nf-core-utils/.github/workflows/validation.yml at main · nf-core/nf-core-utils · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
name: Plugin Validation

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]

env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  NFT_DIFF: pdiff
  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
  NXF_ANSI_LOG: false
  NXF_AGENT_MODE: false
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
jobs:
  validation:
    name: Nextflow ${{ matrix.nextflow }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        # Latest patch of every supported stable line, plus the minimum supported version (25.10.4).
        nextflow: ["25.10.4", "25.10.8", "26.04.7", "26.10.2"]
    env:
      NXF_VER: ${{ matrix.nextflow }}

    steps:
      - name: Checkout code
        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1

      - name: Set up tools
        uses: jdx/mise-action@b44d12e7d0d8ee7461bb893e1b1993500433185b # v5.2.7
        with:
          version: 2026.11.5

      - name: Set up Gradle and cache
        uses: gradle/actions/setup-gradle@8da46b539cd8fe6ab27ca75128919a18d757604c # v6.4.1

      - name: Install snapshot diff formatter
        run: python -m pip install pdiff

      - name: Conda setup
        uses: conda-incubator/setup-miniconda@be893c923ea9cf1cf7cd510fbdde27c7e18cbdcb # v4.1.0
        with:
          auto-update-conda: true
          channels: conda-forge, bioconda
          channel-priority: strict
          conda-remove-defaults: true

      - name: Clean workspace
        run: mise run clean

      - name: Set NFT_WORKDIR dynamically
        run: echo "NFT_WORKDIR=$HOME" >> $GITHUB_ENV

      - name: Build and validate plugin
        run: |
          mise exec -- nextflow -version
          mise run validate

      - name: Upload validation artifacts
        if: always()
        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
        with:
          name: validation-results-${{ matrix.nextflow }}
          path: |
            validation/*/work/pipeline_info/
            validation/*/work/*.log
            validation/*/work/.nextflow.log
            validation/.nf-test/reports/
            validation/**/*.nf.test.snap
          retention-days: 7

      - name: Upload test logs
        if: failure()
        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
        with:
          name: validation-logs-${{ matrix.nextflow }}
          path: |
            validation/*/.nextflow.log
            validation/*/work/**/*.log
            validation/.nf-test/**/*.log
          retention-days: 7

  # Single required check, so matrix changes need no ruleset change
  ci-pass:
    name: CI pass
    needs: [validation]
    if: always()
    runs-on: ubuntu-latest
    steps:
      - name: Check the job results
        env:
          RESULTS: ${{ join(needs.*.result, ' ') }}
        run: |
          echo "$RESULTS"
          case "$RESULTS" in
            *failure*|*cancelled*) exit 1 ;;
          esac