refactor: access sample data by position (#113) #44
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: tests | |
| on: | |
| pull_request: | |
| branches: | |
| - dev | |
| push: | |
| branches: | |
| - '*' | |
| jobs: | |
| static-code-analysis: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| activate-environment: mirflowz | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: Update mirflowz env with dev packages | |
| run: mamba env update -n mirflowz -f environment.dev.yml | |
| - name: display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: flake8 | |
| working-directory: ./scripts | |
| run: flake8 ./*.py --exclude oligomapOutputToSam_nhfiltered.py | |
| - name: mypy | |
| working-directory: ./scripts | |
| run: mypy ./*.py | |
| - name: pylint | |
| working-directory: ./scripts | |
| run: pylint --rcfile=../pylint.cfg ./*.py | |
| - name: Check workflow descriptor files for lints | |
| working-directory: ./test | |
| run: | | |
| snakemake --snakefile="../workflow/Snakefile" --configfile="config.yaml" --lint | |
| snakemake --snakefile="../workflow/rules/common.smk" --configfile="config.yaml" --lint | |
| snakemake --snakefile="../workflow/rules/prepare.smk" --configfile="config.yaml" --lint | |
| snakemake --snakefile="../workflow/rules/map.smk" --configfile="config.yaml" --lint | |
| snakemake --snakefile="../workflow/rules/quantify.smk" --configfile="config.yaml" --lint | |
| snakemake-test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v4 | |
| - name: setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| activate-environment: mirflowz | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: update mirflowz env with root packages | |
| run: mamba env update -n mirflowz -f environment.root.yml | |
| - name: display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run test for rule graph | |
| run: bash test/test_rule_graph.sh | |
| - name: run local test with Singularity | |
| run: bash test/test_workflow_local_with_singularity.sh | |
| - name: run local test with Conda | |
| run: bash test/test_workflow_local_with_conda.sh | |
| unit-testing: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v4 | |
| - name: setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| activate-environment: mirflowz | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: update mirflowz env with dev packages | |
| run: mamba env update -n mirflowz -f environment.dev.yml | |
| - name: display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run unit tests | |
| working-directory: ./scripts/tests | |
| run: pytest --cov=scripts --cov-branch --cov-report=term-missing |