Upgrade to Snakemake version 9 #716
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| jobs: | |
| snakemake-graphs-format: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout ZARP repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge with ZARP environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: install/environment.dev.yml | |
| miniforge-version: latest | |
| conda-remove-defaults: true | |
| channel-priority: strict | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: zarp | |
| - name: Display Conda and environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Run test script for snakemake format | |
| run: bash tests/test_format/test_snakefmt.sh | |
| - name: Run test script for snakemake lint | |
| run: bash tests/test_format/test_snakemake_lint.sh | |
| - name: Run test script for snakemake rulegraph | |
| run: bash tests/test_create_rule_graph/test.sh | |
| - name: Run test script for snakemake DAG | |
| run: bash tests/test_create_dag_image/test.sh | |
| integration-apptainer: | |
| needs: | |
| - snakemake-graphs-format | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout ZARP repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge with ZARP environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: install/environment.dev.yml | |
| miniforge-version: latest | |
| conda-remove-defaults: true | |
| channel-priority: strict | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: zarp | |
| - name: Install Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.3.6 | |
| - name: Display Conda and environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Run test script | |
| run: bash tests/test_integration_workflow/test.local.sh | |
| - name: Run htsinfer test script | |
| run: bash tests/test_htsinfer_with_apptainer/test.local.sh | |
| - name: Run SRA downloads workflow | |
| run: bash tests/test_sra_download_with_apptainer/test.local.sh | |
| integration-apptainer-tempflag: | |
| needs: | |
| - snakemake-graphs-format | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout ZARP repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge with ZARP environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: install/environment.dev.yml | |
| miniforge-version: latest | |
| conda-remove-defaults: true | |
| channel-priority: strict | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: zarp | |
| - name: Display Conda and environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Install Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.3.6 | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Run test script | |
| run: bash tests/test_integration_workflow/test.temp.flag.sh | |
| integration-apptainer-MultipleLanes: | |
| needs: | |
| - snakemake-graphs-format | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout ZARP repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge with ZARP environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: install/environment.dev.yml | |
| miniforge-version: latest | |
| conda-remove-defaults: true | |
| channel-priority: strict | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: zarp | |
| - name: Display Conda and environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Install Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.3.6 | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Run test script | |
| run: bash tests/test_integration_workflow_multiple_lanes/test.local.sh | |
| integration-conda: | |
| needs: | |
| - snakemake-graphs-format | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout ZARP repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge with ZARP environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: install/environment.dev.yml | |
| miniforge-version: latest | |
| conda-remove-defaults: true | |
| channel-priority: strict | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: zarp | |
| - name: Display Conda and environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Run test script | |
| run: bash tests/test_integration_workflow_with_conda/test.local.sh | |
| - name: Run HTSinfer workflow test script | |
| run: bash tests/test_htsinfer_with_conda/test.local.sh | |
| - name: Run SRA downloads workflow test script | |
| run: bash tests/test_sra_download_with_conda/test.local.sh | |
| integration-docker: | |
| needs: | |
| - snakemake-graphs-format | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout ZARP repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge with ZARP environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: install/environment.dev.yml | |
| miniforge-version: latest | |
| conda-remove-defaults: true | |
| channel-priority: strict | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: zarp | |
| - name: Run test script | |
| run: bash tests/test_integration_workflow_with_docker/test.local.sh | |
| - name: Clean up | |
| run: rm -rf data% |