run prettier

docs/PROTOTYPING.md

@@ -1,11 +1,11 @@
 # Prototyping using components from `nf-neuro`
 
-* [Prototyping using components from `nf-neuro`](#prototyping-using-components-from-nf-neuro)
-  * [Environment configuration](#environment-configuration)
-  * [Basic prototype pipeline creation](#basic-prototype-pipeline-creation)
-    * [`main.nf`](#mainnf)
-      * [`main.nf` example](#mainnf-example)
-    * [`nextflow.config`](#nextflowconfig)
+- [Prototyping using components from `nf-neuro`](#prototyping-using-components-from-nf-neuro)
+  - [Environment configuration](#environment-configuration)
+  - [Basic prototype pipeline creation](#basic-prototype-pipeline-creation)
+    - [`main.nf`](#mainnf)
+      - [`main.nf` example](#mainnf-example)
+    - [`nextflow.config`](#nextflowconfig)
 
 ## Environment configuration
 

docs/environment/DEVCONTAINER.md

@@ -4,18 +4,18 @@
 your development. They provide `pre-installed` environments for you to start programming
 new `pipelines` or `nf-neuro components`.
 
-* [Using `nf-neuro` development containers](#using-nf-neuro-development-containers)
-  * [Requirements](#requirements)
-    * [Configuring Docker for easy usage](#configuring-docker-for-easy-usage)
-  * [Prototyping environment](#prototyping-environment)
-    * [Usage](#usage)
-      * [Available in the container](#available-in-the-container)
-      * [Available in the VS Code IDE through extensions](#available-in-the-vs-code-ide-through-extensions)
-  * [Production environment](#production-environment)
-  * [Development environment](#development-environment)
-    * [Usage](#usage-1)
-      * [Available in the container](#available-in-the-container-1)
-      * [Available in the VS Code IDE through extensions](#available-in-the-vs-code-ide-through-extensions-1)
+- [Using `nf-neuro` development containers](#using-nf-neuro-development-containers)
+  - [Requirements](#requirements)
+    - [Configuring Docker for easy usage](#configuring-docker-for-easy-usage)
+  - [Prototyping environment](#prototyping-environment)
+    - [Usage](#usage)
+      - [Available in the container](#available-in-the-container)
+      - [Available in the VS Code IDE through extensions](#available-in-the-vs-code-ide-through-extensions)
+  - [Production environment](#production-environment)
+  - [Development environment](#development-environment)
+    - [Usage](#usage-1)
+      - [Available in the container](#available-in-the-container-1)
+      - [Available in the VS Code IDE through extensions](#available-in-the-vs-code-ide-through-extensions-1)
 
 ## Requirements
 
@@ -51,23 +51,23 @@ for a few minutes and enjoy your fully configured development environment.
 
 #### Available in the container
 
-  - `nf-core` accessible through the terminal, which is configured to access `nf-neuro` modules and subworkflows
-  - `git`, `github-cli`
-  - `curl`, `wget`, `apt-get`
-  - `nextflow`, `docker`, `tmux`
+- `nf-core` accessible through the terminal, which is configured to access `nf-neuro` modules and subworkflows
+- `git`, `github-cli`
+- `curl`, `wget`, `apt-get`
+- `nextflow`, `docker`, `tmux`
 
 #### Available in the VS Code IDE through extensions
 
-  - Docker images and containers management
-  - Nextflow execution environemnt
-  - Python and C++ linting, building and debugging tools
-  - Github Pull Requests management
-  - Github flavored markdown previewing
-  - Neuroimaging data viewer
-  - Test Data introspection
-  - Resource monitoring
-  - Remote development
-  - Live sharing with collaborators
+- Docker images and containers management
+- Nextflow execution environemnt
+- Python and C++ linting, building and debugging tools
+- Github Pull Requests management
+- Github flavored markdown previewing
+- Neuroimaging data viewer
+- Test Data introspection
+- Resource monitoring
+- Remote development
+- Live sharing with collaborators
 
 ## Production environment
 
@@ -84,22 +84,22 @@ few minutes and enjoy your fully configured development environment.
 
 #### Available in the container
 
-  - `nf-neuro`, `nf-core` all accessible through the terminal, which is configured to load
-    the `poetry` environment in shells automatically
-  - `nf-neuro` configured as the main repository for all `nf-core` commands, using `NFCORE_-` environment variables
-  - `git`, `github-cli`
-  - `curl`, `wget`, `apt-get`
-  - `nextflow`, `nf-test`, `docker`, `tmux`
+- `nf-neuro`, `nf-core` all accessible through the terminal, which is configured to load
+  the `poetry` environment in shells automatically
+- `nf-neuro` configured as the main repository for all `nf-core` commands, using `NFCORE_-` environment variables
+- `git`, `github-cli`
+- `curl`, `wget`, `apt-get`
+- `nextflow`, `nf-test`, `docker`, `tmux`
 
 #### Available in the VS Code IDE through extensions
 
-  - Docker images and containers management
-  - Nextflow execution environemnt
-  - Python and C++ linting, building and debugging tools
-  - Github Pull Requests management
-  - Github flavored markdown previewing
-  - Neuroimaging data viewer
-  - Test Data introspection
-  - Resource monitoring
-  - Remote development
-  - Live sharing with collaborators
+- Docker images and containers management
+- Nextflow execution environemnt
+- Python and C++ linting, building and debugging tools
+- Github Pull Requests management
+- Github flavored markdown previewing
+- Neuroimaging data viewer
+- Test Data introspection
+- Resource monitoring
+- Remote development
+- Live sharing with collaborators

docs/environment/DEVOPS.md

@@ -1,14 +1,14 @@
 # Developing within `nf-neuro`
 
-* [Developing within `nf-neuro`](#developing-within-nf-neuro)
-  * [Development container](#development-container)
-  * [Manual installation](#manual-installation)
-    * [Dependencies](#dependencies)
-    * [Python environment](#python-environment)
-    * [Loading the project's environment](#loading-the-projects-environment)
-    * [Global environment](#global-environment)
-    * [Working with VS Code](#working-with-vs-code)
-* [Installing Prettier and editorconfig](#installing-prettier-and-editorconfig)
+- [Developing within `nf-neuro`](#developing-within-nf-neuro)
+  - [Development container](#development-container)
+  - [Manual installation](#manual-installation)
+    - [Dependencies](#dependencies)
+    - [Python environment](#python-environment)
+    - [Loading the project's environment](#loading-the-projects-environment)
+    - [Global environment](#global-environment)
+    - [Working with VS Code](#working-with-vs-code)
+- [Installing Prettier and editorconfig](#installing-prettier-and-editorconfig)
 
 ## Development container
 

docs/environment/NFCORE.md

@@ -1,10 +1,10 @@
 # Basic environment setup
 
-* [Basic environment setup](#basic-environment-setup)
-  * [Development container](#development-container)
-  * [Manual installation](#manual-installation)
-    * [Dependencies](#dependencies)
-    * [Configuration](#configuration)
+- [Basic environment setup](#basic-environment-setup)
+  - [Development container](#development-container)
+  - [Manual installation](#manual-installation)
+    - [Dependencies](#dependencies)
+    - [Configuration](#configuration)
 
 ## Development container