Snakedeploy Tests #2
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/main' }} | |
| jobs: | |
| runtime_tests: | |
| env: | |
| THREADS: 5 | |
| strategy: | |
| max-parallel: 5 | |
| fail-fast: false | |
| matrix: | |
| # python-version: [ "3.11"] | |
| 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 | |
| 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: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: snakemake | |
| auto-update-conda: true | |
| environment-file: tests/conda_snakedeploy_env.yaml | |
| - name: Snakedeploy | |
| # snakedeploy will issue error message if workflow/ or config/ exist, i.e. if tests/ was not sparsely checked out | |
| run: | | |
| snakedeploy deploy-workflow "$(git remote get-url origin)" . --branch "$(git rev-parse HEAD)" | |
| - name: Configure | |
| run: | | |
| virus="${{ matrix.virus }}" | |
| threads="${THREADS}" | |
| trim_primers="false" | |
| # samples data | |
| data_root="tests/data/${virus}" | |
| mkdir -p samples | |
| mv -v "${data_root}"/*/ samples/ | |
| if [ -e "${data_root}/samples.tsv" ]; then | |
| mv -v "${data_root}/samples.tsv" samples/ | |
| # automatically turn trimming on if 4-columns format in TSV | |
| # shellcheck disable=SC2162 | |
| while read s b l p o; do | |
| # no proto? | |
| if [[ -z "${p}" ]]; then | |
| continue | |
| fi | |
| # proto => trim! | |
| trim_primers="true" | |
| echo "with trimming" | |
| break | |
| : "${s} ${b} ${l} ${o}" are unused | |
| done < "samples/samples.tsv" | |
| fi | |
| # configuration file | |
| cat > config/config.yaml <<CONFIG | |
| general: | |
| virus_base_config: "${virus}" | |
| output: | |
| snv: true | |
| local: true | |
| global: false | |
| visualization: true | |
| diversity: true | |
| QA: true | |
| upload: true | |
| trim_primers: ${trim_primers} | |
| upload: | |
| orig_cram: true | |
| snv: | |
| threads: ${threads} | |
| CONFIG | |
| # does this test data provides extra configuration options | |
| if [ -e "${data_root}/config-extra.yaml" ]; then | |
| echo "with extra config:" | |
| cat "${data_root}/config-extra.yaml" | |
| echo | |
| # recursively merge using go-yq | |
| yq eval-all --inplace '. as $item ireduce ({}; . * $item )' config/config.yaml "${data_root}/config-extra.yaml" | |
| fi | |
| - name: Run test | |
| run: | |
| PYTHONUNBUFFERED=1 snakemake \ | |
| --use-conda \ | |
| --cores ${THREADS} \ | |
| --dry-run | |
| echo | |
| cat config/samples.tsv | |
| echo | |
| PYTHONUNBUFFERED=1 snakemake \ | |
| --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 |