Create reusable workflow

.github/workflows/run-pipeline.yml

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+name: Run pipeline
+
+
+on:
+  workflow_call:
+    inputs:
+      environment_file:
+        required: true
+        type: str
+      pipeline_cmd:
+        required: true
+        type: str
+      name:
+        required: true
+        type: str
+
+jobs:
+  Run-Pipeline:
+      runs-on: ubuntu-latest
+      steps:
+        - name: Check out repository code
+          uses: actions/checkout@v4
+        - uses: mamba-org/[email protected]
+          with:
+            environment-name: pipeline-env
+            environment-file: ${{inputs.environment_file}}
+            cache-environment: true
+            cache-downloads: true
+        - name: ${{inputs.name}}
+          run: ${{inputs.pipeline_cmd}}
+          shell: micromamba-shell {0}

.github/workflows/smoke-tests.yml

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+name: DeepRVAT Pipeline tests
+run-name: DeepRVAT Pipeline tests 🧬🧪💻🧑‍🔬
+on: [ push ]
+
+jobs:
+  Smoke-RunTraining:
+    uses: /.github/workflow/run-pipeline.yml
+    with:
+      environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
+      name: Smoke-RunTraining
+      pipeline_cmd: |
+            python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \
+            --snakefile ${{ github.workspace }}/pipelines/run_training.snakefile --show-failed-logs
+
+
+#  Pipeline-Tests-RunTraining:
+#    runs-on: ubuntu-latest
+#    needs: Smoke-RunTraining
+#    steps:
+#      - name: Check out repository code
+#        uses: actions/checkout@v4
+#      - uses: mamba-org/[email protected]
+#        with:
+#          environment-name: deeprvat-gh-action
+#          environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
+#          cache-environment: true
+#          cache-downloads: true
+#      - name: Install DeepRVAT
+#        run: pip install -e ${{ github.workspace }}
+#        shell: micromamba-shell {0}
+#      # There are no GPUs on the gh worker, so we disable it in the config
+#      - name: Update config to use no gpus
+#        run: "sed -i 's/gpus: 1/gpus: 0/' ${{ github.workspace }}/example/config.yaml"
+#        shell: bash -el {0}
+#      - name: Run run_training pipeline
+#        run: |
+#          python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
+#          --snakefile ${{ github.workspace }}/pipelines/run_training.snakefile --show-failed-logs -F
+#        shell: micromamba-shell {0}
+