fix(sra): improve layout extraction from NCBI db #516
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| jobs: | |
| snakemake-graphs-format: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout zarp repository | |
| uses: actions/checkout@v4 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.10" | |
| mamba-version: "*" | |
| channels: conda-forge | |
| channel-priority: true | |
| auto-update-conda: false | |
| activate-environment: zarp | |
| environment-file: install/environment.yml | |
| auto-activate-base: false | |
| - name: Update zarp env with root. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml | |
| - name: Update zarp env with dev. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml | |
| - name: Display all miniconda & env 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-singularity: | |
| needs: | |
| - snakemake-graphs-format | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout zarp repository | |
| uses: actions/checkout@v4 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.10" | |
| mamba-version: "*" | |
| channels: conda-forge | |
| channel-priority: true | |
| auto-update-conda: false | |
| activate-environment: zarp | |
| environment-file: install/environment.yml | |
| auto-activate-base: false | |
| - name: Update zarp env with root. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml | |
| - name: Update zarp env with dev. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml | |
| - name: Display all miniconda & env 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_workflow/test.local.sh | |
| - name: Run SRA downloads workflow | |
| run: bash tests/test_sra_download_with_singularity/test.local.sh | |
| integration-singularity-tempflag: | |
| needs: | |
| - snakemake-graphs-format | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout zarp repository | |
| uses: actions/checkout@v4 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.10" | |
| mamba-version: "*" | |
| channels: conda-forge | |
| channel-priority: true | |
| auto-update-conda: false | |
| activate-environment: zarp | |
| environment-file: install/environment.yml | |
| auto-activate-base: false | |
| - name: Update zarp env with root. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml | |
| - name: Update zarp env with dev. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml | |
| - 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-singularity-MultipleLanes: | |
| needs: | |
| - snakemake-graphs-format | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout zarp repository | |
| uses: actions/checkout@v4 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.10" | |
| mamba-version: "*" | |
| channels: conda-forge | |
| channel-priority: true | |
| auto-update-conda: false | |
| activate-environment: zarp | |
| environment-file: install/environment.yml | |
| auto-activate-base: false | |
| - name: Update zarp env with root. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml | |
| - name: Update zarp env with dev. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml | |
| - 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-20.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout zarp repository | |
| uses: actions/checkout@v4 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.10" | |
| mamba-version: "*" | |
| channels: conda-forge | |
| channel-priority: true | |
| auto-update-conda: false | |
| activate-environment: zarp | |
| environment-file: install/environment.yml | |
| auto-activate-base: false | |
| - name: Update zarp env with dev. packages | |
| run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml | |
| - name: Display all miniconda & env info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: Run test script | |
| run: bash tests/test_integration_workflow_with_conda/test.local.sh | |
| - name: Run SRA downloads workflow | |
| run: bash tests/test_sra_download_with_conda/test.local.sh | |