Himito/.github/workflows/test-small.yml at 0dc87955e6fcf9de21b644542c46fa0348b25a0a · broadinstitute/Himito · GitHub

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name: Small Integration Tests

on:
  push:
    branches: [ main, master ]
  pull_request:
    branches: [ main, master ]
  workflow_dispatch:

permissions:
  contents: read

jobs:
  quick-test:
    name: Quick Integration Test
    runs-on: ubuntu-latest
    timeout-minutes: 30

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libcurl4-openssl-dev \
            libssl-dev \
            zlib1g-dev \
            libbz2-dev \
            liblzma-dev \
            samtools \
            bcftools

      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@stable

      - name: Build project
        run: cargo build --release

      - name: Test help command
        run: |
          cargo run --release -- --help || true
          cargo run --release -- quick-start --help || true
          cargo run --release -- filter --help || true
          cargo run --release -- build --help || true
          cargo run --release -- correct --help || true
          cargo run --release -- call --help || true
          cargo run --release -- asm --help || true
          cargo run --release -- methyl --help || true

      - name: Test Himito quick-start command
        run: |
          if [ -f "test_data/HG005_100x.bam" ] && [ -f "test_data/HG005_100x.bai" ]; then
            cargo run --release -- quick-start \
              -i test_data/HG005_100x.bam \
              -c "chrM" \
              -k 21 \
              --sampleid HG005 \
              -r test_data/rCRS.fasta \
              --output-prefix test_output/himito_test || echo "Himito test skipped - may require additional dependencies"
          else
            echo "Test data not available, skipping evaluate test"
          fi


      - name: Cleanup
        if: always()
        run: rm -rf test_output test_data