nf-test.yml

name: Run nf-test
on:
  push:
    branches:
      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
      - "renovate/**" # branches Renovate creates
  pull_request:
    branches: [master]
  merge_group:
    types: [checks_requested]
    branches: [master]
  workflow_dispatch:
    inputs:
      runners:
        description: "Runners to test on"
        type: choice
        options:
          - "ubuntu-latest"
          - "self-hosted"
        default: "self-hosted"

# 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 }}
  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
  NFT_VER: "0.9.2"
  NXF_ANSI_LOG: false
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
  NXF_VER: "24.10.2"

jobs:
  nf-test-changes:
    name: nf-test-changes
    runs-on: ubuntu-latest
    outputs:
      # Expose detected tags as 'modules' and 'workflows' output variables
      paths: ${{ steps.list.outputs.components }}
      modules: ${{ steps.components.outputs.modules }}
      subworkflows: ${{ steps.components.outputs.subworkflows}}
      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: List nf-test files
        id: list
        uses: adamrtalbot/detect-nf-test-changes@de3c3c8e113031b4f15a3c1104b5f135e8346997 # v0.0.6
        with:
          head: ${{ github.sha }}
          base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }}
          n_parents: 0
          exclude_tags: "gpu"

      - name: Separate modules and subworkflows
        id: components
        run: |
          echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT
          echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT

      - name: get number of shards
        id: set-shards
        if: ${{ steps.list.outputs.components != '[]' }}
        uses: ./.github/actions/get-shards
        env:
          NFT_VER: ${{ env.NFT_VER }}
        with:
          max_shards: 15
          paths: "${{ join(fromJson(steps.list.outputs.components ), ' ') }}"

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

  nf-test:
    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
    name: "Test | ${{ matrix.profile }} | ${{ matrix.shard }}"
    needs: [nf-test-changes]
    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
    strategy:
      fail-fast: false
      matrix:
        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
        profile: [conda, docker_self_hosted, singularity]
    env:
      NXF_ANSI_LOG: false
      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
    outputs:
      filtered_paths: ${{ steps.filter.outputs.filtered_paths }}

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

      - name: Filter paths
        id: filter
        run: |
          PATHS='${{ needs.nf-test-changes.outputs.paths }}'
          FILTERED=$(jq -n -c \
            --arg profile "${{ matrix.profile }}" \
            --argjson input_paths "$PATHS" \
            '
            def get_skip_list: inputs | .[$profile] // [];

            # Get skip list and filter
            get_skip_list as $skip_patterns |

            # Debug output
            ($skip_patterns | "Skip patterns: " + (map("  - " + .) | join(","))) |
            debug |

            # Do the actual filtering
            $input_paths | map(
              . as $path |
              select($skip_patterns | all(. as $pattern | ($path | startswith($pattern)) | not))
            ) as $result |

            # Debug what was skipped
            (if ($input_paths - $result) | length > 0 then
              "Skipped: " + (($input_paths - $result) | map("  - " + .) | join(","))
            else
              "No paths skipped"
            end) |
            debug |

            $result
            ' .github/skip_nf_test.json)

          echo "filtered_paths=${FILTERED}" >> $GITHUB_OUTPUT

      - name: Run nf-test Action
        if: ${{steps.filter.outputs.filtered_paths != '[]'}}
        uses: ./.github/actions/nf-test-action
        env:
          SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
          SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
          SENTIEON_AUTH_MECH: "GitHub Actions - token"
        with:
          profile: ${{ matrix.profile }}
          shard: ${{ matrix.shard }}
          total_shards: ${{ env.TOTAL_SHARDS }}
          paths: "${{ join(fromJson(steps.filter.outputs.filtered_paths), ' ') }}"

  confirm-pass:
    runs-on: ubuntu-latest
    needs: [nf-test]
    if: always()
    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: If no tests run, but filtered_paths was not empty and no tests succeeded, fail
        if: ${{ needs.nf-test.outputs.filtered_paths != '[]' && !contains(needs.*.result, 'success') }}
        run: exit 1

      - 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 "DEBUG: toJSON(needs.nf-test.outputs.filtered_paths) = ${{ needs.nf-test.outputs.filtered_paths }}"
          echo "::endgroup::"