workflow updates

.github/workflows/main.yaml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout with submodules
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: recursive
         fetch-depth: 0
@@ -25,7 +25,7 @@ jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Linting
       uses: snakemake/[email protected]
       with:
@@ -40,18 +40,18 @@ jobs:
       - formatting
     steps:
     - name: Checkout repository with submodules
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: recursive
     - name: Test workflow
       uses: snakemake/[email protected]
       with:
         directory: .test
         snakefile: workflow/Snakefile
-        args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
-    # - name: Test report
-    #   uses: snakemake/[email protected]
-    #   with:
-    #     directory: .test
-    #     snakefile: workflow/Snakefile
-    #     args: "--use-conda --cores 2 --report report.zip"
+        args: "--software-deployment-method conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
+    - name: Test report
+      uses: snakemake/[email protected]
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--software-deployment-method conda --cores 2 --report report.zip"