Merge branch 'master' into workspaceFolder

Author: maxulysse

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
 FROM ghcr.io/nextflow-io/training:latest
 
 ENV NXF_VER=24.10.0
-ENV NXF_EDGE=0
+ENV NXF_EDGE=0

.editorconfig

@@ -0,0 +1,16 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js}]
+indent_size = 2
+
+# ignore python and markdown
+[*.{py,md}]
+indent_style = unset

.github/workflows/docker.yml

@@ -5,40 +5,40 @@
 name: Build GitPod Docker image
 
 on:
-    pull_request:
-    push:
-        branches: [master]
-    release:
-        types: [published]
+  pull_request:
+  push:
+    branches: [master]
+  release:
+    types: [published]
 
 jobs:
-    push_to_registry:
-        if: github.repository == 'nextflow-io/training'
-        name: Build + Push Gitpod Docker image
-        runs-on: ubuntu-latest
-        steps:
-            - name: Check out the repo
-              uses: actions/checkout@v4
+  push_to_registry:
+    if: github.repository == 'nextflow-io/training'
+    name: Build + Push Gitpod Docker image
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
 
-            - name: Login to GitHub Container Registry
-              uses: docker/login-action@v3
-              with:
-                  registry: ghcr.io
-                  username: ${{ github.repository_owner }}
-                  password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
-            - name: Build / push latest image
-              uses: docker/build-push-action@v5
-              if: github.event_name != 'release'
-              with:
-                  file: .github/gitpod.Dockerfile
-                  push: ${{ github.event_name == 'push' }}
-                  tags: ghcr.io/nextflow-io/training:latest
+      - name: Build / push latest image
+        uses: docker/build-push-action@v5
+        if: github.event_name != 'release'
+        with:
+          file: .github/gitpod.Dockerfile
+          push: ${{ github.event_name == 'push' }}
+          tags: ghcr.io/nextflow-io/training:latest
 
-            - name: Push release image
-              uses: docker/build-push-action@v5
-              if: github.event_name == 'release'
-              with:
-                  file: .github/gitpod.Dockerfile
-                  push: true
-                  tags: ghcr.io/nextflow-io/training:${{ github.event.release.tag_name }}
+      - name: Push release image
+        uses: docker/build-push-action@v5
+        if: github.event_name == 'release'
+        with:
+          file: .github/gitpod.Dockerfile
+          push: true
+          tags: ghcr.io/nextflow-io/training:${{ github.event.release.tag_name }}

.github/workflows/mkdocs-docker.yml

@@ -3,29 +3,29 @@
 name: Build mkdocs docker image
 
 on:
-    pull_request:
-    push:
-        branches: [master]
+  pull_request:
+  push:
+    branches: [master]
 
 jobs:
-    mkdocs_docker:
-        if: github.repository == 'nextflow-io/training'
-        name: Build + push mkdocs docker image
-        runs-on: ubuntu-latest
-        steps:
-            - name: Check out the repo
-              uses: actions/checkout@v4
+  mkdocs_docker:
+    if: github.repository == 'nextflow-io/training'
+    name: Build + push mkdocs docker image
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
 
-            - name: Login to GitHub Container Registry
-              uses: docker/login-action@v3
-              with:
-                  registry: ghcr.io
-                  username: ${{ github.repository_owner }}
-                  password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
-            - name: Build / push latest image
-              uses: docker/build-push-action@v5
-              with:
-                  file: .github/mkdocs.Dockerfile
-                  push: ${{ github.event_name == 'push' }}
-                  tags: ghcr.io/nextflow-io/training-mkdocs:latest
+      - name: Build / push latest image
+        uses: docker/build-push-action@v5
+        with:
+          file: .github/mkdocs.Dockerfile
+          push: ${{ github.event_name == 'push' }}
+          tags: ghcr.io/nextflow-io/training-mkdocs:latest

.github/workflows/precommit.yml

@@ -0,0 +1,15 @@
+name: Pre-commit checks
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/[email protected]

.github/workflows/prettier.yml

@@ -2,51 +2,51 @@ workspaceLocation: gitpod/gitpod-ws.code-workspace
 checkoutLocation: gitpod
 
 github:
-    prebuilds:
-        # enable for the master/default branch (defaults to true)
-        master: true
-        # enable for all branches in this repo (defaults to false)
-        branches: false
-        # enable for pull requests coming from this repo (defaults to true)
-        pullRequests: true
-        # enable for pull requests coming from forks (defaults to false)
-        pullRequestsFromForks: true
-        # add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
-        addComment: true
-        # add a "Review in Gitpod" button to pull requests (defaults to false)
-        addBadge: false
+  prebuilds:
+    # enable for the master/default branch (defaults to true)
+    master: true
+    # enable for all branches in this repo (defaults to false)
+    branches: false
+    # enable for pull requests coming from this repo (defaults to true)
+    pullRequests: true
+    # enable for pull requests coming from forks (defaults to false)
+    pullRequestsFromForks: true
+    # add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
+    addComment: true
+    # add a "Review in Gitpod" button to pull requests (defaults to false)
+    addBadge: false
 
 # See .github/Dockerfile
 image: ghcr.io/nextflow-io/training:latest
 
 tasks:
-    - before: printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc && exit
+  - before: printf 'unset JAVA_TOOL_OPTIONS\n' >> $HOME/.bashrc && exit
 
-    - name: Start web server
-      command: gp ports await 23000 && gp preview https://training.nextflow.io/hello_nextflow
+  - name: Start web server
+    command: gp ports await 23000 && gp preview https://training.nextflow.io/hello_nextflow
 
-    - name: Load Nextflow Tutorial
-      command: docker pull -q nextflow/rnaseq-nf
+  - name: Load Nextflow Tutorial
+    command: docker pull -q nextflow/rnaseq-nf
 
-    - name: Start Nextflow Tutorial
-      env:
-          NXF_HOME: "/workspace/gitpod/.nextflow"
-      command: |
-          cd hello-nextflow
-          source $HOME/.bashrc
-          export PS1='\[\e[3;36m\]${PWD/*\//} ->\[\e[0m\] '
-          unset JAVA_TOOL_OPTIONS
-          clear
+  - name: Start Nextflow Tutorial
+    env:
+      NXF_HOME: "/workspace/gitpod/.nextflow"
+    command: |
+      cd hello-nextflow
+      source $HOME/.bashrc
+      export PS1='\[\e[3;36m\]${PWD/*\//} ->\[\e[0m\] '
+      unset JAVA_TOOL_OPTIONS
+      clear
 
 vscode:
-    extensions: # based on nf-core.nf-core-extensionpack
-        - codezombiech.gitignore # Language support for .gitignore files
-        - cssho.vscode-svgviewer # SVG viewer
-        - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-        - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
-        - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
-        # - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-        - nextflow.nextflow # Nextflow syntax highlighting
-        # - oderwat.indent-rainbow # Highlight indentation level
-        - streetsidesoftware.code-spell-checker # Spelling checker for source code
-        - ms-vscode.live-server
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore # Language support for .gitignore files
+    - cssho.vscode-svgviewer # SVG viewer
+    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+    # - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
+    - nextflow.nextflow # Nextflow syntax highlighting
+    # - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - ms-vscode.live-server

.gitpod.yml

@@ -1,23 +1,23 @@
 repos:
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: "v3.1.0"
-      hooks:
-          - id: prettier
-            additional_dependencies:
-                - [email protected]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - [email protected]
 
-    - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-      rev: "2.7.3"
-      hooks:
-          - id: editorconfig-checker
-            alias: ec
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
 
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v5.0.0
-      hooks:
-          - id: trailing-whitespace
-            exclude_types:
-                - svg
-          - id: end-of-file-fixer
-            exclude_types:
-                - svg
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        exclude_types:
+          - svg
+      - id: end-of-file-fixer
+        exclude_types:
+          - svg

.pre-commit-config.yaml

@@ -2,20 +2,20 @@
 
 Table of contents:
 
--   [Contributing](#contributing)
-    -   [Contribution model](#contribution-model)
-    -   [Installation](#installation)
-        -   [Docker](#docker)
-        -   [Python](#python)
-        -   [Social cards](#social-cards)
-    -   [Figures \& diagrams](#figures--diagrams)
-    -   [Content style and formatting](#content-style-and-formatting)
-        -   [Formatting / linting](#formatting--linting)
-        -   [Admonitions](#admonitions)
-    -   [Known limitations](#known-limitations)
-        -   [Code annotations](#code-annotations)
-        -   [Word highlighting](#word-highlighting)
-    -   [TODO / FIXME](#todo--fixme)
+- [Contributing](#contributing)
+  - [Contribution model](#contribution-model)
+  - [Installation](#installation)
+    - [Docker](#docker)
+    - [Python](#python)
+    - [Social cards](#social-cards)
+  - [Figures \& diagrams](#figures--diagrams)
+  - [Content style and formatting](#content-style-and-formatting)
+    - [Formatting / linting](#formatting--linting)
+    - [Admonitions](#admonitions)
+  - [Known limitations](#known-limitations)
+    - [Code annotations](#code-annotations)
+    - [Word highlighting](#word-highlighting)
+  - [TODO / FIXME](#todo--fixme)
 
 ## Contribution model
 
@@ -92,11 +92,11 @@ If there is an announcement banner, you can enable and customise it using the fo
 
 ```yaml
 extra:
-    # Announcement banner for upcoming training
-    announcement:
-        active: false
-        date_text: March 5-6, 2024
-        register_url: https://nf-co.re/events/2024/training-foundational-march
+  # Announcement banner for upcoming training
+  announcement:
+    active: false
+    date_text: March 5-6, 2024
+    register_url: https://nf-co.re/events/2024/training-foundational-march
 ```
 
 If you need more customisation, edit `docs/assets/overrides/main.html`
@@ -136,9 +136,9 @@ There is a GitHub action that checks pull-requests for valid formatting.
 We use admonitions extensively to make certain pieces of content stand out.
 Please see the [official docs](https://squidfunk.github.io/mkdocs-material/reference/admonitions/) for an explanation.
 
--   Note that we have two custom admonitions: `exercise` and `result` (alias `solution`).
--   `!!!` does a regular admonition, `???` makes it collapsed (click to expand).
--   Intendation is important! Make sure you check the rendered site, as it's easy to make a mistake.
+- Note that we have two custom admonitions: `exercise` and `result` (alias `solution`).
+- `!!!` does a regular admonition, `???` makes it collapsed (click to expand).
+- Intendation is important! Make sure you check the rendered site, as it's easy to make a mistake.
 
 ## Known limitations
 
@@ -168,4 +168,4 @@ I recommend the [Todo Tree VSCode extension](https://marketplace.visualstudio.co
 
 A list of key ones also included here:
 
--   Remove plugin install from Phil's GitHub fork in `requirements.txt` and `.github/mkdocs.Dockerfile` when [this PR](https://github.com/timvink/mkdocs-enumerate-headings-plugin/pull/33) is merged
+- Remove plugin install from Phil's GitHub fork in `requirements.txt` and `.github/mkdocs.Dockerfile` when [this PR](https://github.com/timvink/mkdocs-enumerate-headings-plugin/pull/33) is merged