Bump github/super-linter from 4 to 7 #570
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| name: MosaiCatcher basic checks | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| schedule: | |
| - cron: "0 0 * * 0" | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/[email protected] | |
| - name: Formatting using Super-Linter | |
| uses: github/super-linter@v7 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository without submodules | |
| uses: actions/checkout@v4 | |
| # with: | |
| # submodules: "recursive" # Ensures all submodules are checked out | |
| # lfs: true # Ensures LFS objects for the main repo are pulled | |
| # - name: Pull LFS objects in submodules | |
| # run: | | |
| # git submodule foreach --recursive 'git pull origin main' | |
| - name: List contents of .tests-mock | |
| run: | | |
| tree -h github-actions-runner/.tests-mock | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Add Conda to system path | |
| run: | | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| conda install -c conda-forge mamba | |
| - name: Setup snakemake | |
| run: | | |
| mamba install -c conda-forge -c bioconda snakemake==7.32.4 | |
| - name: Run Snakemake Lint | |
| run: | | |
| snakemake --config data_location=github-actions-runner/.tests-mock/data_CHR17 --lint | |
| Testing-basic-v7: | |
| runs-on: ubuntu-latest | |
| # needs: | |
| # - Formatting | |
| # - Linting | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| # Update references | |
| - name: Git Submodule Update | |
| run: | | |
| # git pull --recurse-submodules | |
| git submodule update --remote --recursive --force --init | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: List contents of .tests | |
| run: | | |
| tree -h .tests | |
| - name: Show config file | |
| run: | | |
| cat .tests/config/simple_config_mosaicatcher.yaml | |
| - name: List contents of workflow/data | |
| run: | | |
| tree -h workflow/data | |
| - name: Add Conda to system path | |
| run: echo "$CONDA/bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: conda install -c conda-forge mamba | |
| - name: Setup Snakemake | |
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | |
| - name: List options of workflow | |
| run: | | |
| snakemake --cores 1 --config list_commands=True --verbose --debug | |
| - name: Run workflow | |
| run: | | |
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml \ | |
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | |
| Testing-basic-with-ashleys: | |
| runs-on: ubuntu-latest | |
| # needs: | |
| # - Formatting | |
| # - Linting | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| # lfs: true | |
| - name: Git Submodule Update | |
| run: | | |
| # git pull --recurse-submodules | |
| git submodule update --remote --recursive --force --init | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: List contents of .tests | |
| run: | | |
| tree -h .tests | |
| - name: Show config file | |
| run: | | |
| cat .tests/config/simple_config_mosaicatcher.yaml | |
| - name: List contents of workflow/data | |
| run: | | |
| tree -h workflow/data | |
| - name: Add Conda to system path | |
| run: echo "$CONDA/bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: conda install -c conda-forge mamba | |
| - name: Setup Snakemake | |
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | |
| - name: List options of workflow | |
| run: | | |
| snakemake --cores 1 --config list_commands=True --verbose --debug | |
| - name: Run workflow | |
| run: | | |
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config ashleys_pipeline=True \ | |
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile |