longraredisease/.github/workflows/nf-test.yml at 7538ccb999df25707a40f8a8134f8bf04a90f67f · nf-core/longraredisease · GitHub

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name: nf-test
on:
  push:
    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:
  find-tests:
    runs-on: ubuntu-latest
    outputs:
      tags: ${{ steps.find.outputs.tags }}
    steps:
      - uses: actions/checkout@v4

      - name: get subworkflows
        id: find
        uses: ./.github/actions/find-tests

      - name: debug
        run: |
          echo ${{ steps.find.outputs.tags }}

  nf-test:
    name: "${{ matrix.tag }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }}"
    needs: [find-tests]
    runs-on:
      - "ubuntu-latest"
    strategy:
      fail-fast: false
      matrix:
        profile: [docker, singularity]
        tag: ${{ fromJson(needs.find-tests.outputs.tags) }}
        isMain:
          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
        exclude:
          - isMain: false
            profile: "singularity"
          - isMain: false
            tag: "samplesheet_target_regions_null"
        NXF_VER:
          - "24.04.2"
          - "24.10.5"
          - "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: Clean up Disk space
        if: startsWith(matrix.tag, 'samplesheet')
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
        with:
          android: true
          dotnet: false
          haskell: false
          large-packages: false
          docker-images: false
          swap-storage: false

      - name: Run nf-test
        uses: ./.github/actions/nf-test
        env:
          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
        with:
          profile: ${{ matrix.profile }}
          tags: ${{ matrix.tag }}
          shard: 1
          total_shards: 1

  confirm-pass:
    needs: [nf-test]
    if: always()
    runs-on:
      - "ubuntu-latest"
    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
        if: always()
        run: |
          ls -la ./
          rm -rf ./* || true
          rm -rf ./.??* || true
          ls -la ./