Update GHAs

Author: matrulda

.github/workflows/run_tests.yml

@@ -8,32 +8,27 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v6
 
-      - name: Cache singularity images
-        uses: actions/cache@v4.2.2
+      - name: Cache singularity/apptainer images
+        uses: actions/cache@v5.0.2
         with:
           path: work/singularity
           key: singularity-${{ hashFiles('config/nextflow_config/singularity.config') }}
           restore-keys: singularity-
 
-      - name: Install Singularity
-        uses: eWaterCycle/setup-singularity@v7
+      - name: Install apptainer 
+      - uses: eWaterCycle/setup-apptainer@v2
         with:
-          singularity-version: 3.8.3
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          curl -fsSL https://github.com/nextflow-io/nextflow/releases/download/v24.10.4/nextflow -o nextflow | bash
-          sudo mv nextflow /usr/local/bin/
-      
-      - name: Make Nextflow binary executable
-        run: chmod +x /usr/local/bin/nextflow
+          apptainer-version: 1.3.6
 
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: 25.10.2
+
       - name: Set up python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v6
         with:
           python-version: 3.11
           architecture: x64