Add pixi to my template

.github/workflows/main.yml

@@ -1,44 +1,19 @@
 name: CI
 
-# Controls when the action will run.
 on:
-  # Triggers the workflow on push or pull request events but only for the main branch
   push:
-    branches: [main, master]
+    branches: [main]
   pull_request:
-    branches: [main, master]
+    branches: [main]
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  Formatting:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: psf/black@stable
-        with:
-          options: ". --check --verbose"
-
-  Linting:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Test linting
-        uses: snakemake/[email protected]
-        with:
-          directory: .
-          snakefile: workflow/Snakefile
-          args: "--lint"
-
-  run-workflow:
-    needs: Formatting
+  # pixi test
+  Test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Test CI
-        uses: snakemake/[email protected]
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/[email protected]
         with:
-          directory: .
-          snakefile: workflow/Snakefile
+          pixi-version: v0.37.0
+          cache: true
+      - run: pixi run test

.gitignore

@@ -5,3 +5,6 @@ logs/**
 .snakemake/**
 **.code-workspace
 temp/**
+.ruff_cache/**
+.pixi/**
+.DS_Store

README.md

@@ -5,3 +5,23 @@
 This is a Snakemake project template. The `Snakefile` is under `workflow`.
 
 [Slides](https://mrvollger.github.io/SmkTemplate/slides) describing and justifying the use of this template.
+
+## Install
+
+Please start by installing [pixi](https://pixi.sh/latest/) which handles the environment of this Snakemake workflow.
+
+You can then setup of the `pixi` environment by cloning this repository and running:
+
+```bash
+pixi install
+```
+
+## Usage
+
+I have decided to use `pixi` to handle execution of my Snakemake workflows.
+
+```bash
+pixi run snakemake ...
+```
+
+And in place of `...` use all the normal Snakemake arguments for your workflow.