Symlink micromamba

.github/workflows/main.yaml

@@ -13,12 +13,16 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Lint workflow
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
-      # uses: snakemake/[email protected]
+      #uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/[email protected]
       with:
         directory: .
         snakefile: workflow/Snakefile
         args: "--lint"
+        stagein:
+          - micromamba install -y -c conda-forge rsync
+          - ln -s /usr/bin/micromamba /usr/bin/mamba
+          - ln -s /usr/bin/micromamba /usr/bin/conda
 
   Testing:
     runs-on: ubuntu-latest
@@ -28,13 +32,16 @@ jobs:
     - name: Checkout repository and submodules
       uses: actions/checkout@v4
     - name: Test workflow (local test data)
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
-      #uses: snakemake/[email protected]
+      #uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/[email protected]
       with:
         directory: .test
         snakefile: workflow/Snakefile
-        args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --wrapper-prefix file:///github/workspace/workflow/wrappers"
-        stagein: mamba install -y -c conda-forge rsync
+        args: "--use-conda --conda-backend mamba--show-failed-logs -j 10 --conda-cleanup-pkgs cache --wrapper-prefix file:///github/workspace/workflow/wrappers"
+        stagein:
+          - micromamba install -y -c conda-forge rsync
+          - ln -s /usr/bin/micromamba /usr/bin/mamba
+          - ln -s /usr/bin/micromamba /usr/bin/conda
     - name: Test report
       uses: snakemake/[email protected]
       with: