[hack] temporary workaround against default #186
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| name: Snakedeploy | |
| on: | |
| push: | |
| pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} | |
| jobs: | |
| snakedeploy_tests: | |
| env: | |
| THREADS: 5 | |
| strategy: | |
| max-parallel: 5 | |
| fail-fast: false | |
| matrix: | |
| virus: ["hiv", "sars-cov-2"] | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout test data | |
| uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: | | |
| tests | |
| resources/*/gffs | |
| sparse-checkout-cone-mode: false | |
| lfs: false | |
| # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS | |
| - name: Install conda environment dependencies | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| miniforge-variant: Miniforge3 | |
| python-version: "3.11" # temporary fix for snakemake issue #2480 | |
| mamba-version: "*" | |
| use-mamba: true | |
| no-implicit-channels: true | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: snakemake | |
| auto-update-conda: true | |
| environment-file: tests/conda_snakedeploy_env.yaml | |
| - name: Snakedeploy | |
| # snakedeploy will issue error message if workflow/ or config/ exist, i.e. if tests/ was not sparsely checked out | |
| run: | | |
| snakedeploy deploy-workflow "$(git remote get-url origin)" . --branch "$(git rev-parse HEAD)" | |
| - name: Configure | |
| run: | | |
| tests/configure_for_virus.sh "${{ matrix.virus }}" | |
| # HACK: currently remote URL aren't supported as directories | |
| cp -vrf "resources/${{ matrix.virus }}/gffs" ./ | |
| - name: Run test | |
| run: | | |
| PYTHONUNBUFFERED=1 snakemake \ | |
| --config "input={gff_directory: 'gffs'}" \ | |
| --use-conda \ | |
| --cores "${THREADS}" \ | |
| --dry-run | |
| echo | |
| cat config/samples.tsv | |
| echo | |
| PYTHONUNBUFFERED=1 snakemake \ | |
| --config "input={gff_directory: 'gffs'}" \ | |
| --use-conda \ | |
| --cores "${THREADS}" \ | |
| -p \ | |
| --keep-going | |
| - name: Archive test results | |
| if: ${{ success() }} || ${{ failure() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test_output_${{ matrix.virus }} | |
| path: | | |
| ./* | |
| !./.git | |
| !./.snakemake/conda/*/ | |
| include-hidden-files: true | |
| if-no-files-found: ignore |