main.yml

name: CI-main
on:
  push:
    branches:
      - main
  pull_request:

jobs:
  smoke:
    strategy:
      fail-fast: true
      max-parallel: 1
      matrix:
        python-version: ["3.8", "3.12"]
        poetry-version: ["1.5.1"]
        sentieon-version: ["202308.01", "202308.02"]
        os: [ubuntu-22.04] #, macos-latest, windows-latest]
    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Run image
        uses: abatilo/actions-poetry@v2
        with:
          poetry-version: ${{ matrix.poetry-version }}
      - name: Install the project dependencies
        run: |
          poetry config virtualenvs.in-project true
          poetry install
      - name: Install bcftools
        run: |
          sudo apt-get update
          sudo apt-get install -y bcftools
      - name: Install samtools
        run: |
          curl -L https://github.com/samtools/samtools/releases/download/1.19.2/samtools-1.19.2.tar.bz2 | tar -jxf -
          cd samtools-1.19.2
          ./configure && sudo make install
      - name: Install bedtools
        run: |
          sudo curl -L -o /usr/local/bin/bedtools "https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static"
          sudo chmod ugo+x /usr/local/bin/bedtools
      - name: Install sentieon
        run: |
          curl -L https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-$SENTIEON_VERSION.tar.gz | tar -zxf -
        env:
          SENTIEON_VERSION: ${{ matrix.sentieon-version }}
      - name: Download model
        run: |
          curl -L "https://s3.amazonaws.com/sentieon-release/other/DNAscopePacBio2.1.bundle" \
            > "DNAscope PacBio2.1.bundle"
      - name: Smoke test
        run: |
          SENTIEON_AUTH_DATA=$(python3 .github/scripts/license_message.py encrypt --key "$ENCRYPTION_KEY" --message "$LICENSE_MESSAGE")
          export SENTIEON_AUTH_DATA
          . .venv/bin/activate
          export PATH=$(pwd)/sentieon-genomics-$SENTIEON_VERSION/bin:$PATH
          gzip -dc tests/smoke/ref.fa.bgz > "tests/smoke/r ef.fa"
          mv tests/smoke/ref.fa.fai "tests/smoke/r ef.fa.fai"
          mv tests/smoke/sample.cram "tests/smoke/sam ple.cram"
          mv tests/smoke/sample.cram.crai "tests/smoke/sam ple.cram.crai"

          sentieon-cli dnascope-longread -t 1 -r "tests/smoke/r ef.fa" \
            -i "tests/smoke/sam ple.cram" -m "DNAscope PacBio2.1.bundle" \
            --repeat-model tests/smoke/sample_repeat.model -g \
            -b "tests/smoke/diploid.bed" \
            --haploid-bed "tests/smoke/haploid.bed" \
            "output hifi.vcf.gz"
          sentieon driver -r "tests/smoke/r ef.fa" -t 1 --algo GVCFtyper \
            -v "output hifi.g.vcf.gz" output_hifi_gvcftyper.vcf.gz
          if [ ! -f "output hifi.sv.vcf.gz" -o ! -f "output hifi.haploid.vcf.gz" ]; then
            exit 1
          fi

          sentieon-cli dnascope-longread --tech ONT -t 1 -r "tests/smoke/r ef.fa" \
            -i "tests/smoke/sam ple.cram" -m "DNAscope PacBio2.1.bundle" \
            --repeat-model tests/smoke/sample_repeat.model -g "output ont.vcf.gz"
          sentieon driver -r "tests/smoke/r ef.fa" -t 1 --algo GVCFtyper \
            -v "output ont.g.vcf.gz" output_hifi_gvcftyper.vcf.gz
          if [ ! -f "output ont.sv.vcf.gz" ]; then
            exit 1
          fi

          sentieon-cli dnascope-longread -t 1 -r "tests/smoke/r ef.fa" \
            -i "tests/smoke/sam ple.cram" -m "DNAscope PacBio2.1.bundle" \
            --repeat-model tests/smoke/sample_repeat.model --align \
            --input_ref "tests/smoke/r ef.fa" "output realigned.vcf.gz"
          if [ ! -f "output realigned.vcf.gz" -o ! -f "output realigned_mm2_sorted_0.cram" ]; then
            exit 1
          fi

          samtools fastq --reference "tests/smoke/r ef.fa" \
            "tests/smoke/sam ple.cram" | \
            gzip -c > sample.fq.gz
          sentieon-cli dnascope-longread -t 1 -r "tests/smoke/r ef.fa" \
            --fastq sample.fq.gz --readgroups '@RG\tID:sample-1\tSM:sample' \
            -m "DNAscope PacBio2.1.bundle" \
            --repeat-model tests/smoke/sample_repeat.model "output fq.vcf.gz"
          if [ ! -f "output fq.vcf.gz" -o ! -f "output fq_mm2_sorted_fq_0.cram" -o ! -f "output fq.sv.vcf.gz" ]; then
            exit 1
          fi

        env:
          SENTIEON_LICENSE: ${{ secrets.SENTIEON_LICENSE }}
          SENTIEON_AUTH_MECH: "GitHub Actions - token"
          ENCRYPTION_KEY: ${{ secrets.ENCRYPTION_KEY }}
          LICENSE_MESSAGE: ${{ secrets.LICENSE_MESSAGE }}
          SENTIEON_VERSION: ${{ matrix.sentieon-version }}