Build workflow (v2) website on public Alzheimer dataset (for protein groups) #61
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| name: Build workflow website on smaller development dataset (for protein groups) | |
| on: | |
| pull_request: | |
| branches: [main, dev] | |
| release: | |
| schedule: | |
| - cron: '0 2 * * 3,6' | |
| jobs: | |
| run-workflow-and-build-website: | |
| runs-on: "ubuntu-latest" | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Set up Miniconda | |
| # ! change action https://github.com/mamba-org/setup-micromamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| # miniforge-version: latest | |
| use-mamba: true | |
| channel-priority: disabled | |
| python-version: "3.8" | |
| environment-file: environment.yml | |
| activate-environment: vaep | |
| auto-activate-base: true | |
| # auto-update-conda: true | |
| - name: Run demo workflow (integration test) | |
| continue-on-error: true | |
| run: | | |
| cd project | |
| snakemake -p -c1 -n | |
| snakemake -p -c4 -k | |
| - name: Run demo workflow again (in case of installation issues) | |
| run: | | |
| cd project | |
| snakemake -p -c1 -n | |
| snakemake -p -c4 -k | |
| - name: Install website dependencies | |
| run: | | |
| pip install .[docs] | |
| - name: Build imputation comparison website | |
| run: | | |
| pimms-setup-imputation-comparison -f project/runs/dev_dataset_small/proteinGroups_N50/ | |
| cd project/runs/dev_dataset_small/proteinGroups_N50/ | |
| sphinx-build -n --keep-going -b html ./ ./_build/ | |
| - name: Archive results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: example-workflow-results-${{ matrix.os }} | |
| path: project/runs/dev_dataset_small/proteinGroups_N50/_build/ | |
| - name: Publish workflow as website | |
| uses: peaceiris/actions-gh-pages@v4 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: project/runs/dev_dataset_small/proteinGroups_N50/_build/ |