fix: correct indentation in test_config.yaml for sample definition #12
This file contains hidden or 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: Test GHCR Container | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| test-container: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Pull container presto-0.7.4:latest from GHCR | |
| run: | | |
| docker pull ghcr.io/lewisl23/presto-0.7.4:latest | |
| - name: Test container presto-0.7.4:latest runs | |
| run: | | |
| docker run --rm ghcr.io/lewisl23/presto-0.7.4:latest AssemblePairs.py --help | |
| echo "Container works" | |
| - name: Pull container igblast-1.21.0:latest from GHCR | |
| run: | | |
| docker pull ghcr.io/lewisl23/igblast-1.21.0:latest | |
| - name: Test container igblast-1.21.0:latest runs | |
| run: | | |
| docker run --rm ghcr.io/lewisl23/igblast-1.21.0:latest igblastn -help | |
| echo "Container works" | |
| test-workflow: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.9" | |
| - name: Install Snakemake | |
| run: | | |
| pip install snakemake | |
| pip install pulp==2.7.0 | |
| - name: Run test pipeline | |
| run: | | |
| snakemake --cores 1 \ | |
| --configfile tests/config/test_config.yaml \ | |
| --use-singularity \ | |
| --printshellcmds \ | |
| --reason |