foodme2 announcement #254
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: [ master ] | |
| workflow_dispatch: | |
| jobs: | |
| Testing_ASV: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Test workflow | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: '.tests' | |
| snakefile: 'workflow/Snakefile' | |
| args: "-j 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/config/config.yaml" | |
| stagein: | | |
| conda config --set channel_priority strict | |
| - name: Archive logs on fail | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: foodme-fail-asv | |
| path: .tests/logs/ | |
| if-no-files-found: error | |
| retention-days: 3 | |
| Testing_OTU: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Test workflow | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: '.tests' | |
| snakefile: 'workflow/Snakefile' | |
| args: "-j 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/config/config_otu.yaml" | |
| stagein: | | |
| conda config --set channel_priority strict | |
| - name: Archive logs on fail | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: foodme-fail-otu | |
| path: .tests/logs/ | |
| if-no-files-found: error | |
| retention-days: 3 | |
| Testing_benchmark: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Test benchmark | |
| uses: snakemake/snakemake-github-action@v1.23.0 | |
| with: | |
| directory: '.tests' | |
| snakefile: 'workflow/benchmark' | |
| args: "-j 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/config/config.yaml" | |
| stagein: | | |
| conda config --set channel_priority strict | |
| - name: Archive logs on fail | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: foodme-fail-benchmark | |
| path: .tests/logs/ | |
| if-no-files-found: error | |
| retention-days: 3 | |
| Testing_paramspace: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Test workflow | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: '.tests' | |
| snakefile: 'workflow/paramspace' | |
| args: "-j 1 --use-conda --conda-cleanup-pkgs cache --conda-prefix envs --show-failed-logs --configfile .tests/config/config_paramspace.yaml" | |
| stagein: | | |
| conda config --set channel_priority strict | |
| - name: Archive logs on fail | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: foodme-fail-pspace | |
| path: .tests/logs/ | |
| if-no-files-found: error | |
| retention-days: 3 |