tests.yml

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