black linting #157
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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 | |