chore: update github CI #271
Workflow file for this run
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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/**' | |
defaults: | |
run: | |
shell: bash -el {0} | |
jobs: | |
Dryrun_Tests: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
lfs: 'true' | |
- name: Setup conda | |
uses: ./.github/actions/conda-cache | |
with: | |
python-version: ${{ matrix.python-version }} | |
environment-file: environment.yml | |
- name: Test workflow (local FASTQs) | |
uses: snakemake/snakemake-github-action@cebcb23c87aa3a23efddff3f79b3a4bd143d4120 | |
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 | |
snakemake-version: 7.32.4 | |
Tests: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: | |
- "3.12" | |
needs: | |
- Dryrun_Tests | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
lfs: 'true' | |
- name: Setup conda | |
uses: ./.github/actions/conda-cache | |
with: | |
python-version: ${{ matrix.python-version }} | |
environment-file: environment.yml | |
- name: Test workflow (local FASTQs) | |
uses: snakemake/snakemake-github-action@cebcb23c87aa3a23efddff3f79b3a4bd143d4120 | |
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 | |
snakemake-version: 7.32.4 | |