name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  push:
    branches:
      - dev
  pull_request:
  release:
    types: [published]

env:
  NXF_ANSI_LOG: false

concurrency:
  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
  cancel-in-progress: true

jobs:
  test:
    name: Run pipeline with test data
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
    steps:
      - name: Free some space
        run: |
          sudo rm -rf "/usr/local/share/boost"
          sudo rm -rf "$AGENT_TOOLSDIRECTORY"

      - name: Check out pipeline code
        uses: actions/checkout@v3

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

  profiles:
    name: Run workflow profile
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        # Run remaining test profiles with minimum nextflow version
        profile:
          [
            test_host_rm,
            test_hybrid,
            test_hybrid_host_rm,
            test_busco_auto,
            test_ancient_dna,
            test_adapterremoval,
            test_binrefinement,
            test_virus_identification,
          ]
    steps:
      - name: Free some space
        run: |
          sudo rm -rf "/usr/local/share/boost"
          sudo rm -rf "$AGENT_TOOLSDIRECTORY"

      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - name: Run pipeline with ${{ matrix.profile }} test profile
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results

  checkm:
    name: Run single test to checkm due to database download
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}
    runs-on: ubuntu-latest

    steps:
      - name: Free some space
        run: |
          sudo rm -rf "/usr/local/share/boost"
          sudo rm -rf "$AGENT_TOOLSDIRECTORY"

      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - name: Download and prepare CheckM database
        run: |
          mkdir -p databases/checkm
          wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz -P databases/checkm
          tar xzvf databases/checkm/checkm_data_2015_01_16.tar.gz -C databases/checkm/

      - name: Run pipeline with ${{ matrix.profile }} test profile
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --binqc_tool checkm --checkm_db databases/checkm
