Fix packaging issue #73
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: | |
| push: | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Linting-and-testing: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: cache-conda | |
| uses: actions/cache@v2 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: .snakemake/conda | |
| key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.environments.yaml.txt') }} | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v1.23.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint" | |
| - name: Checkout submodules | |
| uses: textbook/git-checkout-submodule-action@2.0.0 | |
| - name: Remove failing qualimap from tests | |
| run: "sed -i -e \"s/, 'qualimap'//g\" .test/config/config.yaml" | |
| - name: Install workflow environments | |
| uses: snakemake/snakemake-github-action@v1.23.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache --wrapper-prefix file:///github/workspace/workflow/wrappers --conda-create-envs-only" | |
| - name: Test workflow (local test data) | |
| uses: snakemake/snakemake-github-action@v1.23.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache --wrapper-prefix file:///github/workspace/workflow/wrappers" | |
| stagein: 'mamba install -y -c conda-forge -c bioconda -c defaults subversion svn snakemake-wrapper-utils; | |
| ./workflow/scripts/manticore_install_popoolation.py --snakefile workflow/Snakefile --env-dir .test/.snakemake/conda' | |
| - name: Test report | |
| uses: snakemake/snakemake-github-action@v1.21.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--report report.zip --wrapper-prefix file:///github/workspace/workflow/wrappers" |