Move gpu conf fix

.github/workflows/run-pipeline.yml

@@ -15,6 +15,11 @@ on:
       name:
         required: true
         type: string
+      no_gpu:
+        required: false
+        type: boolean
+        default: false
+
 jobs:
   Run-Pipeline:
       runs-on: ubuntu-latest
@@ -34,6 +39,11 @@ jobs:
           if: inputs.prerun_cmd
           run: ${{inputs.prerun_cmd}}
           shell: bash -el {0}
+        - name: Set to 0 Gpu in conf
+          if: inputs.no_gpu
+          # There are no GPUs on the gh worker, so we can disable it in the config
+          run: "sed -i 's/gpus: 1/gpus: 0/' ./example/config.yaml"
+          shell: bash -el {0}
         - name: ${{inputs.name}}
           run: ${{inputs.pipeline_cmd}}
           shell: micromamba-shell {0}

.github/workflows/smoke-tests.yml

@@ -18,8 +18,7 @@ jobs:
     with:
       environment_file: ./deeprvat_env_no_gpu.yml
       name: Run run_training pipeline
-     # There are no GPUs on the gh worker, so we disable it in the config
-      prerun_cmd: "sed -i 's/gpus: 1/gpus: 0/' ./example/config.yaml"
+      no_gpu: true
       pipeline_cmd: |
           python -m snakemake -j 2 --directory ./example \
           --snakefile ./pipelines/run_training.snakefile --show-failed-logs -F