action.yml

name: "nf-test Action"
description: "Runs nf-test with common setup steps"
inputs:
  profile:
    description: "Profile to use"
    required: true
  shard:
    description: "Shard number for this CI job"
    required: true
  total_shards:
    description: "Total number of test shards(NOT the total number of matrix jobs)"
    required: true
  paths:
    description: "Test paths"
    required: true
  tags:
    description: "Tags to pass as argument for nf-test --tag parameter"
    required: false
runs:
  using: "composite"
  steps:
    - name: Setup Nextflow
      uses: nf-core/setup-nextflow@v2
      with:
        version: "${{ env.NXF_VERSION }}"

    - name: Set up Python
      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
      with:
        python-version: "3.13"

    - name: Install nf-test
      uses: nf-core/setup-nf-test@v1
      with:
        version: "${{ env.NFT_VER }}"
        install-pdiff: true

    - name: Setup apptainer
      if: contains(inputs.profile, 'singularity')
      uses: eWaterCycle/setup-apptainer@main

    - name: Set up Singularity
      if: contains(inputs.profile, 'singularity')
      shell: bash
      run: |
        mkdir -p $NXF_SINGULARITY_CACHEDIR
        mkdir -p $NXF_SINGULARITY_LIBRARYDIR

    - name: Conda setup
      if: contains(inputs.profile, 'conda')
      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
      with:
        auto-update-conda: true
        conda-solver: libmamba
        conda-remove-defaults: true

    - name: Run nf-test
      shell: bash
      env:
        NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
      run: |
        nf-test test \
          --profile=+${{ inputs.profile }} \
          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
          --ci \
          --changed-since HEAD^ \
          --verbose \
          --tap=test.tap \
          --shard ${{ inputs.shard }}/${{ inputs.total_shards }}

          # Save the absolute path of the test.tap file to the output
          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT

    - name: Generate test summary
      if: always()
      shell: bash
      run: |
        # Add header if it doesn't exist (using a token file to track this)
        if [ ! -f ".summary_header" ]; then
          echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
          echo "" >> $GITHUB_STEP_SUMMARY
          echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
          echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
          touch .summary_header
        fi

        if [ -f test.tap ]; then
          while IFS= read -r line; do
            if [[ $line =~ ^ok ]]; then
              test_name="${line#ok }"
              # Remove the test number from the beginning
              test_name="${test_name#* }"
              echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
            elif [[ $line =~ ^not\ ok ]]; then
              test_name="${line#not ok }"
              # Remove the test number from the beginning
              test_name="${test_name#* }"
              echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
            fi
          done < test.tap
        else
          echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
        fi

    - name: Clean up
      if: always()
      shell: bash
      run: |
        sudo rm -rf /home/ubuntu/tests/