Prepare version 0.3.0 #149
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: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - '**/*.md' | |
| pull_request: | |
| branches_ignore: [] | |
| paths-ignore: | |
| - '**/*.md' | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout with submodules | |
| uses: actions/checkout@v3.5.2 | |
| - name: Formatting | |
| uses: github/super-linter@v5 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3.5.2 | |
| - name: Linting | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| snakefile: "workflow/Snakefile" | |
| args: "--lint" | |
| run-workflow: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Maximize build space | |
| uses: easimon/maximize-build-space@master | |
| with: | |
| root-reserve-mb: 1024 | |
| swap-size-mb: 1024 | |
| overprovision-lvm: 'true' | |
| remove-dotnet: 'true' | |
| remove-android: 'true' | |
| remove-haskell: 'true' | |
| remove-codeql: 'true' | |
| remove-docker-images: 'true' | |
| - name: Checkout repository | |
| uses: actions/checkout@v3.5.2 | |
| - name: Set up conda environment and singularity | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yaml | |
| create-args: >- | |
| apptainer | |
| - name: Test workflow | |
| shell: bash -l {0} | |
| run: | | |
| mkdir -p temp | |
| workdir=$(pwd -P) | |
| TMPDIR=$workdir/temp | |
| snakemake --directory .test --configfile .test/config/config.yaml --config samples=config/samples_testSRA.tsv --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --use-singularity --default-resources mem_mb=1000 --until fastp_mergedout | |
| snakemake --directory .test --configfile .test/config/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --use-singularity --default-resources mem_mb=1000 | |
| - name: Test report | |
| shell: bash -l {0} | |
| run: | | |
| snakemake --directory .test --configfile .test/config/config.yaml --cores 2 --report report.html |