refactor!: use pydantic models for validation #91
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: | |
| # always run tests when pushing to main | |
| push: | |
| branches: [ main ] | |
| # only run tests on pull requests which actually modify files that affect the tests | |
| pull_request: | |
| branches_ignore: [] | |
| # for now, the tests defined in this file are only run when any of the following paths are modified: | |
| paths: | |
| # workflow definitions | |
| - '.tests/**' | |
| # github workflow configurations | |
| - '.github/**' | |
| # 'base' files of snappy-pipeline | |
| - 'snappy_pipeline/*' | |
| - 'snappy_pipeline/workflows/abstract/**' | |
| # steps used in the test workflows | |
| - 'snappy_pipeline/workflows/ngs_mapping/**' | |
| - 'snappy_pipeline/workflows/somatic_variant_calling/**' | |
| - 'snappy_pipeline/workflows/somatic_variant_annotation/**' | |
| - 'snappy_pipeline/workflows/somatic_variant_filtration/**' | |
| # 'base' files of snappy_wrappers | |
| - 'snappy_wrappers/*' | |
| # wrappers used in the test workflows | |
| - 'snappy_wrappers/wrappers/alfred/**' | |
| - 'snappy_wrappers/wrappers/bcftools/**' | |
| - 'snappy_wrappers/wrappers/bwa/**' | |
| - 'snappy_wrappers/wrappers/link_in_bam/**' | |
| - 'snappy_wrappers/wrappers/mutect/**' | |
| - 'snappy_wrappers/wrappers/mutect_par/**' | |
| - 'snappy_wrappers/wrappers/mutect2/**' | |
| - 'snappy_wrappers/wrappers/mutect2_par/**' | |
| - 'snappy_wrappers/wrappers/ngs_chew/**' | |
| - 'snappy_wrappers/wrappers/somatic_variant_filtration/**' | |
| - 'snappy_wrappers/wrappers/vep/**' | |
| jobs: | |
| Dryrun_Tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Test workflow (local FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .tests/test-workflow | |
| snakefile: .tests/test-workflow/workflow/Snakefile | |
| args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| Tests: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Dryrun_Tests | |
| steps: | |
| - name: update apt | |
| run: sudo apt-get update | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Test workflow (local FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .tests/test-workflow | |
| snakefile: .tests/test-workflow/workflow/Snakefile | |
| args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache" | |
| show-disk-usage-on-error: true | |