lint main workflow and integration workflow

Author: irm-codebase

.github/workflows/template-pr-ci.yml

@@ -22,7 +22,9 @@ jobs:
         continue-on-error: true
       - name: Run snakemake linting
         id: linting
-        run: pixi run snakemake --lint
+        run: |
+          pixi run snakemake --lint --snakefile workflow/Snakefile
+          pixi run snakemake --lint --snakefile tests/integration/Snakefile
         continue-on-error: true
       - name: Save integration logs
         if: ${{ always() }}