Add GitHub test action (#85)

* update gh action

* trigger on PR

* remove PR trigger

* use all cores

* fix snakemake style

* trigger on PR

* remove PR trigger

Author: hoferand

.github/workflows/ci.yml

@@ -0,0 +1,72 @@
+name: CI
+
+on:
+  workflow_dispatch:
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  packages: read
+  statuses: write
+
+jobs:
+  format:
+    name: Format workflow
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Format code base
+        uses: super-linter/super-linter@v8.5.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_ALL_CODEBASE: true
+          DEFAULT_BRANCH: main
+
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+          VALIDATE_PYTHON_BLACK: true
+          VALIDATE_YAML_PRETTIER: true
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Set up R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: styler
+
+      - name: Check R style
+        run: Rscript -e 'changed <- styler::style_dir(".", dry = "on"); if (any(changed$changed)) quit(status = 1)'
+
+  test:
+    name: Test example data
+    runs-on: ubuntu-latest
+    timeout-minutes: 45
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+        with:
+          persist-credentials: false
+
+      - name: Run workflow on example data
+        uses: snakemake/snakemake-github-action@v2
+        with:
+          directory: .
+          snakefile: workflow/Snakefile
+          snakemake-version: 8.25.3
+          args: >-
+            --cores all
+            --sdm conda
+            --conda-cleanup-pkgs cache
+            --show-failed-logs
+          show-disk-usage-on-error: true

.github/workflows/lint.yml

@@ -21,6 +21,8 @@ report: os.path.join("report", "workflow.rst")
 
 ##### load and validate config and sample annotation sheets #####
 configfile: os.path.join("config", "config.yaml")
+
+
 validate(config, os.path.join("schemas", "config.schema.yaml"))