bump 3.0.1 version #171
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_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 |