Merge pull request #37 from hydra-genetics/Smeds-patch-1

feat: update to snakemake 8

.github/workflows/compatibility.yaml

@@ -20,10 +20,10 @@ jobs:
         id: branch-name
         uses: tj-actions/[email protected]
       - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt

.github/workflows/lint.yaml

@@ -17,10 +17,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Add conda to system path
         run: |
           echo $CONDA/bin >> $GITHUB_PATH

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

@@ -17,10 +17,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.8
+      - name: Set up Python 3.11
         uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Add conda to system path
         run: |
           echo $CONDA/bin >> $GITHUB_PATH

requirements.txt

@@ -1,8 +1,6 @@
 drmaa==0.7.9
-hydra-genetics==0.15.0
+hydra-genetics==1.14.0
 jinja2==3.0.1
 pandas>=1.3.1
-pulp<2.8.0
 singularity==3.0.0
-snakemake>=7.13.0,<8
-tabulate<0.9.0
+snakemake>=8,<9