ci.yml

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

env:
  NXF_ANSI_LOG: false
  NFTEST_VER: "0.7.3"

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

jobs:
  define_nxf_versions:
    name: Choose nextflow versions to test against depending on target branch
    runs-on: ubuntu-latest
    outputs:
      matrix: ${{ steps.nxf_versions.outputs.matrix }}
    steps:
      - id: nxf_versions
        run: |
          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
          else
            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
          fi

  test:
    name: nf-test
    needs: define_nxf_versions
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
        tags:
          - "test"
          - "test_single"
          - "test_fasta"
          - "test_multi"
          - "test_reftaxcustom"
          - "test_doubleprimers"
          - "test_iontorrent"
          - "test_novaseq"
          - "test_pacbio_its"
          - "test_sintax"
          - "test_pplace"
        profile:
          - "docker"

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

      - name: Check out test data
        uses: actions/checkout@v3
        with:
          repository: nf-core/test-datasets
          ref: ampliseq
          path: test-datasets/
          fetch-depth: 1

      - name: Replace remote paths in samplesheets
        run: |
          for f in ${{ github.workspace }}/test-datasets/samplesheets/*.tsv; do
            sed -i "s=https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/=${{ github.workspace }}/test-datasets/=g" $f
            echo "========== $f ============"
            cat $f
            echo "========================================"
          done;

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

      - name: Install nf-test
        run: |
          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
          sudo mv nf-test /usr/local/bin/

      - name: Run nf-test
        run: |
          nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml

      - name: Output log on failure
        if: failure()
        run: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml

      - name: Publish Test Report
        uses: mikepenz/action-junit-report@v3
        if: always() # always run even if the previous step fails
        with:
          report_paths: "*.xml"