Disable linter for templates #160
Workflow file for this run
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: Snakedeploy | |
| on: | |
| push: | |
| pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} | |
| jobs: | |
| snakedeploy_tests: | |
| env: | |
| THREADS: 5 | |
| strategy: | |
| max-parallel: 5 | |
| fail-fast: false | |
| matrix: | |
| virus: ["hiv", "sars-cov-2"] | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout test data | |
| uses: actions/checkout@v3 | |
| with: | |
| sparse-checkout: | | |
| tests | |
| resources/*/gffs | |
| sparse-checkout-cone-mode: false | |
| lfs: false | |
| # NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS | |
| - name: Install conda environment dependencies | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-version: latest | |
| miniforge-variant: Mambaforge | |
| python-version: "3.11" # temporary fix for snakemake issue #2480 | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: snakemake | |
| auto-update-conda: true | |
| environment-file: tests/conda_snakedeploy_env.yaml | |
| - name: Snakedeploy | |
| # snakedeploy will issue error message if workflow/ or config/ exist, i.e. if tests/ was not sparsely checked out | |
| run: | | |
| snakedeploy deploy-workflow "$(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 | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test_output | |
| path: | | |
| ./* | |
| !./.git | |
| !./.snakemake/conda/*/ | |
| if-no-files-found: ignore |