setting up github actions #108
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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@v2 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint --configfile config/config_test.yaml" | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Linting | |
| - Formatting | |
| steps: | |
| - uses: nschloe/action-cached-lfs-checkout@v1 | |
| - name: Download busco lineage | |
| run: | | |
| mkdir -p test_data/busco_db | |
| cd test_data/busco_db | |
| wget https://busco-data.ezlab.org/v5/data/lineages/saccharomycetes_odb10.2024-01-08.tar.gz | |
| tar -xzf saccharomycetes_odb10.2024-01-08.tar.gz | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: ncbi_fcsgx | |
| environment-file: workflow/envs/fcsgx.yaml | |
| auto-activate-base: false | |
| - name: Download FCS-GX test database | |
| shell: bash -l {0} | |
| run: | | |
| conda activate ncbi_fcsgx | |
| mkdir -p test_data/gx_test_db | |
| cd test_data/gx_test_db | |
| sync_files.py get --mft https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.manifest --dir ./test-only | |
| - name: Install and set up time command (needed by FCS-GX for debug purposes) | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y time | |
| - name: Test workflow | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--configfile config/config_test.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp" | |
| - name: Test report | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--report report.zip" |