Merge pull request #348 from genomic-medicine-sweden/develop

chore: dev to master

.github/workflows/lint.yaml

@@ -30,4 +30,4 @@ jobs:
       - name: Linting
         working-directory: .tests/integration
         run: |
-          snakemake --lint -n -s ../../workflow/Snakefile --configfile config/config.yaml
+          snakemake --lint -n -s ../../workflow/Snakefile --configfiles ../../config/config.yaml config/config.yaml

.github/workflows/snakefmt.yaml

@@ -21,7 +21,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Lint Code Base
-        uses: github/super-linter@v4.9.0
+        uses: super-linter/super-linter@v5.3.1
         env:
           VALIDATE_ALL_CODEBASE: false
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/snakemake-dry-run.yaml

@@ -30,4 +30,8 @@ jobs:
       - name: snakemake dry run
         working-directory: .tests/integration
         run: |
-          snakemake -n -s ../../workflow/Snakefile --configfile config/config.yaml
+          snakemake -n -s ../../workflow/Snakefile --configfiles ../../config/config.yaml config/config.yaml
+      - name: snakemake dry run reference
+        working-directory: .tests/integration
+        run: | 
+          snakemake -s ../../workflow/Snakefile_references.smk --configfiles ../../config/config.yaml ../../config/config_references.yaml config/config.yaml config/config_reference.yaml -n

.github/workflows/test-build-mkdocs.yaml

@@ -0,0 +1,33 @@
+name: build mkdocs
+
+on:
+  push:
+    branches:
+     - develop
+     - master
+  pull_request:
+    branches:
+     - develop
+     - master
+  workflow_dispatch:
+
+jobs:
+  build-mkdocs:
+    name: build mkdocs
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.8
+      - name: Install requirements.txt
+        run: |
+          pip install -r requirements.txt
+      - name: Install requirements.test.txt
+        run: |
+          pip install -r requirements.test.txt
+          pip install -r docs/requirements.txt
+      - name: build mkdocs
+        run: |
+          mkdocs build