Use official nf-test CI #376

	name: nf-core CI
	# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
	on:
	push:
	branches:
	- dev
	pull_request:
	release:
	types: [published]

	env:
	NXF_ANSI_LOG: false
	NFT_VER: "0.8.4"
	NFT_WORKDIR: "~"
	NFT_DIFF: "pdiff"
	NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"

	concurrency:
	group: "${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}"
	cancel-in-progress: true

	jobs:
	test:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	shard: [1, 2, 3, 4]
	NXF_VER: ["23.04.0", ""]
	profile: ["docker"]
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
	with:
	fetch-depth: 0

	# - name: Set up JDK 11
	# uses: actions/setup-java@v2
	# with:
	# java-version: "11"
	# distribution: "adopt"

	- uses: actions/setup-python@v4
	with:
	python-version: "3.11"
	architecture: "x64"

	- name: Install pdiff to see diff between nf-test snapshots
	run: \|
	python -m pip install --upgrade pip
	pip install pdiff

	- uses: nf-core/setup-nextflow@v2
	with:
	version: "${{ matrix.NXF_VER }}"

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

	- name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
	run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} --changed-since HEAD^ --profile "+${{ matrix.profile }}"

	- name: Publish Test Report
	uses: mikepenz/action-junit-report@v3
	if: always() # always run even if the previous step fails
	with:
	report_paths: test.xml

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