test

Add in content need for tests to pass on Azure #62

	name: test
	on:
	push:
	branches: [main]
	paths-ignore:
	- "!*/.md"
	pull_request:
	branches: [main]
	paths-ignore:
	- "!*/.md"
	merge_group:
	types: [checks_requested]
	branches: [main]

	# Cancel if a newer run is started
	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	prettier:
	runs-on: ubuntu-latest
	steps:
	- name: Check out repository
	uses: actions/checkout@v3

	- name: Install NodeJS
	uses: actions/setup-node@v3

	- name: Install Prettier
	run: npm install -g prettier

	- name: Run Prettier --check
	run: prettier --check .

	nf-test:
	runs-on: ubuntu-20.04
	env:
	NXF_ANSI_LOG: false
	steps:
	- uses: actions/checkout@v3

	- uses: actions/setup-java@v3
	with:
	distribution: "temurin"
	java-version: "17"

	- name: Cache software installation
	id: cache-software
	uses: actions/cache@v3
	with:
	path: \|
	/usr/local/bin/nextflow
	/usr/local/bin/nf-test
	/home/runner/.nf-test/nf-test.jar
	key: ${{ runner.os }}-software-${{ github.workspace }}

	- name: Install Nextflow
	env:
	CAPSULE_LOG: none
	if: steps.cache-software.outputs.cache-hit != 'true'
	run: \|
	wget -qO- get.nextflow.io \| bash
	sudo mv nextflow /usr/local/bin/

	- name: Install nf-test
	if: steps.cache-software.outputs.cache-hit != 'true'
	run: \|
	wget -qO- https://code.askimed.com/install/nf-test \| bash
	sudo mv nf-test /usr/local/bin/
	nf-test update-plugins

	- name: Run pipeline and cache dependencies
	run: \|
	nextflow run main.nf

	# Test the module
	- name: Run nf-test
	run: \|
	java -version
	nf-test test --tap=test.tap

	- uses: pcolby/tap-summary@v1
	with:
	path: >-
	test.tap

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