test.yml

name: Test

on:
  push:
    branches:
      - master
      - dev
  pull_request:
    branches:
      - master

env:
  JAVA_VERSION: 17
  JAVA_DISTRO: zulu

jobs:
  pipeline-test:
    name: Pipeline tests
    runs-on: ubuntu-latest
    needs: workflow-test

    strategy:
      fail-fast: false
      matrix:
        profile:
          - gemflux
          - starrsem
          - starflux
          - markdup
          - rmdup
          - ihec

    steps:
      - uses: actions/checkout@v4
      - name: Set up Java
        uses: actions/setup-java@v4
        with:
          distribution: ${{ env.JAVA_DISTRO }}
          java-version: ${{ env.JAVA_VERSION }}
          java-package: jre
      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v2
      - name: Install nf-test
        uses: nf-core/setup-nf-test@v1
      - name: Run tests
        run: nf-test test --tag pipeline --profile +${CI_PROFILE}
        env:
          CI_PROFILE: ${{ matrix.profile }}

  workflow-test:
    name: Workflow tests
    runs-on: ubuntu-latest
    needs: module-test

    steps:
      - uses: actions/checkout@v4
      - name: Set up Java
        uses: actions/setup-java@v4
        with:
          distribution: ${{ env.JAVA_DISTRO }}
          java-version: ${{ env.JAVA_VERSION }}
          java-package: jre
      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v2
      - name: Install nf-test
        uses: nf-core/setup-nf-test@v1
      - name: Run tests
        run: nf-test test --tag workflow

  module-test:
    name: Module tests
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
      - name: Set up Java
        uses: actions/setup-java@v4
        with:
          distribution: ${{ env.JAVA_DISTRO }}
          java-version: ${{ env.JAVA_VERSION }}
          java-package: jre
      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v2
      - name: Install nf-test
        uses: nf-core/setup-nf-test@v1
      - name: Run tests
        run: nf-test test --tag module