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]

env:
  NXF_ANSI_LOG: false
  CAPSULE_LOG: none

jobs:
  test:
    name: Run pipeline with test data
    # 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/nanoseq') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        # Nextflow versions
        include:
          # Test pipeline minimum Nextflow version
          - NXF_VER: "21.10.3"
            NXF_EDGE: ""
          # Test latest edge release of Nextflow
          - NXF_VER: ""
            NXF_EDGE: "1"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

      - name: Install Nextflow
        env:
          NXF_VER: ${{ matrix.NXF_VER }}
          # Uncomment only if the edge release is more recent than the latest stable release
          # See https://github.com/nextflow-io/nextflow/issues/2467
          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
        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 --outdir ./results

  profile:
    name: Run profile tests
    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}"
    runs-on: ubuntu-latest
    env:
      NXF_VER: "21.10.3"
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        profiles:
          - "test_bc_nodx"
          - "test_nobc_dx"
          - "test_nobc_nodx_vc"
          - "test_nobc_nodx_stringtie"
          - "test_nobc_nodx_noaln"
          - "test_nobc_nodx_rnamod"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - name: Run pipeline with different profiles
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profiles }},docker --outdir ./results

  parameters:
    name: Run parameter tests
    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nanoseq') }}"
    runs-on: ubuntu-latest
    env:
      NXF_VER: "21.10.3"
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        parameters:
          - "--aligner graphmap2"
          - "--skip_alignment"
          - "--skip_qc"
          - "--skip_quantification"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - name: Run pipeline with different parameters
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}

#
