added test #25
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| name: Tests | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Formatting | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint" | |
| Dryrun: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2.2.0 | |
| with: | |
| channels: conda-forge,bioconda,defaults | |
| - run: conda install -y snakemake | |
| - run: snakemake --version | |
| - name: Dryrun | |
| run: bash .test/dryrun.sh | |
| Testing: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - run: pwd; ls -la | |
| - name: Test workflow with spades | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| stagein: .test/copy_example_data.sh .test/spades | |
| directory: .test/spades | |
| snakefile: workflow/Snakefile | |
| args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp" | |
| - name: Test report spades | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: .test/spades | |
| snakefile: workflow/Snakefile | |
| args: "--report report.zip" | |
| - name: Test workflow with megahit | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| stagein: .test/copy_example_data.sh .test/megahit | |
| directory: .test/megahit | |
| snakefile: workflow/Snakefile | |
| args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp --config assembler=megahit " | |
| - name: Test report megahit | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: .test/megahit | |
| snakefile: workflow/Snakefile | |
| args: "--report report.zip" |