Fix matching of sample names in DESeq2.R script #101
Workflow file for this run
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| name: 3t-seq test run | |
| on: | |
| release: | |
| types: [ published ] | |
| pull_request: | |
| branches-ignore: [] | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout with submodules | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Formatting | |
| uses: github/super-linter@v5 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Linting | |
| uses: snakemake/snakemake-github-action@v1.22.0 | |
| with: | |
| directory: tests | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .tests/integration/config.yaml --lint" | |
| run-unit-tests: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| lfs: true | |
| - name: Setup Python 3.11 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.11 | |
| - 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 apptainer=1.2.5 | |
| - name: Pytest | |
| run: | | |
| pytest .tests/unit | |
| run-integration-tests: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| lfs: true | |
| - name: Setup Python 3.11 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.11 | |
| - name: Add Conda to system path | |
| run: | | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| conda install -c conda-forge mamba | |
| - name: Setup snakemake | |
| run: | | |
| mamba install -c conda-forge -c bioconda snakemake=7.32.4 apptainer=1.2.5 | |
| - name: Run workflow | |
| run: | | |
| ROOT=$(realpath .) | |
| snakemake \ | |
| --directory .tests/integration \ | |
| --configfile .tests/integration/config.yaml \ | |
| --profile .tests/integration/profile \ | |
| --snakefile workflow/Snakefile \ | |
| --all-temp \ | |
| --singularity-args="--bind $ROOT --bind $HOME" | |