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:
  test:
    name: Run workflow tests
    # 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/methylseq') }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        # Nextflow versions: check pipeline minimum and current latest
        nxf_ver: ['20.07.1', '21.03.0-edge']
        aligner: ['bismark', 'bismark_hisat', 'bwameth']
        include:
          - aligner: 'bismark'
            ref_index: --bismark_index results/reference_genome/BismarkIndex/
          - aligner: 'bismark_hisat'
            ref_index: --bismark_index results/reference_genome/BismarkIndex/
          - aligner: 'bwameth'
            ref_index: --bwa_meth_index results/reference_genome/genome.fa
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

      - name: Check if Dockerfile or Conda environment changed
        uses: technote-space/get-diff-action@v4
        with:
          FILES: |
            Dockerfile
            environment.yml

      - name: Build new docker image
        if: env.MATCHED_FILES
        run: docker build --no-cache . -t nfcore/methylseq:1.6

      - name: Pull docker image
        if: ${{ !env.MATCHED_FILES }}
        run: |
          docker pull nfcore/methylseq:dev
          docker tag nfcore/methylseq:dev nfcore/methylseq:1.6

      - name: Install Nextflow
        env:
          CAPSULE_LOG: none
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/

      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --save_reference
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}}
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --skip_trimming --rrbs
