Merge pull request #34 from hydra-genetics/action_v3

test: update depricated github action to v3

.github/workflows/integration.yaml

@@ -16,33 +16,20 @@ jobs:
     name: integration small data set singularity
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: 3.8
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-            miniforge-variant: Mambaforge
-            miniforge-version: latest
-            activate-environment: my-env
-            use-mamba: true
-      - name: Set strict channel
-        run: |
-          conda config --set channel_priority strict
-      - name: Add conda to system path
+      - name: Install apptainer/singularity
         run: |
-          echo $CONDA/bin >> $GITHUB_PATH
+          sudo add-apt-repository -y ppa:apptainer/ppa && sudo apt install -y software-properties-common && sudo apt install -y apptainer-suid
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt
       - name: Install requirements.test.txt
         run: |
           pip install -r requirements.test.txt
-      - name: Install singularity
-        run: |
-          mamba install -c conda-forge -c bioconda singularity=3.8.6
       - name: Integration test - small dataset
         working-directory: .tests/integration
         run: |

.github/workflows/lint.yaml

@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Linting
         uses: snakemake/[email protected]
         with:

.github/workflows/snakefmt.yaml

@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Lint Code Base

.github/workflows/snakemake-dry-run.yaml

@@ -18,16 +18,13 @@ on:
 jobs:
   snakemake-dry-run:
     name: Run snakemake dry run
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: 3.8
-      - name: Add conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH
       - name: Install dependencies
         run: |
           conda install -c conda-forge mamba
@@ -40,5 +37,4 @@ jobs:
       - name: snakemake dry run
         working-directory: .tests/integration
         run: |
-          mamba install -c conda-forge -c bioconda snakemake singularity
           snakemake -n -s ../../workflow/Snakefile --configfile config.yaml