Merge pull request #23 from BU-ISCIII/develop #170
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_taranys: | |
| 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: taranys_env | |
| environment-file: environment.yml | |
| - name: Verify conda environment | |
| run: conda env list | |
| - name: Activate env and install taranys | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate taranys_env | |
| python -m pip install . | |
| - name: Testing analyze schema allele | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate taranys_env | |
| taranys 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 taranys_env | |
| taranys reference-alleles -s test/MLST_listeria/reference_allele -o reference_allele_test --cpus 1 | |
| - name: Testing allele calling | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate taranys_env | |
| taranys reference-alleles -s analyze_schema_test/new_schema -o reference_allele --cpus 1 | |
| taranys allele-calling --force --schema analyze_schema_test/new_schema --reference reference_allele --annotation analyze_schema_test/allele_annotation.tar.gz --output allele_calling_test --cpus 1 --snp --alignment test/samples_listeria/*.fasta | |
| - name: Testing distance matrix | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate taranys_env | |
| mkdir distance_matrix_result | |
| taranys distance-matrix --alleles allele_calling_test/allele_calling_match.csv --force --output distance_matrix_result |