Test pipeline on GHA #26
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| name: Test snakemake 🐍 pipeline | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| test-pipeline: | |
| runs-on: ubuntu-latest | |
| services: | |
| mysql: | |
| image: mysql:8.0 | |
| env: | |
| MYSQL_ROOT_PASSWORD: root | |
| ports: | |
| - "8888:3306" | |
| options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3 | |
| steps: | |
| - name: Setup pipeline 🚰 | |
| uses: actions/checkout@v4 | |
| - name: Setup slurm 🐌 | |
| uses: koesterlab/setup-slurm-action@v1 | |
| - name: Cache conda 🏦 | |
| id: cache-conda | |
| uses: actions/cache@v4 | |
| env: | |
| # Increase this value to reset cache if environment.yml has not changed | |
| CACHE_NUMBER_CONDA: 1 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ runner.os }}-conda-${{ env.CACHE_NUMBER_CONDA }}-${{hashFiles('environment.yml') }} | |
| - if: ${{ steps.cache-conda.outputs.cache-hit != 'true' }} | |
| name: Setup conda 🐍 | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: aatrnaseqpipe | |
| environment-file: environment.yml | |
| # https://github.com/conda-incubator/setup-miniconda/issues/267 | |
| # XXX don't use this: use-only-tar-bz2: true | |
| - if: ${{ steps.cache-conda.outputs.cache-hit == 'true' }} | |
| name: Activate conda 🐍 | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: aatrnaseqpipe | |
| - run: conda info | |
| - run: conda list | |
| - run: conda config --show | |
| - name: Cache test data 🏦 | |
| id: cache-test | |
| uses: actions/cache@v4 | |
| env: | |
| # Increase this value to reset cache if environment.yml has not changed | |
| CACHE_NUMBER_TEST_DATA: 0 | |
| with: | |
| path: ./.test | |
| key: | |
| # hash based on the FASTA reference | |
| ${{ runner.os }}-test-data-${{ env.CACHE_NUMBER_TEST_DATA }}-${{hashFiles('./.test/sacCer3-mature-tRNAs-dual-adapt-v2.fa')}} | |
| - if: ${{ steps.cache-test.outputs.cache-hit != 'true' }} | |
| name: Download test data ⬇️ | |
| working-directory: ./.test | |
| run: | | |
| echo ">> working directory: $(pwd)" | |
| bash download_test_data.sh | |
| echo ">> directory contents:" | |
| ls -l | |
| - if: false | |
| name: Dry-run snakemake | |
| run: | | |
| conda init | |
| conda activate aatrnaseqpipe | |
| snakemake -n \ | |
| --configfile=config/config-test.yaml \ | |
| --profile-cluster/slurm |