nf-test.yml

name: Run nf-test
on:
  push:
    branches:
      - dev
      - master
      - main
    paths-ignore:
      - "docs/**"
      - "**/meta.yml"
      - "**/*.md"
      - "**/*.png"
      - "**/*.svg"
  pull_request:
    paths-ignore:
      - "docs/**"
      - "**/meta.yml"
      - "**/*.md"
      - "**/*.png"
      - "**/*.svg"
  release:
    types: [published]
  workflow_dispatch:

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  NFT_VER: "0.9.2"
  NFT_WORKDIR: "~"
  NXF_ANSI_LOG: false
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity

jobs:
  nf-test-changes:
    name: nf-test-changes
    runs-on: # use self-hosted runners
      - runs-on=$-nf-test-changes
      - runner=4cpu-linux-x64
    outputs:
      shard: ${{ steps.set-shards.outputs.shard }}
      total_shards: ${{ steps.set-shards.outputs.total_shards }}
    steps:
      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
        run: |
          ls -la ./
          rm -rf ./* || true
          rm -rf ./.??* || true
          ls -la ./
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
        with:
          fetch-depth: 0

      - name: get number of shards
        id: set-shards
        uses: ./.github/actions/get-shards
        env:
          NFT_VER: ${{ env.NFT_VER }}
        with:
          max_shards: 15
          tags: modules_local,subworkflows_local

      - name: debug
        run: |
          echo ${{ steps.set-shards.outputs.shard }}
          echo ${{ steps.set-shards.outputs.total_shards }}

  nf-test:
    name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
    needs: [nf-test-changes]
    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
    runs-on: # use self-hosted runners
      - runs-on=$-nf-test
      - runner=4cpu-linux-x64
      - disk=large
    strategy:
      fail-fast: false
      matrix:
        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
        profile: [conda, docker, singularity]
        isMain:
          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
        # Exclude conda and singularity on dev
        exclude:
          - isMain: false
            profile: "conda"
          - isMain: false
            profile: "singularity"
        NXF_VER:
          - "24.04.2"
          - "latest-everything"
    env:
      NXF_ANSI_LOG: false
      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}

    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
        with:
          fetch-depth: 0

      - name: Run nf-test
        uses: ./.github/actions/nf-test
        env:
          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
        with:
          profile: ${{ matrix.profile }}
          shard: ${{ matrix.shard }}
          total_shards: ${{ env.TOTAL_SHARDS }}
          tags: modules_local,subworkflows_local

  pipeline-tests:
    name: "Pipeline Test | ${{ matrix.test_name }} | ${{ matrix.NXF_VER }} | ${{ matrix.profile }}"
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        test_name:
          - "default"
          - "main_pipeline_build"
          - "main_pipeline_extend"
          - "main_pipeline_sub"
          - "main_pipeline_qc"
          - "main_pipeline_reference_mapping"
        profile: [conda, docker, singularity]
        isMain:
          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
        # Exclude conda and singularity on dev
        exclude:
          - isMain: false
            profile: "conda"
          - isMain: false
            profile: "singularity"
        NXF_VER:
          - "24.04.2"
          - "latest-everything"
    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
        with:
          fetch-depth: 0

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

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

      - name: Set up Python
        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
        with:
          python-version: "3.13"

      - name: Install nf-test
        uses: nf-core/setup-nf-test@v1
        with:
          version: ${{ env.NFT_VER }}
          install-pdiff: true

      - name: Setup apptainer
        if: contains(matrix.profile, 'singularity')
        uses: eWaterCycle/setup-apptainer@main

      - name: Set up Singularity
        if: contains(matrix.profile, 'singularity')
        shell: bash
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      - name: Conda setup
        if: contains(matrix.profile, 'conda')
        uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
        with:
          auto-update-conda: true
          conda-solver: libmamba
          conda-remove-defaults: true

      - name: Run nf-test
        shell: bash
        env:
          NFT_DIFF: ${{ env.NFT_DIFF }}
          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
        run: |
          # Make it clear that we're ONLY running tests from the tests directory
          # and not including any module or subworkflow tests
          nf-test test \
            --profile=+${{ matrix.profile }} \
            --ci \
            --verbose \
            --tap=test.tap \
            tests/${{ matrix.test_name }}.nf.test

      - name: Generate test summary
        if: always()
        shell: bash
        run: |
          # Add header if it doesn't exist (using a token file to track this)
          if [ ! -f ".summary_header" ]; then
            echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
            echo "" >> $GITHUB_STEP_SUMMARY
            echo "| Status | Test Name | Profile | Nextflow Version |" >> $GITHUB_STEP_SUMMARY
            echo "|:------:|-----------|---------|-----------------|" >> $GITHUB_STEP_SUMMARY
            touch .summary_header
          fi

          if [ -f test.tap ]; then
            while IFS= read -r line; do
              if [[ $line =~ ^ok ]]; then
                test_name="${line#ok }"
                # Remove the test number from the beginning
                test_name="${test_name#* }"
                echo "| ✅ | ${test_name} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
              elif [[ $line =~ ^not\ ok ]]; then
                test_name="${line#not ok }"
                # Remove the test number from the beginning
                test_name="${test_name#* }"
                echo "| ❌ | ${test_name} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
              fi
            done < test.tap
          else
            echo "| ⚠️ | No test results found | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
          fi

  confirm-pass:
    needs: [nf-test, pipeline-tests]
    if: always()
    runs-on: # use self-hosted runners
      - runs-on=$-confirm-pass
      - runner=2cpu-linux-x64
    steps:
      - name: One or more tests failed
        if: ${{ contains(needs.*.result, 'failure') }}
        run: exit 1

      - name: One or more tests cancelled
        if: ${{ contains(needs.*.result, 'cancelled') }}
        run: exit 1

      - name: All tests ok
        if: ${{ contains(needs.*.result, 'success') }}
        run: exit 0

      - name: debug-print
        if: always()
        run: |
          echo "::group::DEBUG: `needs` Contents"
          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
          echo "::endgroup::"

      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
        if: always()
        run: |
          ls -la ./
          rm -rf ./* || true
          rm -rf ./.??* || true
          ls -la ./