SLURM migration of Zooma mappings #204
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| name: Test experiment_metadata tasks | |
| on: [pull_request] | |
| jobs: | |
| setup: | |
| name: ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Add workspace to path | |
| run: | | |
| echo "${GITHUB_WORKSPACE}" >> $GITHUB_PATH | |
| - name: Cache conda | |
| uses: actions/cache@v2 | |
| env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| CACHE_NUMBER: 1 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{hashFiles('test-environment.yml') }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: test | |
| environment-file: test-environment.yml | |
| mamba-version: "*" | |
| python-version: 3.6 | |
| channels: ebi-gene-expression-group,conda-forge,bioconda,defaults | |
| allow-softlinks: true | |
| channel-priority: flexible | |
| show-channel-urls: true | |
| use-only-tar-bz2: true | |
| - name: Run tests | |
| run: | | |
| atlas-experiment-metadata-test.bats | |
| #- name: Linting | |
| # uses: snakemake/snakemake-github-action@v1 | |
| # with: | |
| # directory: 'test_data' | |
| # snakefile: 'zooma-mappings-wf/Snakefile' | |
| # args: '--lint --config mode="atlas" working_dir=../test_data debugging=true zooma_logs=../test_data zooma_exclusions=../test_data/zooma_exclusions.yml load_zooma_jobs=30 prot_magetabfiles=/magetab_path/ temp_dir=../test_data zoomaMetadataUrl=zoomaMetadataUrl notifEmail=false retryWithoutZooma=no experiment_metadata_dir=experiment_metadata_dir atlas_prod_co=atlas_prod_co lsf_config=lsf_config previousRunDate=previous_run dest=dest keep_backup_sdrf=false' | |