conda.yml

name: test conda profiles on demand and on publish

on:
  release:
      types: [published]
  workflow_dispatch:

jobs:
  preload_ancestry:
    uses: ./.github/workflows/preload-reference.yml

  test_mamba_ancestry:
    uses: ./.github/workflows/ancestry-conda.yml
    needs: [preload_ancestry]
    with:
      ancestry-cache-key: ${{ needs.preload_ancestry.outputs.cache-key }}

  test_mamba_standard:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    strategy:
      fail-fast: false
      matrix:
        test_profile: ["test"]
        profile: ["mamba"]
        nxf_ver: ["23.10.0", ""]

    env:
      NXF_VER: ${{ matrix.nxf_ver }}

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v2
        with:  
          channels: conda-forge,bioconda,defaults
          miniforge-variant: Mambaforge
          miniforge-version: latest
          python-version: "3.10"
          
      - uses: actions/setup-java@v3
        with:
          distribution: 'corretto'
          java-version: '17'

      - name: install nxf
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/

      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile}},${{ matrix.profile }}