Fix GitHub action by enforcing Snakemake 7.32

Prevents automatic usage of Snakemake 8 and avoids snakemake/snakemake-github-action#37
PathoGenOmics-Lab · Jan 5, 2024 · 77f3678 · 77f3678
1 parent 70958c3
commit 77f3678
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Showing 2 changed files with 37 additions and 16 deletions.
diff --git a/.github/workflows/install.yml b/.github/workflows/install.yml
@@ -25,23 +25,37 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
-      - name: Create environments
-        uses: snakemake/snakemake-github-action@v1
+      - name: Setup mamba
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          directory: ".test"
-          snakefile: "workflow/Snakefile"
-          args: "--configfile config/config.yaml .test/targets.yaml --cores 1 --conda-create-envs-only --use-conda"
-
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: true
+          activate-environment: ""
+      - name: Install Snakemake 7.32
+        run: |
+          pip install snakemake==7.32.4
+      - name: Create environments
+        run: |
+          snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --conda-create-envs-only --use-conda -c1
+
   Dry_run:
     needs: skip_duplicate
     if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }}
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
-      - name: Dry run
-        uses: snakemake/snakemake-github-action@v1
+      - name: Setup mamba
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          directory: ".test"
-          snakefile: "workflow/Snakefile"
-          args: "--configfile config/config.yaml .test/targets.yaml --dry-run"
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: true
+          activate-environment: ""
+      - name: Install Snakemake 7.32
+        run: |
+          pip install snakemake==7.32.4
+      - name: Dry run
+        run: |
+          snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --dry-run
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -34,12 +34,19 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
-      - name: Run test pipeline
-        uses: snakemake/snakemake-github-action@v1
+      - name: Setup mamba
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          directory: ".test"
-          snakefile: "workflow/Snakefile"
-          args: "--configfile config/config.yaml .test/targets.yaml --cores 1 --use-conda"
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          auto-activate-base: true
+          activate-environment: ""
+      - name: Install Snakemake 7.32
+        run: |
+          pip install snakemake==7.32.4
+      - name: Run test pipeline
+        run: |
+          snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --use-conda -c1  
       - name: Pack logs
         shell: bash
         run: |