feat: Add results for nf-core/sarek 3.4.3 (#47) #255
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: benchmark | |
| on: | |
| - push | |
| 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@v2 | |
| - name: Download reference genome | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: "--cores 1 --use-conda --conda-cleanup-pkgs cache resources/reference/genome.fasta" | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http | |
| - name: Download truthsets | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: "--use-conda --cores 1 --conda-cleanup-pkgs cache --until benchmark_get_truth" | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo 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@v1 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: "--cores 1 --touch resources/regions/*/test-regions.cov-*.bed" | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http | |
| - name: Run analysis | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: > | |
| --cores 2 --use-conda --conda-cleanup-pkgs cache | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http | |
| - name: Create report | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: "." | |
| snakefile: "workflow/Snakefile" | |
| args: "--report report.zip" | |
| stagein: | | |
| pip install snakemake-storage-plugin-zenodo snakemake-storage-plugin-http | |
| - name: Upload report as artifact | |
| uses: actions/upload-artifact@v3 | |
| 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 }} |