2.1.1 PR (#113) #36

	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:1.2.1 \
	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 --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

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