feat: bump to dna-seq-benchmark 1.14.1 #314
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| name: benchmark | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| workflow_dispatch: | |
| concurrency: | |
| # Cancel concurrent flows | |
| group: ci-${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| evaluate: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| actions: write | |
| env: | |
| FTP_PASSWORD: ${{ secrets.FTP_PASSWORD }} | |
| ZENODO_TOKEN: ${{ secrets.ZENODO_TOKEN }} | |
| BENCHMARK_GIAB_NA12878_AGILENT_TOKEN: ${{ secrets.BENCHMARK_GIAB_NA12878_AGILENT_TOKEN }} | |
| BO_AGILENT_TOKEN: ${{ secrets.BO_AGILENT_TOKEN }} | |
| CO_AGILENT_TOKEN: ${{ secrets.CO_AGILENT_TOKEN }} | |
| BO_CORE_UNIT_TOKEN: ${{ secrets.BO_CORE_UNIT_TOKEN }} | |
| BENCHMARK_GIAB_NA12878_TWIST_TOKEN: ${{ secrets.BENCHMARK_GIAB_NA12878_TWIST_TOKEN }} | |
| SNAKEMAKE_STORAGE_ZENODO_ACCESS_TOKEN: ${{ secrets.SNAKEMAKE_STORAGE_ZENODO_ACCESS_TOKEN }} | |
| steps: | |
| - uses: 8BitJonny/[email protected] | |
| id: pr | |
| with: | |
| sha: ${{ github.event.pull_request.head.sha }} | |
| filterOutClosed: true | |
| - run: | | |
| echo "is PR: ${{ steps.pr.outputs.pr_found }}" | |
| echo "current branch: ${{ github.ref }}" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/[email protected] | |
| with: | |
| # this might remove tools that are actually needed, | |
| # if set to "true" but frees about 6 GB | |
| tool-cache: false | |
| # all of these default to true, but feel free to set to | |
| # "false" if necessary for your workflow | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| swap-storage: true | |
| docker-images: false | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - name: Download reference genome | |
| uses: snakemake/snakemake-github-action@v2 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: "--cores 1 --sdm conda --conda-cleanup-pkgs cache resources/reference/genome.fasta" | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo | |
| pip install snakemake-storage-plugin-http | |
| - name: Download truthsets | |
| uses: snakemake/snakemake-github-action@v2 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: "--sdm conda --cores 1 --conda-cleanup-pkgs cache --until benchmark_get_truth" | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo | |
| pip install snakemake-storage-plugin-http | |
| # This step is necessary (after downloading the truthsets above) to ensure | |
| # that the files coming from the git repo are not triggering reruns | |
| # because their modification dates are too new or too old. | |
| # (as git does not preserve modification dates) | |
| - name: Fix modification dates | |
| uses: snakemake/snakemake-github-action@v2 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: "--cores 1 --sdm conda --touch resources/regions/*/test-regions.cov-*.bed" | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo | |
| pip install snakemake-storage-plugin-http | |
| - name: Run analysis | |
| uses: snakemake/snakemake-github-action@v2 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: > | |
| --cores 4 --sdm conda --conda-cleanup-pkgs cache --rerun-triggers mtime --all-temp | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo | |
| pip install snakemake-storage-plugin-http | |
| - name: Create report | |
| uses: snakemake/snakemake-github-action@v2 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: "--report report.zip" | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo | |
| pip install snakemake-storage-plugin-http | |
| - name: Upload report as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: report | |
| path: report.zip | |
| - name: Trigger homepage build | |
| if: ${{ (steps.pr.outputs.pr_found != 'true') && (github.ref == 'refs/heads/main') }} | |
| uses: benc-uk/workflow-dispatch@v1 | |
| with: | |
| workflow: deploy-page | |
| repo: ncbench/ncbench.github.io | |
| token: ${{ secrets.WORKFLOW_DISPATCH_TOKEN }} |