Merge pull request #2 from MPUSP/dev

feat: updated docs and added linting wf for repo content

Author: m-jahn

.github/workflows/yaml-formatting.yml

@@ -0,0 +1,20 @@
+name: YAML Workflow Formatting
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Formatting
+        uses: super-linter/super-linter@v8
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_YAML_PRETTIER: true

README.md

@@ -1,4 +1,3 @@
-
 # MPUSP GitHub Actions
 
 This repository contains reusable GitHub Actions workflows for the [MPUSP](https://www.mpusp.mpg.de/), the Max Planck Unit for the Science of Pathogens.
@@ -8,21 +7,104 @@ This repository contains reusable GitHub Actions workflows for the [MPUSP](https
 These workflows are designed to streamline CI processes across MPUSP projects by providing standardized, reusable automation templates.
 Their main purpose is to secure a harmonized, easy-to-maintain, and up-to-date collection of reusable CI workflows for our [Snakemake pipelines](https://github.com/orgs/MPUSP/repositories).
 
+## Workflows
+
+Currently available workflows include:
+
+- `snakemake-tests`: Runs standardized tests for Snakemake workflows.
+- `deploy-apptainer`: Builds and deploys Apptainer containers for Snakemake workflows to GitHub Packages ([GHCR](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry)). **Note**: work in progress, use carefully!
+- `release-please`: Automates the release process using the [release-please](https://github.com/googleapis/release-please) tool.
+- `conventional-prs`: Lints pull requests for conventional commit messages.
+
 ## Usage
 
-To use these workflows in your repository, reference them in your workflow files:
+To use these workflows in your repository, reference them in your workflow files as outlined below.
+Note: workflows can be pinned to a specific version tag (`@v1.0`), but it is recommended to use the latest stable version (`@main`) in order to keep manual intervention in workflows to a minimum.
+
+### Snakemake Tests
 
 ```yaml
+name: Snakemake Tests
+
+on:
+  pull_request:
+    branches: [main]
+
 jobs:
-    my-job:
-        uses: mpusp/mpusp-github-actions/.github/workflows/workflow-name.yml@main
+  snakemake-tests:
+    uses: MPUSP/mpusp-github-actions/.github/workflows/snakemake-tests.yml@main
+    with:
+      cores: 2
+      dryrun: false
 ```
 
-## Workflows
+### Deploy Apptainer
 
-Documentation for individual workflows coming soon.
+```yaml
+name: Deploy Apptainer
+
+on:
+  workflow_run:
+    workflows: ["Release Please"]
+    types:
+      - completed
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  deploy-apptainer:
+    if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
+    uses: MPUSP/mpusp-github-actions/.github/workflows/deploy-apptainer.yml@main
+```
+
+### Release Please
+
+```yaml
+name: Release Please
+
+on:
+  push:
+    branches: [main]
+
+permissions:
+  contents: write
+  pull-requests: write
+  issues: write
+
+jobs:
+  release-please:
+    uses: MPUSP/mpusp-github-actions/.github/workflows/release-please.yml@main
+```
+
+### Conventional PRs
+
+```yaml
+name: Conventional PRs
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+permissions:
+  pull-requests: read
+
+jobs:
+  conventional-prs:
+    uses: MPUSP/mpusp-github-actions/.github/workflows/conventional-prs.yml@main
+```
 
 ## Contributing
 
 For issues and comments, please leave an issue on [Github](https://github.com/MPUSP/mpusp-github-actions/issues).
 For further questions, please contact bioinformatics@mpusp.mpg.de.
+
+## Authors
+
+- MPUSP bioinformatics team (http://mpusp.github.io/)