build: upgrade tool versions #453
Workflow file for this run
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: 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@v3 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| 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@v3 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| 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 | |
| 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@v3 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| 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@v3 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| 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@v3 | |
| - name: Setup miniconda & zarp env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| 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 | |