consistency_check.yml

on:
  pull_request:
    branches:
      - main
  push:
    branches:
      - main
  workflow_dispatch:
name: Consistency Check
jobs:
  test:
    name: Check Consistency vs. KevinKuchinski/FluViewer
    strategy:
      fail-fast: false
      matrix:
        python_version:
          - "3.8"
          - "3.9"
          - "3.10"
          - "3.11"
          - "3.12"
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@master
    - name: Create Artifacts Directory
      run: mkdir artifacts
    - name: Install Conda
      run: bash .github/scripts/install_conda.sh
    - name: Create ART Read-Simulation Environment
      run: bash .github/scripts/create_art_environment.sh
    - name: Download Assemblies
      run: bash .github/scripts/download_assemblies.sh
    - name: Simulate Reads
      run: bash .github/scripts/simulate_reads.sh
    - name: Create SRA-Tools Environment
      run: bash .github/scripts/create_sra-tools_environment.sh
    - name: Download SRA Reads
      run: bash .github/scripts/download_sra_reads.sh
    - name: Download FluViewer db
      run: bash .github/scripts/download_fluviewer_db.sh
    - name: Install KevinKuchinski/FluViewer
      run: bash .github/scripts/install_fluviewer_kkuchinski.sh
    - name: Run analysis with KevinKuchinski/FluViewer
      run: bash .github/scripts/run_analysis_upstream.sh
    - name: Install BCCDC-PHL/FluViewer
      run: bash .github/scripts/install_fluviewer_bccdc-phl.sh
    - name: Run analysis with BCCDC-PHL/FluViewer
      run: bash .github/scripts/run_analysis_origin.sh
    - name: Check Outputs
      run: bash .github/scripts/check_outputs.sh
    - name: Prepare Artifacts
      if: always()
      run: bash .github/scripts/prepare_artifacts.sh
    - name: Upload Artifacts
      uses: actions/upload-artifact@v4
      if: always()
      with:
        name: artifacts-BCCDC-PHL-FluViewer-python-v${{ matrix.python_version }}-${{ github.run_id }}.${{ github.run_attempt }}
        path: artifacts