juno_mapping_singularity.yaml

# Testing for pipeline python wrapper and scripts used inside rules

name: Singularity e2e test

on: [pull_request]

env:
  KRAKEN_DEFAULT_DB: /mnt/kraken-database

jobs:
  singularity_end_to_end:
    runs-on: ${{ matrix.config.os }}
    strategy:
      fail-fast: false
      matrix:
        config: 
          - {os: ubuntu-latest}
    name: Singularity Juno_mapping pipeline ${{ matrix.config.os }}

    steps:
      - name: check space 1
        shell: bash -l {0}
        run: |
          echo "Checking space: ."
          df -h .
          echo "Checking space: /mnt"
          df -h /mnt
      - uses: actions/checkout@v4
      - uses: eWaterCycle/setup-singularity@v7
        with:
          singularity-version: 3.8.3
      - name: Install Conda environment with Micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          generate-run-shell: false # see https://github.com/mamba-org/setup-micromamba/issues/130
          cache-downloads: true
          environment-file: envs/juno_mapping.yaml
          environment-path: /mnt/juno_mapping
      - name: Cache minikraken
        id: cache-minikraken
        uses: actions/cache@v3
        with:
          path: ${{ env.KRAKEN_DEFAULT_DB }}
          key: minikraken-${{ runner.os }}
      - name: Download k2 database
        if: steps.cache-minikraken.outputs.cache-hit != 'true'
        run: |
          mkdir -pv ${{ env.KRAKEN_DEFAULT_DB }}
          cd ${{ env.KRAKEN_DEFAULT_DB }}
          curl -k https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20220908.tar.gz > k2_viral_20220908.tar.gz
          tar zxvf k2_viral_20220908.tar.gz
          ls -lh
          rm k2_viral_20220908.tar.gz
      - name: Conda list
        shell: bash -l {0}
        run: conda list
      - name: check space 2
        shell: bash -l {0}
        run: |
          which singularity
          singularity --version
          df -h .
          if [ -d /home/runner ]; then
            sudo rm -rf /usr/share/dotnet
            sudo rm -rf /opt/ghc
            sudo rm -rf "/usr/local/share/boost"
          fi
          echo "Checking space: ."
          df -h .
          echo "Checking space: /mnt"
          df -h /mnt
          which singularity
          singularity --version
      - name: Test juno_mapping pipeline using singularity.
        shell: bash -l {0}
        run: pytest -v tests/test_pipeline_singularity.py
      - name: Test the juno_mapping wrapper
        shell: bash -l {0}
        run: pytest -v tests/test_juno_mapping.py
      - name: check space 3
        if: always()
        shell: bash -l {0}
        run: | 
          echo "Checking space: ."
          df -h .
          echo "Checking space: /mnt"
          df -h /mnt