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
      - documentation
  pull_request:
  release:
    types: [published]
  workflow_dispatch:

env:
  NXF_ANSI_LOG: false
  NFT_VER: "0.9.0"
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
  # env var to force tests
  # TEST_SET: '["tests/workflows/mcmicro.nf.test", "subworkflows/local/utils_nfcore_mcmicro_pipeline/tests/initialisation.nf.test", "tests/main.nf.test"]'

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

jobs:
  #  nf-test-changes:
  #    name: Check for changes
  #    runs-on: ubuntu-latest
  #    outputs:
  #      nf_test_files: ${{ steps.list.outputs.components }}
  #      # nf_test_files: ${{ env.TEST_SET }}
  #
  #    steps:
  #      - uses: actions/checkout@v4
  #        with:
  #          fetch-depth: 0
  #
  #      - name: List nf-test files
  #        id: list
  #        uses: adamrtalbot/detect-nf-test-changes@v0.0.4
  #        with:
  #          head: ${{ github.sha }}
  #          # TODO: check that the following works on pull_request
  #          base: ${{ github.ref_name }}
  #
  #      - name: print list of nf-test files
  #        run: |
  #          echo ${{ steps.list.outputs.components }}

  #  test:
  #    name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})"
  #    needs: [nf-test-changes]
  #    # Only run on push if this is the nf-core dev branch (merged PRs)
  #    if: "${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mcmicro')) && needs.nf-test-changes.outputs.nf_test_files != '[]' }}"
  #    runs-on: ubuntu-latest
  #    strategy:
  #      fail-fast: false
  #      matrix:
  #        NXF_VER:
  #          - "24.04.2"
  #          - "latest-everything"
  #        nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
  #        profile:
  #          # - "conda"
  #          - "docker"
  #          - "singularity"
  #        test_name:
  #          - "test"
  #        isMaster:
  #          - ${{ github.base_ref == 'master' }}
  #        # Exclude conda and singularity on dev
  #        exclude:
  #          - isMaster: false
  #            profile: "conda"
  #          - isMaster: false
  #            profile: "singularity"
  #    steps:
  #      - name: install curl
  #        run: sudo apt update && sudo apt install -y curl wget
  #
  #      - name: Check out pipeline code
  #        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
  #
  #      - name: Set up Nextflow
  #        uses: nf-core/setup-nextflow@v2
  #        with:
  #          version: "${{ 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: Install nf-test
  #        uses: nf-core/setup-nf-test@v1
  #        with:
  #          version: ${{ env.NFT_VER }}
  #
  #      - uses: actions/setup-python@v4
  #        with:
  #          python-version: "3.11"
  #          architecture: "x64"
  #
  #      - name: Install pdiff to see diff between nf-test snapshots
  #        run: |
  #          python -m pip install --upgrade pip
  #          pip install pdiff
  #
  #      - name: Clean up Disk space
  #        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
  #
  #      - name: Run nf-test
  #        run: |
  #          nf-test test \
  #            --verbose ${{ matrix.nf_test_files }} \
  #            --profile "+${{ matrix.profile }},ci" \
  #            --junitxml=test.xml \
  #            --tap=test.tap
  #
  #      - uses: pcolby/tap-summary@v1
  #        with:
  #          path: >-
  #            test.tap
  #
  #      - name: Output log on failure
  #        if: failure()
  #        run: |
  #          sudo apt install bat > /dev/null
  #          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
  #
  #      - name: Publish Test Report
  #        uses: mikepenz/action-junit-report@v3
  #        if: always() # always run even if the previous step fails
  #        with:
  #          report_paths: test.xml

  #  confirm-pass:
  #    runs-on: ubuntu-latest
  #    needs: [test]
  #    if: always()
  #    steps:
  #      - name: All tests ok
  #        if: ${{ !contains(needs.*.result, 'failure') }}
  #        run: exit 0
  #      - name: One or more tests failed
  #        if: ${{ contains(needs.*.result, 'failure') }}
  #        run: exit 1
  #
  #      - name: debug-print
  #        if: always()
  #        run: |
  #          echo "toJSON(needs) = ${{ toJSON(needs) }}"
  #          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

  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/mcmicro') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-java@v4
        with:
          distribution: "zulu" # See 'Supported distributions' for available options
          java-version: "21"

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

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

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

      - name: Run pipeline with test data
        # TODO nf-core: You can customise CI pipeline run tests as required
        # For example: adding multiple test runs with different parameters
        # Remember that you can parallelise this by using strategy.matrix
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results