enhance operations #1220
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| name: NANOME pipelines for CI test | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| # Hardware requirment: https://lifebit.gitbook.io/cloudos/tutorials/adding-ci-testing-in-nextflow-pipelines | |
| on: [push, pull_request, release] | |
| jobs: | |
| docker: | |
| name: Docker | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| nxf_ver: ['20.07.1', ''] | |
| ci_test_name: ['test', 'test_human'] | |
| using_tools_option: [''] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install Nextflow ${{ matrix.nxf_ver }} | |
| run: | | |
| export NXF_VER=${{ matrix.nxf_ver }} | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Basic NANOME workflow test for ${{ matrix.ci_test_name }} | |
| run: | | |
| nextflow -v &&\ | |
| nextflow run ${GITHUB_WORKSPACE} \ | |
| -profile ${{ matrix.ci_test_name }},docker ${{ matrix.using_tools_option }} | |
| - name: File tree for ${{ matrix.ci_test_name }} | |
| run: | | |
| echo "Outputs tree view:" ; tree -a results; ls -lh -R results | |
| - name: Results for ${{ matrix.ci_test_name }} | |
| run: | | |
| echo "CpGs summary:" ; sudo find work -name '*.Report.run.log' -exec tail {} \; | |
| # remove singularity, since it is same with docker container | |
| # singularity: | |
| # name: Singularity | |
| # runs-on: ubuntu-latest | |
| # strategy: | |
| # fail-fast: false | |
| # matrix: | |
| # singularity_version: ['3.6.4'] | |
| # nxf_ver: [''] | |
| # ci_test_name: ['test', 'test_human'] | |
| # steps: | |
| # - uses: actions/checkout@v1 | |
| # - uses: eWaterCycle/setup-singularity@v6 | |
| # with: | |
| # singularity-version: ${{ matrix.singularity_version }} | |
| # - name: Install Nextflow ${{ matrix.nxf_ver }} | |
| # run: | | |
| # export NXF_VER=${{ matrix.nxf_ver }} | |
| # wget -qO- get.nextflow.io | bash | |
| # sudo mv nextflow /usr/local/bin/ | |
| # - name: Basic NANOME workflow tests by ${{ matrix.ci_test_name }} | |
| # run: | | |
| # nextflow -v &&\ | |
| # nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.ci_test_name }},singularity --runMethcall false | |
| # echo "Outputs tree view:" ; tree -a outputs; ls -lh -R outputs |