ci: testing through apptainer

.github/workflows/testing.yml

@@ -10,15 +10,80 @@ on:
 jobs:
   Testing:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0} # Required for Conda environments to activate properly
+
     steps:
-    - name: Checkout repository with submodules
+    # 1. Clear disk space (Crucial for Apptainer + DeepVariant)
+    - name: Free Disk Space (Ubuntu)
+      uses: jlumbroso/free-disk-space@main
+      with:
+        tool-cache: true
+        android: true
+        dotnet: true
+        haskell: true
+        large-packages: true
+        docker-images: true
+        swap-storage: true
+
+    - name: Checkout repository
       uses: actions/checkout@v3
       with:
         submodules: recursive
-    - name: Test workflow
-      uses: snakemake/snakemake-github-action@v1.22.0
+
+    # 2. Install Apptainer on the Host
+    - name: Setup Apptainer
+      uses: eWaterCycle/setup-apptainer@v2
       with:
-        directory: .test
-        snakefile: .test/Snakefile
-        args: "--configfile .test/config/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
-
+        apptainer-version: '1.2.5'
+
+    # 3. Install Snakemake using Mamba (Faster/Native approach)
+    - name: Setup Mamba/Conda and Install Snakemake
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-version: latest
+        activate-environment: snakemake
+        # Installing snakemake directly here
+        environment-config: >
+          name: snakemake
+          channels:
+            - conda-forge
+            - bioconda
+            - nodefaults
+          dependencies:
+            - snakemake
+            - python=3.10
+
+    # 4. Prepare your data (Files & Downloads)
+    - name: Prepare Test Data and Models
+      run: |
+        gzip -d .test/test_data/chr6_cdna.fa.gz
+        gzip -d .test/test_data/genome_chr6.fa.gz
+        mv .test/test_data/genome_chr6.fa.gz.fai .test/test_data/genome_chr6.fa.fai
+
+        mkdir -p workflow/supplementary_res/deepvariant_rna_model
+        BASE_URL="https://storage.googleapis.com/deepvariant/models/DeepVariant/1.4.0/DeepVariant-inception_v3-1.4.0+data-rnaseq_standard"
+
+        wget -q -P workflow/supplementary_res/deepvariant_rna_model "$BASE_URL/model.ckpt.data-00000-of-00001"
+        wget -q -P workflow/supplementary_res/deepvariant_rna_model "$BASE_URL/model.ckpt.example_info.json"
+        wget -q -P workflow/supplementary_res/deepvariant_rna_model "$BASE_URL/model.ckpt.index"
+        wget -q -P workflow/supplementary_res/deepvariant_rna_model "$BASE_URL/model.ckpt.meta"
+
+        echo "Data preparation complete."
+
+    # 5. Run Snakemake directly
+    - name: Test workflow
+      env:
+        # Save disk space by preventing Apptainer from caching the huge SIF files
+        APPTAINER_DISABLE_CACHE: "true"
+      run: |
+        snakemake \
+          --directory .test \
+          --snakefile .test/Snakefile \
+          --configfile .test/config/config.yaml \
+          --use-apptainer \
+          --use-conda \
+          --show-failed-logs \
+          --cores 2 \
+          --conda-cleanup-pkgs cache