Ensure that environment is activated correctly in startup script #67
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| name: BactSeq CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| env: | |
| NXF_ANSI_LOG: false | |
| CAPSULE_LOG: none | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'adamd3/BactSeq') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Nextflow versions | |
| include: | |
| # Test pipeline minimum Nextflow version | |
| - NXF_VER: "21.10.3" | |
| NXF_EDGE: "" | |
| # Test latest edge release of Nextflow | |
| - NXF_VER: "" | |
| NXF_EDGE: "1" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| # Uncomment only if the edge release is more recent than the latest stable release | |
| # See https://github.com/nextflow-io/nextflow/issues/2467 | |
| # NXF_EDGE: ${{ matrix.NXF_EDGE }} | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| chmod +x nextflow | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and publish to docker | |
| run: | | |
| docker build --platform linux/amd64 -t adamd3/bactseq:latest . | |
| docker push adamd3/bactseq:latest | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | |