Feature/allele calling #143
Workflow file for this run
This file contains 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: tests ci | |
| # This workflow runs the pipeline with the minimal test dataset to check | |
| # is completed without any errors | |
| on: | |
| pull_request: | |
| push: | |
| jobs: | |
| test_analyze_schema: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: taranis_env | |
| environment-file: environment.yml | |
| - name: Verify Conda environment | |
| run: conda env list | |
| - name: Activate env and install taranis | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate taranis_env | |
| python -m pip install . | |
| taranis analyze-schema -i test/MLST_listeria/analyze_schema -o analyze_schema_test --cpus 1 --output-allele-annot --remove-no-cds --remove-duplicated --remove-subset | |
| - name: Testing Reference allele | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate taranis_env | |
| taranis reference-alleles -s test/MLST_listeria/reference_allele -o reference_allele_test --cpus 1 | |