diff --git a/README.md b/README.md index 8f7efe60..c18f030c 100644 --- a/README.md +++ b/README.md @@ -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 / ``` -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 @@ -103,9 +103,9 @@ The `nf-neuro` project requires some specific tools to be installed on your syst - Docker ≥ 24 (we recommend using [Docker Desktop](https://www.docker.com/products/docker-desktop)) - Java Runtime ≥ 11, ≤ 17 - On Ubuntu, install `openjdk-jre-` packages -- Nextflow ≥ 21.04.3 -- nf-test ≥ 0.9.0-rc1 -- Node ≥ 14 and Prettier (see [below](#installing-prettier)) +- Nextflow ≥ 23.04.0 +- nf-test ≥ 0.9.0 +- Node ≥ 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 @@ -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_1.jdk`) and use the -> following : `/Library/Java/JavaVirtualMachines/dk_1.jdk/Contents/Home`. +> following : `/Library/Java/JavaVirtualMachines/jdk_1.jdk/Contents/Home`. ### Python environment @@ -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` @@ -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