ci.yml

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]
  workflow_dispatch:

env:
  NXF_ANSI_LOG: false
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity

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

jobs:
  test:
    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "24.04.2"
          - "latest-everything"
        profile:
          - "conda"
          - "docker"
          - "singularity"
        test_name:
          - "test"
        isMaster:
          - ${{ github.base_ref == 'master' }}
        # Exclude conda and singularity on dev
        exclude:
          - isMaster: false
            profile: "conda"
          - isMaster: false
            profile: "singularity"
    steps:
      - name: Free some space
        run: |
          sudo rm -rf "/usr/local/share/boost"
          sudo rm -rf "$AGENT_TOOLSDIRECTORY"

      - name: Check out pipeline code
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Set up Apptainer
        if: matrix.profile == 'singularity'
        uses: eWaterCycle/setup-apptainer@main

      - name: Set up Singularity
        if: matrix.profile == 'singularity'
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      - name: Set up Miniconda
        if: matrix.profile == 'conda'
        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
        with:
          miniconda-version: "latest"
          auto-update-conda: true
          conda-solver: libmamba
          channels: conda-forge,bioconda

      - name: Set up Conda
        if: matrix.profile == 'conda'
        run: |
          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
          echo $(realpath python) >> $GITHUB_PATH

      - name: Clean up Disk space
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

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

  profiles:
    name: Run workflow profile
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        # Run remaining test profiles with minimum nextflow version
        test_name:
          [
            test_host_rm,
            test_hybrid,
            test_hybrid_host_rm,
            test_busco_auto,
            test_ancient_dna,
            test_adapterremoval,
            test_binrefinement,
            test_virus_identification,
            test_single_end,
            test_concoct,
          ]
    steps:
      - name: Free some space
        run: |
          sudo rm -rf "/usr/local/share/boost"
          sudo rm -rf "$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: Clean up Disk space
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

      - name: Run pipeline with ${{ matrix.test_name }} test profile
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},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@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

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

      - name: Clean up Disk space
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

      - name: Download and prepare CheckM database
        run: |
          mkdir -p databases/checkm
          wget https://zenodo.org/records/7401545/files/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