ci.yml

name: Test nf-core Modules

on:
  push:
    branches:
      - 'github_actions_mza'
  workflow_dispatch:
    inputs:
      runners:
        description: 'Runners to test on'
        type: choice
        options:
          - 'ubuntu-latest'
          - 'self-hosted'
        default: 'ubuntu-latest'

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'
  NXF_ANSI_LOG: false
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
  NXF_VER: '24.10.1'

jobs:
  discover-modules:
    name: Discover nf-core Modules with Tests
    runs-on: ubuntu-latest
    outputs:
      module_list: ${{ steps.get-modules.outputs.module_list }}
    steps:
      - name: Checkout Code
        uses: actions/checkout@v4

      - name: List nf-core Modules with Tests
        id: get-modules
        run: |
          modules=$(find modules/nf-core -type d -maxdepth 1 -mindepth 1 | while read module; do
            if [ -d "$module/tests" ]; then
              basename "$module"
            fi
          done | jq -R -s -c 'split("\n") | map(select(length > 0))')
          if [ "$modules" == "[]" ]; then
            echo "No modules with tests found!"
            exit 1
          fi
          echo "module_list=$modules" >> $GITHUB_OUTPUT
        shell: bash

      - name: Display discovered modules
        run: |
          echo "Discovered modules with tests:"
          echo '${{ steps.get-modules.outputs.module_list }}' | jq .
        shell: bash

  nf-test:
    needs: discover-modules
    runs-on: ${{ github.event.inputs.runners || 'ubuntu-latest' }}
    strategy:
      fail-fast: false
      matrix:
        module: ${{ fromJson(needs.discover-modules.outputs.module_list) }}
        profile: [singularity, docker, conda]
    name: '${{ matrix.profile }} | ${{ matrix.module }}'
    env:
      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
    steps:
      - name: Clean Workspace
        run: |
          rm -rf $GITHUB_WORKSPACE/*

      - name: Checkout Code
        uses: actions/checkout@v4
        with:
          fetch-depth: 1

      - name: Run nf-test Action
        uses: ./.github/actions/nf-test-action
        with:
          profile: ${{ matrix.profile }}
          module: ${{ matrix.module }}

      - name: Display Test Summary
        if: always()
        run: |
          echo "Test Summary for ${{ matrix.module }} (${{ matrix.profile }}):"
          cat modules/nf-core/${{ matrix.module }}/test.tap | grep -E '^(not )?ok'
        shell: bash