nf-test.yml

name: Run nf-tests
on:
  pull_request:
    paths-ignore:
      - "docs/**"
      - "**/meta.yml"
      - "**/*.md"
      - "**/*.png"
      - "**/*.svg"
  release:
    types: [published]
  workflow_dispatch:
    inputs:
      runners:
        description: "Runners to test on"
        type: choice
        options:
          - "ubuntu-latest"
          - "self-hosted"
        default: "ubuntu-latest"

# 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: "0.9.3"
  NFT_WORKDIR: "~"
  NXF_ANSI_LOG: false
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
  # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
  NXF_VER: "24.10.5"

jobs:
  get-shards:
    runs-on:
      - runs-on=${{ github.run_id }}-nf-test-get-shards
      - runner=2cpu-linux-x64
    name: "Get Shards"
    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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
        with:
          fetch-depth: 0

      - name: run nf-test-shard action
        id: set-shards
        uses: ./.github/actions/nf-test-shard
        env:
          NFT_VER: ${{ env.NFT_VER }}
        with:
          tags: "cpu"
          max_shards: 15

      - name: Set outputs
        id: set-outputs
        run: |
          echo "shard=${{ steps.set-shards.outputs.shard }}" >> $GITHUB_ENV
          echo "total_shards=${{ steps.set-shards.outputs.total_shards }}" >> $GITHUB_ENV

  nf-test:
    name: "Test | ${{ matrix.profile }} | ${{ matrix.shard }} | ${{ matrix.NXF_VER }} | ${{ matrix.filters }}"
    needs: [get-shards]
    runs-on: # use self-hosted runners
      - runs-on=${{ github.run_id }}-nf-test
      - runner=4cpu-linux-x64
      - image=ubuntu22-full-x64
    env:
      NXF_VER: ${{ matrix.NXF_VER }}
      NXF_ANSI_LOG: false

    # Only run on push if this is the nf-core dev branch (merged PRs)
    # and number of shards is greater than 0
    if: |
      needs.get-shards.outputs.total_shards > 0 &&
      (
        github.event_name != 'push' ||
        ( github.event_name == 'push' && github.repository == 'nf-core/methylseq' )
      )

    strategy:
      fail-fast: false
      matrix:
        profile: [conda, docker, singularity]
        shard: ${{ fromJson(needs.get-shards.outputs.shard) }}
        NXF_VER:
          - "25.04.0"
          - "latest-everything"
        filters: [pipeline]

    steps:
      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
        with:
          fetch-depth: 0

      - name: Run nf-test
        id: run_nf_test
        uses: ./.github/actions/nf-test
        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
        env:
          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
          NXF_VERSION: ${{ matrix.NXF_VER }}
        with:
          profile: ${{ matrix.profile }}
          shard: ${{ matrix.shard }}
          total_shards: ${{ needs.get-shards.outputs.total_shards }}
          filters: ${{ matrix.filters }}
          tags: "cpu"

      - name: Report test status
        if: ${{ always() }}
        run: |
          if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then
            echo "::error::Test with ${{ matrix.NXF_VER }} failed"
            # Add to workflow summary
            echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ needs.get-shards.outputs.total_shards }}" >> $GITHUB_STEP_SUMMARY
            if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then
              echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
            fi
            if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
              exit 1
            fi
          fi

  confirm-pass:
    runs-on:
      - runs-on=${{ github.run_id }}-confirm-pass
      - runner=2cpu-linux-x64
    needs: [nf-test]
    if: always()
    steps:
      - name: One or more tests failed (excluding latest-everything)
        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::"