fixes

.devcontainer/devops/devcontainer.json

@@ -8,8 +8,8 @@
         }
     },
     "forwardPorts": [3000],
-    "onCreateCommand": "bash .devcontainer/onCreateCommand.sh",
-    "updateContentCommand": "bash .devcontainer/updateContentCommand.sh",
+    "onCreateCommand": "bash .devcontainer/devops/onCreateCommand.sh",
+    "updateContentCommand": "bash .devcontainer/devops/updateContentCommand.sh",
     "postStartCommand": "git config --global --add safe.directory ${containerWorkspaceFolder}",
     "containerEnv": {
         "WORKSPACE": "${containerWorkspaceFolder}"

.devcontainer/prototyping/devcontainer.json

@@ -7,8 +7,8 @@
         }
     },
     "forwardPorts": [3000],
-    "onCreateCommand": "bash .devcontainer/onCreateCommand.sh",
-    "updateContentCommand": "bash .devcontainer/updateContentCommand.sh",
+    "onCreateCommand": "bash .devcontainer/prototyping/onCreateCommand.sh",
+    "updateContentCommand": "bash .devcontainer/prototyping/updateContentCommand.sh",
     "postStartCommand": "git config --global --add safe.directory ${containerWorkspaceFolder}",
     "containerEnv": {
         "WORKSPACE": "${containerWorkspaceFolder}"

README.md

@@ -11,24 +11,24 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 ![Checks](https://github.com/scilus/nf-neuro/workflows/Merge%20to%20main%20checks/badge.svg)
 
-Welcome to the `nf-neuro` project ! A __Nextflow__ modules and workflows repository for neuroimaging
+Welcome to the `nf-neuro` project ! A **Nextflow** modules and workflows repository for neuroimaging
 maintained by the [SCIL team](https://scil-documentation.readthedocs.io/en/latest/). The
 primary focus of the library is to provide pre-built processes and processing sequences for
-__neuroimaging__, optimized for _Nextflow DSL2_, based on open-source
+**neuroimaging**, optimized for _Nextflow DSL2_, based on open-source
 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,_
+**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
+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 !
+development in **neuroimaging** and produces better research outcomes for all !
 
 ---
 
@@ -185,6 +185,7 @@ DENOSING_NLMEANS( input )
 
 > [!WARNING]
 > There are some exceptions here, due to limitations in current `nf-core` tools and standards.
+>
 > 1. some inputs could be associated to different channels. It's almost never the case, but it happens.
 >    We are working hard at changing the behavior of those modules, and at improving the metadata to
 >    help you better. For now, please refer to their implementation in the `modules/nf-neuro/`
@@ -201,7 +202,8 @@ DENOISING_NLMEANS.out.versions.first().view() // [ "versions.yml" ]
 
 > [!WARNING]
 > There are some exceptions here, due to limitations in current `nf-core` tools and standards.
-> 1. `meta` output __is not a channel__ but accompanies all files, produced by other channels.
+>
+> 1. `meta` output **is not a channel** but accompanies all files, produced by other channels.
 > 2. `versions` is a channel, but its output is not accompanied by `meta`
 > 3. Some other outputs are not accompanied by `meta` also. We are currently improving the metadata
 >    files to make it apparent. For now, please refer to their implementation in the `modules/nf-neuro/`
@@ -244,7 +246,7 @@ PREPROC_T1.out.versions.first().view()  // [ "versions.yml" ]
 
 ## Porting prototypes to `nf-` ready pipelines
 
-__SECTION TO COME__
+**SECTION TO COME**
 
 # Developing within `nf-neuro`
 
@@ -362,7 +364,7 @@ The tool can be omitted to run tests for all modules in a category.
 
 # Installing Prettier and editorconfig
 
-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 :
+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

docs/MODULE.md

@@ -29,19 +29,19 @@ nf-core modules create
 You will be prompted several times to configure the new module correctly. Refer
 to the following to ensure configuration abides with `nf-neuro` :
 
-- __Name of tool/subtool__ : `category/tool` of the module you plan creating (e.g. denoising/nlmeans).
-- __Bioconda package__ : select `no`.
-- __Github author__ : use your Github handle, or `@scilus` if you prefer not being identified through nf-neuro.
-- __Resource label__ : select `process_single` for now, for any tool (multiprocessing and acceleration will be delt with later).
-- __Meta map__ : select `yes`.
+- **Name of tool/subtool** : `category/tool` of the module you plan creating (e.g. denoising/nlmeans).
+- **Bioconda package** : select `no`.
+- **Github author** : use your Github handle, or `@scilus` if you prefer not being identified through nf-neuro.
+- **Resource label** : select `process_single` for now, for any tool (multiprocessing and acceleration will be delt with later).
+- **Meta map** : select `yes`.
 
 Alternatively, you can use the following command to supply nearly all information :
 
 ```bash
 nf-core modules create --author @scilus --label process_single --meta <category>/<tool>
 ```
 
-You will still have to interact with the __bioconda__ prompt, still select `no`.
+You will still have to interact with the **bioconda** prompt, still select `no`.
 
 > [!NOTE]
 > Once used to the conventions, adding `--empty-template` to the command will disable
@@ -361,7 +361,7 @@ Available runner classes that superseed `default` :
 | scilus-nf-neuro-bigmem-runners | <ul><li>16Gb RAM</li></ul>              |
 
 > [!IMPORTANT]
-> Specialized runners are limited !!! They are allocated for hungry processes, such as __AI/ML__ models and __large dataset studies__, don't abuse them. _The more they are requested for, the longer PR take to merge_, so don't ask for them for nothing, meaning be smart in designing your modules ! __PRs deemed not needing them will be automatically closed.__
+> Specialized runners are limited !!! They are allocated for hungry processes, such as **AI/ML** models and **large dataset studies**, don't abuse them. _The more they are requested for, the longer PR take to merge_, so don't ask for them for nothing, meaning be smart in designing your modules ! **PRs deemed not needing them will be automatically closed.**
 
 ## Lint your code
 
@@ -419,7 +419,7 @@ process {
 }
 ```
 
-Doing so will affect __ALL__ processes. To scope to a specific process, use the
+Doing so will affect **ALL** processes. To scope to a specific process, use the
 [process selectors](https://www.nextflow.io/docs/latest/config.html#process-selectors)
 (`withName:` or `withLabel:`) :
 
@@ -443,12 +443,12 @@ process {
 ```
 
 > [!IMPORTANT]
-> Modules inherit __selectors__. Thus, a module renamed at import (`import {A as B}`)
+> Modules inherit **selectors**. Thus, a module renamed at import (`import {A as B}`)
 > will be affected both by the selection `withName: "A"` and `withName: "B"`. However,
 > parameters defined by `B` will have precedence on those define in `A`.
 
 > [!IMPORTANT]
-> The same stands for __selectors__ defined on multiple levels, implicit (`withName: WORKFLOW_X*`)
+> The same stands for **selectors** defined on multiple levels, implicit (`withName: WORKFLOW_X*`)
 > or explicit (`withName: WORKFLOW_Y:B`).
 
 # Test data infrastructure

docs/SUBWORKFLOWS.md

@@ -38,7 +38,7 @@ The command will generate a new subworkflow template in the `./subworkflows/nf-n
 You can't select an empty template when you generate a new subworkflow, so the template is based on nf-core. You will need to replace some of their sections for your use case:
 
 - Remove the different comment lines.
-- Include your modules into your subworkflows (a subworkflow should include at least __two__ modules). Remove the modules `{ SAMTOOLS_SORT}` and `{ SAMTOOLS_INDEX }` then includes yours with the good pathway:
+- Include your modules into your subworkflows (a subworkflow should include at least **two** modules). Remove the modules `{ SAMTOOLS_SORT}` and `{ SAMTOOLS_INDEX }` then includes yours with the good pathway:
 
 ```
 include { <MODULES>	} from '../../../modules/nf-neuro/<category>/<tool>/main'