/workflows/push_dockerhub_dev.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index e928e80f27..17e93fb84a 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -2,8 +2,9 @@ name: nf-core Docker push (dev)
 # This builds the docker image and pushes it to DockerHub
 # Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
 on:
-  push:
-    branches: [dev, issues/3466-gitpod]
+  workflow_dispatch
+  #push:
+  #  branches: [dev, issues/3466-gitpod]
 
 # Cancel if a newer run is started
 concurrency:

From 855959347740d56c7d55e4f7fef924563385c60e Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 15:58:48 +0200
Subject: [PATCH 73/79] Testing: Remove repo constraint

---
 .github/workflows/push_dockerhub_dev.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 17e93fb84a..4b003bd0a9 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -16,7 +16,7 @@ jobs:
     name: Push new Docker image to Docker Hub (dev)
     runs-on: ubuntu-latest
     # Only run for the nf-core repo, for releases and merged PRs
-    if: ${{ github.repository == 'nf-core/tools' }}
+    #if: ${{ github.repository == 'nf-core/tools' }}
     env:
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
       DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}

From ce0cf8870f9b34ffd940f87bb3d698eb0746238c Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 16:02:50 +0200
Subject: [PATCH 74/79] Move local features into build-devcontainer

---
 .../local-features/apptainer/devcontainer-feature.json            | 0
 .../{ => build-devcontainer}/local-features/apptainer/install.sh  | 0
 .../local-features/nf-test/devcontainer-feature.json              | 0
 .../{ => build-devcontainer}/local-features/nf-test/install.sh    | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename .devcontainer/{ => build-devcontainer}/local-features/apptainer/devcontainer-feature.json (100%)
 rename .devcontainer/{ => build-devcontainer}/local-features/apptainer/install.sh (100%)
 rename .devcontainer/{ => build-devcontainer}/local-features/nf-test/devcontainer-feature.json (100%)
 rename .devcontainer/{ => build-devcontainer}/local-features/nf-test/install.sh (100%)

diff --git a/.devcontainer/local-features/apptainer/devcontainer-feature.json b/.devcontainer/build-devcontainer/local-features/apptainer/devcontainer-feature.json
similarity index 100%
rename from .devcontainer/local-features/apptainer/devcontainer-feature.json
rename to .devcontainer/build-devcontainer/local-features/apptainer/devcontainer-feature.json
diff --git a/.devcontainer/local-features/apptainer/install.sh b/.devcontainer/build-devcontainer/local-features/apptainer/install.sh
similarity index 100%
rename from .devcontainer/local-features/apptainer/install.sh
rename to .devcontainer/build-devcontainer/local-features/apptainer/install.sh
diff --git a/.devcontainer/local-features/nf-test/devcontainer-feature.json b/.devcontainer/build-devcontainer/local-features/nf-test/devcontainer-feature.json
similarity index 100%
rename from .devcontainer/local-features/nf-test/devcontainer-feature.json
rename to .devcontainer/build-devcontainer/local-features/nf-test/devcontainer-feature.json
diff --git a/.devcontainer/local-features/nf-test/install.sh b/.devcontainer/build-devcontainer/local-features/nf-test/install.sh
similarity index 100%
rename from .devcontainer/local-features/nf-test/install.sh
rename to .devcontainer/build-devcontainer/local-features/nf-test/install.sh

From 22bbccf72c13344ee51ab9c319e4ad59403757ec Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Fri, 18 Jul 2025 19:57:30 +0200
Subject: [PATCH 75/79] Use no cache for build

---
 .github/workflows/push_dockerhub_dev.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 4b003bd0a9..0137558632 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -37,6 +37,7 @@ jobs:
           imageTag: dev
           platform: linux/amd64,linux/arm64
           push: false
+          noCache: true
 
       - name: Push Docker images to DockerHub (dev)
         run: |

From ca5fba7dc2501c2adf0047e643f847df8e44ef23 Mon Sep 17 00:00:00 2001
From: Julian Flesch <julian.flesch@qbic.uni-tuebingen.de>
Date: Sat, 19 Jul 2025 00:03:55 +0200
Subject: [PATCH 76/79] testing buildx config

---
 .github/workflows/push_dockerhub_dev.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 0137558632..0ebace555a 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -26,6 +26,9 @@ jobs:
       - name: Check out code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev
 

From 60a01549b1e5e973c01af6859a3e4eba15bd4be5 Mon Sep 17 00:00:00 2001
From: JulianFlesch <julianflesch@googlemail.com>
Date: Sat, 19 Jul 2025 01:55:20 +0200
Subject: [PATCH 77/79] Testing container deploy

---
 .github/workflows/push_dockerhub_dev.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 0ebace555a..aa192b1517 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -30,14 +30,14 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: Build nfcore/tools:dev docker image
-        run: docker build --no-cache . -t nfcore/tools:dev
+        run: docker build --no-cache . -t fljulian/nfcore-devcontainer:ts-dev
 
       - name: Build nfcore/devcontainer:dev devcontainer image
         uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3
         with:
           configFile: .devcontainer/build-devcontainer/devcontainer.json
-          imageName: nfcore/devcontainer
-          imageTag: dev
+          imageName: fljulian/nfcore-devcontainer
+          imageTag: dc-dev
           platform: linux/amd64,linux/arm64
           push: false
           noCache: true
@@ -45,5 +45,5 @@ jobs:
       - 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/devcontainer:dev
+          docker push fljulian/nfcore-devcontainer:ts-dev
+          docker push fljulian/nfcore-devcontainer:dc-dev

From 66755bee0475dbd993ebbde544e2ad38e02ef70a Mon Sep 17 00:00:00 2001
From: JulianFlesch <julianflesch@googlemail.com>
Date: Sat, 19 Jul 2025 02:08:54 +0200
Subject: [PATCH 78/79] Testing deployed image in codespaces

---
 .devcontainer/devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 3214aa7ad2..fa9d0b81de 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,6 +1,6 @@
 {
     "name": "nfcore",
-    "image": "nfcore/devcontainer", // ToDo: Add version hash once available
+    "image": "fljulian/nfcore-devcontainer:dc-dev", // ToDo: Add version hash once available
 
     // Mount full current path to make mounting into docker-outside-of-docker work
     "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",

From b9a5e946814fbaaf61141267231094bb9f15ddc5 Mon Sep 17 00:00:00 2001
From: JulianFlesch <julianflesch@googlemail.com>
Date: Sat, 19 Jul 2025 02:15:45 +0200
Subject: [PATCH 79/79] Testing: Limit to only devcontainer image build+push

---
 .github/workflows/push_dockerhub_dev.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index aa192b1517..07071d4b80 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -29,15 +29,15 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
-      - name: Build nfcore/tools:dev docker image
-        run: docker build --no-cache . -t fljulian/nfcore-devcontainer:ts-dev
+      #- name: Build nfcore/tools:dev docker image
+      #  run: docker build --no-cache . -t fljulian/nfcore-devcontainer:ts-dev
 
       - name: Build nfcore/devcontainer:dev devcontainer image
         uses: devcontainers/ci@8bf61b26e9c3a98f69cb6ce2f88d24ff59b785c6 # v0.3
         with:
           configFile: .devcontainer/build-devcontainer/devcontainer.json
           imageName: fljulian/nfcore-devcontainer
-          imageTag: dc-dev
+          imageTag: dev
           platform: linux/amd64,linux/arm64
           push: false
           noCache: true
@@ -45,5 +45,6 @@ jobs:
       - name: Push Docker images to DockerHub (dev)
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push fljulian/nfcore-devcontainer:ts-dev
-          docker push fljulian/nfcore-devcontainer:dc-dev
+          docker push fljulian/nfcore-devcontainer:dev
+       # docker push fljulian/nfcore-devcontainer:ts-dev
+