ci-tests.yml

name: CI Tests

on:
  push:
    branches: [main]
  pull_request:

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
  cancel-in-progress: true

jobs:
  test:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Start Kraken Server
        run: |
          docker run -d --name kraken-server --network host \
            -v ${{ github.workspace }}/tests/test-data:/data \
            quay.io/biowilko/scylla:latest \
            kraken2_server --max-requests 4 --thread-pool 1 \
            --port 8080 --host-ip localhost \
            --db /data/database/testdb-kraken2/ \
            --confidence 0.05

      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "25.4.6"

      - name: Install nf-test
        run: |
          wget -qO- https://get.nf-test.com | bash
          sudo mv nf-test /usr/local/bin/

      - name: Run Tests
        run: nf-test test --ci --profile docker,local,ci --tag ci

      - name: upload logs
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: nf-test-work-dirs-${{ github.run_id }}
          include-hidden-files: true
          path: ./.nf-test/*
          retention-days: 1
          if-no-files-found: ignore