Adds new Devcontainer Setup for use with Codespaces (#8983)

* Add devcontainer setup from nf-core/tools for testing. Move nf-test install to setup.sh

* Add the default user again at the end

* Move nf-test install to unprivileged location and add WORKDIR. Add pipefail. Remove copying unnecessary files.

* Move Dockerfile

* Remove docker-in-docker interfering with docker-outside-docker from parent image. Adapt Mounts to use host paths when starting sibling containers

* Fix arm profile

* Remove apptainer install

* Remove efforts for unprivileged user

* Use root user by default

* update welcome message. update prompt

* Remove explicitly setting NFT_WORKDIR

* Add nf-test as local feature

* Remove Dockerfile in favor of features

* Remove env vars

* Add apptainer as local feature

* Fix install

* Fix install script for apptainer by installing dependencies first

* Fix install script for apptainer by installing dependencies first

* Update local feature to have version, name, id

* ftr: new devcontainer config

* Remove redundant tools install

* Remove local features. Already installed in parent image

* Testing: Change to pulling image from controlled location for testing in codespaces. REVERT THIS

* fix: set executable bit flag to run setup.sh

* Change to final container image

* Bumpy hostRequirements to run in more powerful instance in Codespaces

* Switch to using dev tag of our nf-core/devcontainer

Author: JulianFlesch

.devcontainer/devcontainer.json

@@ -1,28 +1,20 @@
 {
-    "name": "nfcore",
-    "image": "nfcore/gitpod:dev",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
-    // 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",
-                "python.linting.enabled": true
-            },
+    "name": "nfcore-modules",
+    "image": "nfcore/devcontainer:dev",
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
     },
-    "features": {
-        "ghcr.io/devcontainers/features/github-cli:1.0.11": {
-            "digest": "sha256:464564228ccdd6028f01f8a62a3cfbaf76e9ba7953b29ac0e53ba2c262604312"
-        },
-        "ghcr.io/devcontainers/features/docker-in-docker:2.9.2": {
-            "digest": "sha256:9074d8eaf4585ab1498c81a8762078992725614fc7a9cfafe799aa22717a6bbf"
-        }
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "remoteUser": "root",
+    "privileged": true,
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }

.devcontainer/setup.sh

@@ -0,0 +1,15 @@
+#!/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 pre-commit hooks
+pre-commit install --install-hooks
+
+# Update welcome message
+echo "Welcome to nf-core/modules devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt