setup.yml

name: Conda environment testing

on:
  workflow_dispatch:
    branches:
      - main
      - devel
  pull_request:
    branches:
      - main
      - devel

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [macos-latest, ubuntu-latest]
        env: [snakemake, nextflow, jupyter, quarto]
        include:
          - env: snakemake
            os: ubuntu-latest # Conda on MacOS ARM64 doesn't have subread
            cmd: snakemake -c 1 -d tutorials/snakemake/ -s tutorials/snakemake/snakefile_mrsa.smk
          - env: nextflow
            os: ubuntu-latest # Conda on MacOS ARM64 doesn't have subread
            cmd: cd tutorials/nextflow && nextflow run main_mrsa.nf
          - env: jupyter
            cmd: jupyter nbconvert --to HTML tutorials/jupyter/supplementary_material.ipynb
          - env: quarto
            cmd: conda install -c conda-forge quarto && conda install -c conda-forge deno && export QUARTO_DENO=$(which deno) && quarto render tutorials/quarto/quarto-tutorial-example.qmd --to html
    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Conda setup
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          activate-environment: ${{ matrix.env }}-env
          environment-file: tutorials/${{ matrix.env }}/environment.yml
          channel-priority: strict

      - name: Test ${{ matrix.env }} Conda environment
        shell: bash -l {0}
        run: |
          conda list
          ${{ matrix.cmd }}