Feature/allele calling #140
Workflow file for this run
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| 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 | |