Build workflow (v2) website on public Alzheimer dataset (for protein groups) #192
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| name: Build workflow (v2) website on public Alzheimer dataset (for protein groups) | |
| on: | |
| pull_request: | |
| branches: [main, dev] | |
| release: | |
| types: [published] | |
| schedule: | |
| - cron: '0 4 * * 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@v4 | |
| - name: Set up Miniconda | |
| # ! change action https://github.com/mamba-org/setup-micromamba | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| use-mamba: true | |
| # channel-priority: true | |
| python-version: "3.10" | |
| environment-file: snakemake_env.yml | |
| activate-environment: snakemake | |
| auto-activate-base: true | |
| - name: Dry-run workflow | |
| run: | | |
| cd project | |
| snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/config.yaml -p -c1 --use-conda -n | |
| - name: Run demo workflow (integration test) | |
| continue-on-error: true | |
| run: | | |
| cd project | |
| snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/config.yaml -p -c4 -k --use-conda | |
| - name: Run demo workflow again (in case of installation issues) | |
| continue-on-error: true | |
| run: | | |
| cd project | |
| snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/config.yaml -p -c4 -k --use-conda | |
| - name: Run demo workflow again (in case of installation issues) with one thread | |
| run: | | |
| cd project | |
| snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/config.yaml -p -c1 -k --use-conda | |
| - name: Run differential analysis workflow | |
| run: | | |
| cd project | |
| snakemake -s workflow/Snakefile_ald_comparison.smk --configfile config/alzheimer_study/comparison.yaml -p -c4 --use-conda | |
| - name: clean-up environments and pkg cache | |
| run: | | |
| conda clean -a -y | |
| cd project | |
| rm -r .snakemake | |
| ls -la | |
| - name: Install website dependencies | |
| run: | | |
| pip install .[docs] | |
| - name: Build imputation comparison website | |
| run: | | |
| pimms-setup-imputation-comparison -f project/runs/alzheimer_study/ | |
| pimms-add-diff-comp -f project/runs/alzheimer_study/ -sf_cp project/runs/alzheimer_study/diff_analysis/AD | |
| cd project/runs/alzheimer_study/ | |
| sphinx-build -n --keep-going -b html ./ ./_build/ | |
| - name: Archive results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: alzheimer-study | |
| path: project/runs/alzheimer_study/ | |
| - name: Publish workflow as website | |
| uses: peaceiris/actions-gh-pages@v4 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: project/runs/alzheimer_study/_build/ |