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Various fixes on readme
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AlexVCaron authored Sep 18, 2024
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Expand Up @@ -74,13 +74,13 @@ a list of the available modules, run :
nf-core modules --git-remote https://github.com/scilus/nf-neuro.git list remote
```

The same can be done for subworkflows, replacing `modules` in the `nf-core` command by `subworkflows, e.g. :
The same can be done for subworkflows, replacing `modules` in the `nf-core` command by `subworkflows :

```bash
nf-core subworkflows --git-remote https://github.com/scilus/nf-neuro.git install <category>/<subworkflow>
```

It can become heavy to always prepend the commands with `--git-remote`, even so if you need to specify a `--branch` where to fetch the information. You can instead define the `git-remote` and `branch` using _Environment Variables_ :
It can become heavy to always prepend the commands with `--git-remote`, more so if you need to specify a `--branch` where to fetch the information. You can instead define the `git-remote` and `branch` using _Environment Variables_ :

```bash
export NFCORE_MODULES_GIT_REMOTE=https://github.com/scilus/nf-neuro.git
Expand All @@ -103,9 +103,9 @@ The `nf-neuro` project requires some specific tools to be installed on your syst
- Docker &geq; 24 (we recommend using [Docker Desktop](https://www.docker.com/products/docker-desktop))
- Java Runtime &geq; 11, &leq; 17
- On Ubuntu, install `openjdk-jre-<version>` packages
- Nextflow &geq; 21.04.3
- nf-test &geq; 0.9.0-rc1
- Node &geq; 14 and Prettier (see [below](#installing-prettier))
- Nextflow &geq; 23.04.0
- nf-test &geq; 0.9.0
- Node &geq; 14, `Prettier` and `editorconfig` (see [below](#installing-prettier-and-editorconfig))

> [!IMPORTANT]
> Nextflow might not detect the right `Java virtual machine` by default, more so if
Expand All @@ -117,7 +117,7 @@ The `nf-neuro` project requires some specific tools to be installed on your syst
> - MacOS : if the `Java jvm` is the preferential one, use `JAVA_HOME=$(/usr/libexec/java_home)`.
> Else, look into `/Library/Java/JavaVirtualMachines` for the folder with the correct
> runtime version (named `jdk<inner version>_1<runtime version>.jdk`) and use the
> following : `/Library/Java/JavaVirtualMachines/dk<inner version>_1<runtime version>.jdk/Contents/Home`.
> following : `/Library/Java/JavaVirtualMachines/jdk<inner version>_1<runtime version>.jdk/Contents/Home`.
### Python environment

Expand Down Expand Up @@ -185,7 +185,7 @@ This will make it so the `nf-core` commands target the right repository by defau
### Working with VS Code

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).
marketplace](https://marketplace.visualstudio.com/items?itemName=nf-neuro.nf-neuro-extensionpack).

## Configuration via the `devcontainer`

Expand All @@ -201,15 +201,20 @@ environment.
- `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`, `git-lfs`, `github-cli`
- `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
- Test Data introspection
- Resource monitoring
- Remote development
- Live sharing with collaborators

# Contributing to the `nf-neuro` project

Expand Down

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