nf-core-pixelator-tests.yml

#schema: https://github.com/softprops/github-actions-schemas/blob/master/workflow.json
name: "nf-core/pixelator integration tests"

on:
  workflow_dispatch:

env:
  ANNOY_COMPILER_ARGS: "-DANNOYLIB_MULTITHREADED_BUILD,-mno-avx512f"

jobs:
  pre_job:
    continue-on-error: true
    runs-on: ubuntu-latest
    # Map a step output to a job output
    outputs:
      should_skip: ${{ steps.skip_check.outputs.should_skip }}
      paths_result: ${{ steps.skip_check.outputs.paths_result }}
    steps:
      - id: skip_check
        uses: fkirc/skip-duplicate-actions@v5
        if: ${{ !github.event.act }}
        with:
          concurrent_skipping: "same_content_newer"
          skip_after_successful_duplicate: "true"
          do_not_skip: '["workflow_dispatch"]'
          paths_filter: |
            pixelator:
              paths:
                - 'pyproject.toml'
                - 'poetry.lock'
                - 'src/pixelator/**'
                - '**/Taskfile.yml'
                - '.github/**'
              paths_ignore:
                - 'tests/**'


  test:
    name: Test default profile
    if: github.event.act || needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).pixelator.should_skip
    runs-on: ubuntu-latest
    needs: [pre_job]
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - name: Checkout pixelator
        uses: actions/checkout@v4

      - name: Checkout nf-core-pixelator
        uses: actions/checkout@v4
        with:
          repository: PixelgenTechnologies/nf-core-pixelator
          ref: pixelator-next
          path: nf-core-pixelator

      - name: Install Java
        uses: actions/setup-java@v4
        with:
          distribution: 'microsoft'
          java-version: '21'

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "latest-stable"

      - name: Setup conda environment caching
        uses: actions/cache@v3
        with:
          path: ${{ env.CONDA }}/envs
          key:
            conda-${{ runner.os }}--${{ runner.arch }}--${{ env.CACHE_NUMBER }}--${{ hashFiles('environment.yml') }}
        env:
          # Increase this value to reset cache if environment.yml has not changed
          CACHE_NUMBER: 0
        id: cache-conda

      - name: Setup conda environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: pixelator
          miniforge-version: latest
          channels: conda-forge,bioconda,defaults
          use-mamba: true
          environment-file: environment.yml

      - name: Install pixelator
        run: pip install -e .

      - name: Run nf-core/pixelator default profile with current pixelator
        env:
          PIPELINE_SOURCE_DIR: ./nf-core-pixelator
        run: |
          task test-nf-core-pixelator