test.yml

name: Test

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

env:
  JAVA_VERSION: 17
  JAVA_DISTRO: zulu
  AWS_REGION: us-east-1
  
permissions:
  id-token: write   # This is required for requesting the JWT
  contents: read 
      
jobs:
  pipeline-test:
    name: Pipeline tests
    runs-on: ubuntu-latest
    needs: [module-test, 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: Configure AWS credentials
        uses: aws-actions/configure-aws-credentials@v4 # More information on this action can be found below in the 'AWS Credentials' section
        with:
          role-to-assume: arn:aws:iam::566365074765:role/github-actions-role
          aws-region: ${{ env.AWS_REGION }}
      - name: Login to Amazon ECR Public
        id: login-ecr-public
        uses: aws-actions/amazon-ecr-login@v2
        with:
          registry-type: public
      - 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