ci.yml

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

concurrency:
  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
  cancel-in-progress: true

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:
        NXF_VER:
          - "22.10.1"
          - "latest-everything"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - 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: "22.10.3"
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        profiles:
          - "test_nodx_vc"
          - "test_nodx_stringtie"
          - "test_nodx_noaln"
          - "test_nodx_rnamod"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - 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: "22.10.3"
      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 }}

#