Disha/GitHub_ci_nf_test #47

	name: NF Tests
	on: [push, pull_request]

	env:
	NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
	NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
	NFTEST_VER: "0.9.0"
	jobs:
	test:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Set up JDK 11
	uses: actions/setup-java@v4
	with:
	java-version: '11'
	distribution: 'adopt'

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

	- name: Install nf-test
	uses: nf-core/setup-nf-test@v1
	with:
	version: ${{ env.NFTEST_VER }}

	- name: Setup apptainer
	uses: eWaterCycle/setup-apptainer@main

	- name: Set up Singularity
	run: \|
	mkdir -p $NXF_SINGULARITY_CACHEDIR
	mkdir -p $NXF_SINGULARITY_LIBRARYDIR

	- name: Set up Python
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
	with:
	python-version: "3.11"

	- name: Run Tests
	run: nf-test test --ci #this is used to prevent updating the snapshot

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