nextflow.yaml

name: Nextflow Test

on:
  push:
  pull_request:

jobs:
  build:
    uses: ./.github/workflows/build.yml

  nextflow:
    needs: build
    runs-on: ubuntu-latest
    steps:
    - name: Download Funnel
      uses: actions/download-artifact@v4
      with:
        name: funnel

    - name: Start Funnel
      run: |
        chmod +x ./funnel
        ./funnel server --LocalStorage.AllowedDirs $HOME run &
    
    - name: Setup Java
      uses: actions/setup-java@v4
      with:
        distribution: 'temurin'
        java-version: '21'

    - name: Install Nextflow
      run: |
        git clone https://github.com/nextflow-io/nextflow
        cd nextflow
        make compile

    - name: Install nf-canary and GA4GH-TES plugin
      run: |
        git clone https://github.com/seqeralabs/nf-canary
        cd nf-canary
        cat <<EOF >> nextflow.config
          plugins {
            id 'nf-ga4gh'
          }
          process.executor = 'tes'
          tes.endpoint = 'http://localhost:8000'
        EOF

    - name: Run nf-canary tests
      run: |
        ./nextflow/nextflow run nf-canary/main.nf