fix missing column in output. NA column has to be made even if no bmk #214
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| 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 | |