add test nexus tree #71
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| name: Nextflow tests | |
| # This workflow runs the PhyloNext pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| release: | |
| types: [published] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run PhyloNext pipeline with test data | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'vmikk/PhyloNext') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Nextflow versions | |
| include: | |
| # Test pipeline minimum Nextflow version | |
| - NXF_VER: '23.10.0' | |
| NXF_EDGE: '' | |
| # # Test latest edge release of Nextflow | |
| # - NXF_VER: '' | |
| # NXF_EDGE: '1' | |
| env: | |
| NXF_ANSI_LOG: false | |
| # CAPSULE_LOG: none | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: main | |
| fetch-depth: 1 | |
| # pwd = /__w/PhyloNext/PhyloNext | |
| - 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 | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline usning built-in phylogenetic tree | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -work-dir $(pwd)/work1 | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/work/PhyloNext/PhyloNext/.nextflow.log | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: logs-builtin-tree | |
| path: | | |
| /home/runner/work/PhyloNext/PhyloNext/.nextflow.log | |
| /home/runner/work/PhyloNext/PhyloNext/work1/**/.command.log | |
| - name: Run pipeline and fetch phylogenetic tree from OToL | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_ott,docker --maxage 111 -work-dir $(pwd)/work2 -resume | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/work/PhyloNext/PhyloNext/.nextflow.log | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: logs-ott-tree | |
| path: | | |
| /home/runner/work/PhyloNext/PhyloNext/.nextflow.log | |
| /home/runner/work/PhyloNext/PhyloNext/work2/**/.command.log | |
| - name: Check file existence | |
| id: check_files | |
| uses: andstor/file-existence-action@v2 | |
| with: | |
| files: "./03.Plots/Biodiverse_results_merged.txt, ./03.Plots/Choropleth.html, ./03.Plots/Diversity_estimates.gpkg" | |
| - name: File exists | |
| if: steps.check_files.outputs.files_exists == 'true' | |
| run: | | |
| echo "Looks good, all expected output files are in place!" | |
| exit 0 | |
| - name: File is missing | |
| if: steps.check_files.outputs.files_exists == 'false' | |
| run: | | |
| echo "ERROR! Some files are missing!" | |
| exit 1 |