Run quick tests of pipeline #8
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| name: Run quick tests of pipeline | |
| on: | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| jobs: | |
| run-tests: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: rocker/r-ver:4.1.0 | |
| options: --privileged | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Setup Singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| - name: Download Singularity container | |
| run: | | |
| singularity pull library://opain/genopred/genopred_pipeline:latest | |
| - name: Set environment variables | |
| run: | | |
| echo "SIF_FILE=$GITHUB_WORKSPACE/genopred_pipeline_latest.sif" >> $GITHUB_ENV | |
| echo "BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV | |
| - name: Install R dependencies | |
| run: | | |
| Rscript -e 'install.packages("testthat", repos="https://cran.rstudio.com/")' | |
| Rscript -e 'install.packages("data.table", repos="https://cran.rstudio.com/")' | |
| - name: Run tests | |
| run: | | |
| mkdir -p test_results | |
| Rscript -e "testthat::test_dir('pipeline/tests/testthat')" | |
| env: | |
| SIF_FILE: ${{ env.SIF_FILE }} | |
| BRANCH_NAME: ${{ env.BRANCH_NAME }} | |
| - name: Setup tmate session | |
| if: ${{ failure() }} | |
| uses: mxschmitt/action-tmate@v3 | |
| timeout-minutes: 60 |