fix syntax typo #204
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test_rain: | |
| # Avoid running twice: skip push events if there's an open PR for this branch | |
| if: github.event_name != 'push' || github.event.pull_request == null | |
| runs-on: ubuntu-24.04 | |
| services: | |
| docker: | |
| image: docker:dind | |
| options: --privileged --shm-size=2g | |
| volumes: | |
| - /var/run/docker.sock:/var/run/docker.sock:ro | |
| steps: | |
| - name: Get the code | |
| uses: actions/checkout@v4 | |
| # Install/cache OpenJDK | |
| - name: Cache OpenJDK | |
| id: cache-openjdk | |
| uses: actions/cache@v4 | |
| with: | |
| path: /usr/lib/jvm/java-11-openjdk-amd64 | |
| key: ${{ runner.os }}-openjdk-11 | |
| restore-keys: | | |
| ${{ runner.os }}-openjdk-11 | |
| - name: Install OpenJDK | |
| if: steps.cache-openjdk.outputs.cache-hit != 'true' | |
| run: sudo apt-get update && sudo apt-get install -y openjdk-11-jdk | |
| # Install/cache Nextflow | |
| - name: Cache Nextflow | |
| id: cache-nextflow | |
| uses: actions/cache@v4 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }}-nextflow-24.10.6 | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow-24.10.6 | |
| - name: Install Nextflow | |
| if: steps.cache-nextflow.outputs.cache-hit != 'true' | |
| run: export NXF_VER=24.10.6 && curl -s https://get.nextflow.io | bash && sudo mv nextflow /usr/local/bin && sudo chmod +x /usr/local/bin/nextflow | |
| # Cache Docker images | |
| - name: Cache Docker images | |
| id: cache-dockerfiles | |
| uses: actions/cache@v4 | |
| with: | |
| path: docker-images.tar | |
| key: ${{ runner.os }}-dockerfiles-${{ hashFiles('docker/**/*') }} | |
| restore-keys: | | |
| ${{ runner.os }}-dockerfiles- | |
| - name: Load cached Docker images | |
| if: steps.cache-dockerfiles.outputs.cache-hit == 'true' | |
| run: | | |
| echo "Loading cached Docker images..." | |
| docker load -i docker-images.tar | |
| - name: Build Docker images | |
| if: steps.cache-dockerfiles.outputs.cache-hit != 'true' | |
| run: bash build_containers.sh --docker --github_action | |
| # Run test(s) | |
| - name: test short single list | |
| run: nextflow run rain.nf -profile docker,test_short_single_list | |
| - name: test short paired folder | |
| run: nextflow run rain.nf -profile docker,test_short_paired_folder | |
| - name: test csv mix | |
| run: nextflow run rain.nf -profile docker,test_mix_csv | |