diff --git a/.github/workflows/test_pipelines.yml b/.github/workflows/test_pipelines.yml index 2ec48234..765d2332 100755 --- a/.github/workflows/test_pipelines.yml +++ b/.github/workflows/test_pipelines.yml @@ -24,6 +24,7 @@ jobs: key: ${{ runner.os }}-env-${{ hashFiles('**/testing.yml') }} restore-keys: | ${{ runner.os }}-env- + - name: Setup conda uses: conda-incubator/setup-miniconda@v3 with: @@ -36,6 +37,7 @@ jobs: shell: pwsh run: | pip install . + - name: Cache singularity if: matrix.test == 'pipeline' id: cache-singularity @@ -45,6 +47,7 @@ jobs: key: ${{ runner.os }}-singularity-${{ hashFiles('tmp/*') }} restore-keys: | ${{ runner.os }}-singularity- + - uses: eWaterCycle/setup-apptainer@v2 if: matrix.test == 'pipeline' with: @@ -56,6 +59,7 @@ jobs: run: | apptainer remote add --no-login SylabsCloud cloud.sylabs.io apptainer remote use SylabsCloud + - name: Pull singularity images if: matrix.test == 'pipeline' && steps.cache-singularity.outputs.cache-hit != 'true' shell: bash @@ -69,6 +73,7 @@ jobs: elif [[ "${{ matrix.assay }}" == "rna-rx" ]]; then apptainer pull --force library://asmith151/seqnado/seqnado_report:latest fi + - name: Test ${{ matrix.test }} ${{ matrix.assay }} shell: pwsh env: