Merge pull request #13 from AlexVCaron/doc

Update documentation

.editorconfig-checker.json → .ecrc

@@ -1,10 +1,10 @@
 {
-    "Verbose": true,
+    "Verbose": false,
     "Debug": false,
     "IgnoreDefaults": false,
     "SpacesAftertabs": false,
     "NoColor": false,
-    "Exclude": ["^tests/.runs/", "^\\.nf-test/", "^\\.venv/", "^\\node_modules/", "\\.nf-test.log$"],
+    "Exclude": ["^tests/.runs/", "^\\.nf-test/", "^\\.venv/", "^\\node_modules/", "\\.nf-test.log$","^\\.git/"],
     "AllowedContentTypes": [],
     "PassedFiles": [],
     "Disable": {

README.md

@@ -18,6 +18,20 @@ primary focus of the library is to provide pre-built processes and processing se
 technologies and made easily available to pipeline's developers through the `nf-core`
 framework.
 
+# WHY ? `nf-neuro`
+
+**Let's say you develop a pipeline for neuroimaging**. You want to make it the more _efficient,_
+_reliable, reproducible_ and also be able to _evaluate it_ and _control the quality_ of its outputs.
+That's what `nf-neuro` provides to you, **all in one repository**, hosting **all dependencies** you
+need to start developing and analyzing.
+
+The only thing we ask of you is to develop in `Nextflow DSL2`. We use principle and standards
+closely aligned with [nf-core](), but we'll make you adapt to them slowly as you go (we still
+haven't finished complying to all of them ourselves). Using `nf-neuro` helps accelerate
+development in **neuroimaging** and produces better research outcomes for all !
+
+---
+
 - [Using modules from `nf-neuro`](#using-modules-from-nf-neuro)
 - [Developing in `nf-neuro`](#developing-in-nf-neuro)
   - [Manual configuration](#manual-configuration)
@@ -38,6 +52,7 @@ framework.
       - [Edit `tests/main.nf.test`](./docs/MODULE.md#edit-testsmainnftest)
       - [Edit `tests/nextflow.config`](./docs/MODULE.md#edit-testsnextflowconfig)
     - [Generate tests snapshots](./docs/MODULE.md#generate-tests-snapshots)
+    - [Request for more test resources](./docs/MODULE.md#request-for-more-test-resources)
     - [Lint your code](./docs/MODULE.md#lint-your-code)
     - [Submit your PR](./docs/MODULE.md#submit-your-pr)
   - [Defining optional input parameters](./docs/MODULE.md#defining-optional-input-parameters)
@@ -57,6 +72,8 @@ framework.
 - [Configuring Docker for easy usage](#configuring-docker-for-easy-usage)
 - [Installing Prettier and editorconfig](#installing-prettier-and-editorconfig)
 
+---
+
 # Using modules from `nf-neuro`
 
 To import modules from `nf-neuro`, you first need to install [nf-core](https://github.com/nf-core/tools)

docs/MODULE.md

@@ -10,6 +10,7 @@
     - [Edit `tests/main.nf.test`](#edit-testsmainnftest)
     - [Edit `tests/nextflow.config`](#edit-testsnextflowconfig)
   - [Generate tests snapshots](#generate-tests-snapshots)
+  - [Request for more test resources](#request-for-more-test-resources)
   - [Lint your code](#lint-your-code)
   - [Submit your PR](#submit-your-pr)
 - [Defining optional input parameters](#defining-optional-input-parameters)
@@ -295,7 +296,7 @@ Make sure there is no more comments generated by the `nf-core` template, and you
 The `nextflow.config` file does not exist by default, so you will have to create it if needed. This is not mandatory, except if you have defined optional parameters with `task.ext` and want to alter their values for some test cases. Refer to [this section](#defining-optional-input-parameters) to
 see how to scope those parameters to specific tests using `selectors`.
 
-### Generate tests snapshots
+## Generate tests snapshots
 
 > [!WARNING]
 > Verify you are located at the root of `nf-neuro` (not inside modules) before
@@ -315,7 +316,7 @@ smoothly, look at the snapshot file produced at `tests/main.nf.test.snap` in you
 directory and validate that ALL outputs produced by test cases are caught. Their `md5sum` is
 critical to ensure future executions of your test produce valid outputs.
 
-### Request for more test resources
+## Request for more test resources
 
 Test runners are tailored to restrain their resources usage to specifically what is asked for by
 Nextflow through the configuration files. For `nf-neuro` tests, you can find this configuration in