Replace singular cd aind-ephys-pipeline/pipeline in two steps #69

	name: Test Nextflow Pipeline

	on:
	pull_request:
	branches: [main]
	types: [synchronize, opened, reopened]
	jobs:
	test:
	runs-on: ubuntu-latest

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

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"

	- name: Free up disk space
	run: \|
	echo "Before cleanup:"
	df -h
	sudo rm -rf /usr/local/lib/android
	sudo rm -rf /opt/ghc
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /opt/hostedtoolcache
	echo "After cleanup:"
	df -h

	- name: Install packages
	run: \|
	python -m pip install --upgrade pip
	pip install spikeinterface neuroconv "pynwb<3"

	- name: Generate test NWB files
	run: \|
	python sample_dataset/create_test_nwb.py

	- name: Set up Nextflow
	uses: nf-core/setup-nextflow@v1
	with:
	version: latest-stable

	- name: Run Nextflow pipeline
	run: \|
	DATA_PATH="$(pwd)/sample_dataset/nwb" RESULTS_PATH="$(pwd)/sample_dataset/nwb/results" \
	nextflow -C "$(pwd)/.github/workflows/nextflow_test.config" run pipeline/main_multi_backend.nf \
	--params_file "$(pwd)/.github/workflows/params_test.json"

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