name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  push:
    branches:
      - dev
  pull_request:
  release:
    types: [published]

jobs:
  ##############################
  ### SMALL INTEGRATION TEST ###
  ##############################
  test:
    name: Run standard pipeline test
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
    strategy:
      matrix:
        # Nextflow versions
        include:
          # Test pipeline minimum Nextflow version
          - NXF_VER: '21.10.3'
          # Test latest nextflow version
          - NXF_VER: ''
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/

      # Work around for the unexpected end of file error that github actions seems to get when downloading compressed
      # files during pipelie execution
      - name: Download data
        run: |
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

      - name: Run pipeline
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

  ##############################
  ### LARGE INTEGRATION TEST ###
  ##############################
  test_full_small:
    name: Run extended pipeline test
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
    strategy:
      matrix:
        # Nextflow versions: check pipeline minimum and current latest
        nxf_ver: ['21.10.3', '']
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/

      # Work around for the unexpected end of file error that github actions seems to get when downloading compressed
      # files during pipelie execution
      - name: Download data
        run: |
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip

  #####################################
  ### EDGE VERSION INTEGRATION TEST ###
  #####################################
  test_edge:
    name: Run standard pipeline test (edge version)
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ''
      NXF_EDGE: 1
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
          nextflow self-update

      # Work around for the unexpected end of file error that github actions seems to get when downloading compressed
      # files during pipelie execution
      - name: Download data
        run: |
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

  ##############################
  ###      UNIT TESTS        ###
  ##############################
  unit_tests:
    name: ${{ matrix.nxf_version }} ${{ matrix.tags }}
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
    runs-on: ubuntu-20.04
    env:
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
    strategy:
      fail-fast: false
      matrix:
        nxf_version: ['21.10.3', '']
        tags: ["samplesheet", "verify_output_input", "verify_output_align_short", "verify_output_align_long", "verify_output_peak_calling", "verify_output_reporting", "verify_output_save", "verify_output_skip"]
    steps:
      - uses: actions/checkout@v2

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: "3.x"

      - uses: actions/cache@v2
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: "3.x"

      - name: Install Python dependencies
        run: python -m pip install --upgrade pip pytest-workflow

      - uses: actions/cache@v2
        with:
          path: /usr/local/bin/nextflow
          key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
          restore-keys: |
            ${{ runner.os }}-nextflow-
      - name: Install Nextflow
        env:
          NXF_VER: ${{ matrix.nxf_version }}
          CAPSULE_LOG: none
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Run pytest-workflow
        run: pytest --tag ${{ matrix.tags }} --kwdof

      - name: Upload logs on failure
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
          path: |
            /tmp/pytest_workflow_*/*/.nextflow.log
            /tmp/pytest_workflow_*/*/log.out
            /tmp/pytest_workflow_*/*/log.err
            /tmp/pytest_workflow_*/*/work
