Merge pull request #2 from AlexVCaron/fix/port_workflow_errors

Fix port workflow errors

.editorconfig

@@ -13,3 +13,11 @@ indent_size = 2
 
 [LICENSE]
 indent_size = unset
+
+[tests/.runs]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset

.editorconfig-checker.json

@@ -0,0 +1,18 @@
+{
+    "Verbose": true,
+    "Debug": false,
+    "IgnoreDefaults": false,
+    "SpacesAftertabs": false,
+    "NoColor": false,
+    "Exclude": ["^tests/.runs/", "^\\.nf-test/", "^\\.venv/", "^\\node_modules/", "\\.nf-test.log$"],
+    "AllowedContentTypes": [],
+    "PassedFiles": [],
+    "Disable": {
+        "EndOfLine": false,
+        "Indentation": false,
+        "IndentSize": false,
+        "InsertFinalNewline": false,
+        "TrimTrailingWhitespace": false,
+        "MaxLineLength": false
+    }
+}

.gitignore

@@ -22,6 +22,7 @@ yarn-error.log
 .work/
 .nextflow*
 .nf-test*
+tests/.runs/
 
 # Misc
 .DS_Store

.prettierignore

@@ -5,7 +5,7 @@
 .nextflow/
 .nf-test/
 .pytest_cache/
-.test_data/
+tests/.runs/
 venv/
 .venv/
 .vscode/

README.md

@@ -18,45 +18,44 @@ 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.
 
-* [Using modules from `nf-neuro`](#using-modules-from-nf-neuro)
-* [Developing in `nf-neuro`](#developing-in-nf-neuro)
-  * [Manual configuration](#manual-configuration)
-    * [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)
-  * [Configuration via the `devcontainer` :](#configuration-via-the-devcontainer-)
-* [Contributing to the `nf-neuro` project](#contributing-to-the-nf-neuro-project)
-  * [Adding a new module to nf-neuro](./docs/MODULE.md#adding-a-new-module-to-nf-neuro)
-    * [Generate the template](./docs/MODULE.md#generate-the-template)
-    * [Edit the template](./docs/MODULE.md#edit-the-template)
-      * [Edit `main.nf`:](./docs/MODULE.md#edit-mainnf)
-      * [Edit `environment.yml`:](./docs/MODULE.md#edit-environmentyml)
-      * [Edit `meta.yml`:](./docs/MODULE.md#edit-metayml)
-    * [Create test cases](./docs/MODULE.md#create-test-cases)
-      * [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)
-    * [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)
-  * [Test data infrastructure](./docs/MODULE.md#test-data-infrastructure)
-  * [Adding a new subworkflow to nf-neuro](./docs/SUBWORKFLOWS.md#adding-a-new-subworkflow-to-nf-neuro)
-    * [Generate the template](./docs/SUBWORKFLOWS.md#generate-the-template)
-    * [Edit the template](./docs/SUBWORKFLOWS.md#edit-the-template)
-      * [Edit `main.nf`](./docs/SUBWORKFLOWS.md#edit-mainnf)
-        * [Define your subworkflow inputs](./docs/SUBWORKFLOWS.md#define-your-subworkflow-inputs)
-        * [Fill the `main:` section](./docs/SUBWORKFLOWS.md#fill-the-main-section)
-        * [Define your Workflow outputs](./docs/SUBWORKFLOWS.md#define-your-workflow-outputs)
-      * [Edit `meta.yml`](./docs/SUBWORKFLOWS.md#edit-metayml)
-      * [Create test cases](./docs/SUBWORKFLOWS.md#create-test-cases)
-    * [Lint your code](./docs/SUBWORKFLOWS.md#lint-your-code)
-    * [Submit your PR](./docs/SUBWORKFLOWS.md#submit-your-pr)
-* [Running tests](#running-tests)
-* [Configuring Docker for easy usage](#configuring-docker-for-easy-usage)
-* [Installing Prettier](#installing-prettier)
-
+- [Using modules from `nf-neuro`](#using-modules-from-nf-neuro)
+- [Developing in `nf-neuro`](#developing-in-nf-neuro)
+  - [Manual configuration](#manual-configuration)
+    - [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)
+  - [Configuration via the `devcontainer`](#configuration-via-the-devcontainer)
+- [Contributing to the `nf-neuro` project](#contributing-to-the-nf-neuro-project)
+  - [Adding a new module to nf-neuro](./docs/MODULE.md#adding-a-new-module-to-nf-neuro)
+    - [Generate the template](./docs/MODULE.md#generate-the-template)
+    - [Edit the template](./docs/MODULE.md#edit-the-template)
+      - [Edit `main.nf`](./docs/MODULE.md#edit-mainnf)
+      - [Edit `environment.yml`](./docs/MODULE.md#edit-environmentyml)
+      - [Edit `meta.yml`](./docs/MODULE.md#edit-metayml)
+    - [Create test cases](./docs/MODULE.md#create-test-cases)
+      - [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)
+    - [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)
+  - [Test data infrastructure](./docs/MODULE.md#test-data-infrastructure)
+  - [Adding a new subworkflow to nf-neuro](./docs/SUBWORKFLOWS.md#adding-a-new-subworkflow-to-nf-neuro)
+    - [Generate the template](./docs/SUBWORKFLOWS.md#generate-the-template)
+    - [Edit the template](./docs/SUBWORKFLOWS.md#edit-the-template)
+      - [Edit `main.nf`](./docs/SUBWORKFLOWS.md#edit-mainnf)
+        - [Define your subworkflow inputs](./docs/SUBWORKFLOWS.md#define-your-subworkflow-inputs)
+        - [Fill the `main:` section](./docs/SUBWORKFLOWS.md#fill-the-main-section)
+        - [Define your Workflow outputs](./docs/SUBWORKFLOWS.md#define-your-workflow-outputs)
+      - [Edit `meta.yml`](./docs/SUBWORKFLOWS.md#edit-metayml)
+      - [Create test cases](./docs/SUBWORKFLOWS.md#create-test-cases)
+    - [Lint your code](./docs/SUBWORKFLOWS.md#lint-your-code)
+    - [Submit your PR](./docs/SUBWORKFLOWS.md#submit-your-pr)
+- [Running tests](#running-tests)
+- [Configuring Docker for easy usage](#configuring-docker-for-easy-usage)
+- [Installing Prettier and editorconfig](#installing-prettier-and-editorconfig)
 
 # Using modules from `nf-neuro`
 
@@ -188,7 +187,7 @@ This will make it so the `nf-core` commands target the right repository by defau
 The `nf-neuro` project curates a bundle of useful extensions for Visual Studio Code, the `nf-neuro-extensions` package. You can find it easily on the [extension
 marketplace](https://marketplace.visualstudio.com/items?itemName=nf-neuro.nf-neuro-extensions).
 
-## Configuration via the `devcontainer` :
+## Configuration via the `devcontainer`
 
 The `devcontainer` definition for the project contains all required dependencies and setup
 steps are automatically executed. To use this installation method, you need to have **Docker** (refer to [this section](#configuring-docker-for-easy-usage) for configuration requirements or validate your configuration) and **Visual Studio Code** installed on your system.
@@ -239,9 +238,9 @@ sudo usermod -aG docker $USER
 
 After running this command, you need to log out and log back in to apply the changes.
 
-# Installing Prettier
+# Installing Prettier and editorconfig
 
-To install **Prettier** for the project, you need to have `node` and `npm` installed on your system to at least version 14. On Ubuntu, you can do it using snap :
+To install **Prettier** and **editorconfig** for the project, you need to have `node` and `npm` installed on your system to at least version 14. On Ubuntu, you can do it using snap :
 
 ```bash
 sudo snap install node --classic
@@ -256,6 +255,8 @@ curl -fsSL https://deb.nodesource.com/setup_${NODE_MAJOR}.x | bash - &&\
 apt-get install -y nodejs
 
 npm install --save-dev --save-exact prettier
+npm install --save-dev --save-exact editorconfig-checker
 
 echo "function prettier() { npm exec prettier $@; }" >> ~/.bashrc
+echo "function editorconfig-checker() { npm exec editorconfig-checker $@; }" >> ~/.bashrc
 ```

docs/MODULE.md

@@ -1,19 +1,19 @@
 # Contributing to nf-neuro <!-- omit in toc -->
 
-* [Adding a new module to nf-neuro](#adding-a-new-module-to-nf-neuro)
-  * [Generate the template](#generate-the-template)
-  * [Edit the template](#edit-the-template)
-    * [Edit `main.nf`:](#edit-mainnf)
-    * [Edit `environment.yml`:](#edit-environmentyml)
-    * [Edit `meta.yml`:](#edit-metayml)
-  * [Create test cases](#create-test-cases)
-    * [Edit `tests/main.nf.test`:](#edit-testsmainnftest)
-    * [Edit `tests/nextflow.config`:](#edit-testsnextflowconfig)
-  * [Generate tests snapshots](#generate-tests-snapshots)
-  * [Lint your code](#lint-your-code)
-  * [Submit your PR](#submit-your-pr)
-* [Defining optional input parameters](#defining-optional-input-parameters)
-* [Test data infrastructure](#test-data-infrastructure)
+- [Adding a new module to nf-neuro](#adding-a-new-module-to-nf-neuro)
+  - [Generate the template](#generate-the-template)
+  - [Edit the template](#edit-the-template)
+    - [Edit `main.nf`](#edit-mainnf)
+    - [Edit `environment.yml`](#edit-environmentyml)
+    - [Edit `meta.yml`](#edit-metayml)
+  - [Create test cases](#create-test-cases)
+    - [Edit `tests/main.nf.test`](#edit-testsmainnftest)
+    - [Edit `tests/nextflow.config`](#edit-testsnextflowconfig)
+  - [Generate tests snapshots](#generate-tests-snapshots)
+  - [Lint your code](#lint-your-code)
+  - [Submit your PR](#submit-your-pr)
+- [Defining optional input parameters](#defining-optional-input-parameters)
+- [Test data infrastructure](#test-data-infrastructure)
 
 # Adding a new module to nf-neuro
 
@@ -57,7 +57,7 @@ already follow all guidelines. You will find related files in :
 - `modules/nf-neuro/betcrop/fslbetcrop`
 - `tests/modules/nf-neuro/betcrop/fslbetcrop`
 
-### Edit `main.nf`:
+### Edit `main.nf`
 
 - Remove the line `conda "YOUR-TOOL-HERE"`.
 
@@ -148,24 +148,19 @@ already follow all guidelines. You will find related files in :
 
   - Call `touch <file>` to generate empty files for all required outputs.
 
-### Edit `environment.yml`:
+### Edit `environment.yml`
 
-Start by removing the comments added automatically by `nf-core`, then, replace the existing `channels` section by:
+This file is used by `nf-core` to manage `conda` environements for modules. It is not
+used by `nf-neuro` for now, but must be created following a basic format for linting to
+pass. The file should contain the following :
 
-```yml
-channels:
-  - Docker
-  - Apptainer
+```yaml
+name: <category>_<tool>
+channels: []
+dependencies: []
 ```
 
-and add the name of the tools used within your module in the `dependencies` section. For example, if you are using `scilpy` tools, write:
-
-```yml
-dependencies:
-  - scilpy
-```
-
-### Edit `meta.yml`:
+### Edit `meta.yml`
 
 Fill the sections you find relevant. There is a lot of metadata in this file, but we
 don't need to specify them all. At least define the `keywords`, describe the process'
@@ -189,7 +184,7 @@ The module's test infrastructure is auto-generated when creating a module using
 > [!NOTE]
 > Multiple tests can be specified one after the other in the `main.nf.test`, be sure to corner most of the use-case of your module to ensure catching any potential bugs!
 
-### Edit `tests/main.nf.test`:
+### Edit `tests/main.nf.test`
 
 To specify test data, you need to define a `setup` section before the actual test definition. This setup section will use the `LOAD_TEST_DATA` workflow to fetch your test data from an available package (refer to [this section](#test-data-infrastructure) to learn how to find packages). Once you selected the archives and files you need, add a `setup` section before the test section.
 
@@ -295,7 +290,7 @@ Finally, ensure all the tags at the beginning of the process definition include
 
 Make sure there is no more comments generated by the `nf-core` template, and you should be good to go!
 
-### Edit `tests/nextflow.config`:
+### Edit `tests/nextflow.config`
 
 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`.
@@ -316,19 +311,28 @@ nf-core modules test -u <category>/<tool>
 ```
 
 All the test case you defined will be run, watch out for errors ! Once everything runs
-smoothly, look at the snapshot file produced at `tests/main.nf.test.snap` in your module's 
+smoothly, look at the snapshot file produced at `tests/main.nf.test.snap` in your module's
 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.
 
 ## Lint your code
 
-Before submitting to _nf-neuro_, once you've commit and push everything, the code need to be correctly linted, else the checks won't pass. This is done using `prettier` on your new module, through the _nf-core_ command line :
+Before submitting to _nf-neuro_, once you've commit and push everything, the code need to be correctly linted, else the checks won't pass. This is done using `prettier` and `editorconfig-checker` on your new module, through the _nf-core_ command line :
 
 ```bash
 nf-core modules lint <category>/<tool>
 ```
 
-You'll probably get a bunch of _whitespace_ and _indentation_ errors, but also image errors, bad _nextflow_ syntax and more. You need to fix all `errors` and as much as the `warnings`as possible.
+You'll probably get a bunch of _whitespace_ and _indentation_ errors, but also image errors, bad _nextflow_ syntax and more. You need to fix all `errors` and as much as the `warnings` as possible.
+
+If at any point you modified files outside of your module's directory, those also need to be linted. To do so, run the following commands at the root of the repository :
+
+```bash
+prettier --check .
+editorconfig-checker
+```
+
+You'll get lists of syntax errors to fix from both commands. For prettier, you can run `prettier --write .` to fix most of them automatically. For `editorconfig-checker`, you'll have to fix them manually.
 
 ## Submit your PR
 

docs/SUBWORKFLOWS.md

@@ -1,16 +1,16 @@
 # Contributing to nf-neuro <!-- omit in toc -->
 
-* [Adding a new subworkflow to nf-neuro](#adding-a-new-subworkflow-to-nf-neuro)
-  * [Generate the template](#generate-the-template)
-  * [Edit the template](#edit-the-template)
-    * [Edit `main.nf`](#edit-mainnf)
-      * [Define your subworkflow inputs](#define-your-subworkflow-inputs)
-      * [Fill the `main:` section](#fill-the-main-section)
-      * [Define your Workflow outputs](#define-your-workflow-outputs)
-    * [Edit `meta.yml`](#edit-metayml)
-    * [Create test cases](#create-test-cases)
-  * [Lint your code](#lint-your-code)
-  * [Submit your PR](#submit-your-pr)
+- [Adding a new subworkflow to nf-neuro](#adding-a-new-subworkflow-to-nf-neuro)
+  - [Generate the template](#generate-the-template)
+  - [Edit the template](#edit-the-template)
+    - [Edit `main.nf`](#edit-mainnf)
+      - [Define your subworkflow inputs](#define-your-subworkflow-inputs)
+      - [Fill the `main:` section](#fill-the-main-section)
+      - [Define your Workflow outputs](#define-your-workflow-outputs)
+    - [Edit `meta.yml`](#edit-metayml)
+    - [Create test cases](#create-test-cases)
+  - [Lint your code](#lint-your-code)
+  - [Submit your PR](#submit-your-pr)
 
 # Adding a new subworkflow to nf-neuro
 
@@ -152,7 +152,14 @@ Run `prettier` on your new module, through the `nf-core` command line :
 nf-core subworkflows lint <subworkflow>
 ```
 
-and fix all `errors` and as many `warnings` as possible.
+and fix all `errors` and as many `warnings` as possible. If at any point you modified files outside of your module's directory, those also need to be linted. To do so, run the following commands at the root of the repository :
+
+```bash
+prettier --check .
+editorconfig-checker
+```
+
+You'll get lists of syntax errors to fix from both commands. For prettier, you can run `prettier --write .` to fix most of them automatically. For `editorconfig-checker`, you'll have to fix them manually.
 
 ## Submit your PR
 

modules/environment-schema.json

@@ -11,8 +11,8 @@
         "channels": {
             "type": "array",
             "items": {
-            	"type": "string"
-    	    }
+                "type": "string"
+            }
         },
         "dependencies": {
             "type": "array",

nf-test.config

@@ -10,7 +10,7 @@ config {
 
     ignore ".venv/**/*.nf*"
 
-    requires( 
+    requires(
         "nf-test": "0.9.0"
     )
 

tests/nextflow.config

@@ -18,4 +18,4 @@ report {
     overwrite = true
 }
 
-includeConfig "$projectDir/tests/config/nextflow.config"
+includeConfig "$projectDir/tests/config/nextflow.config"