Fix module and workflow tests and snapshots #36

	name: Test

	on:
	push:
	branches:
	- master
	- dev
	pull_request:
	branches:
	- master

	env:
	JAVA_VERSION: 17
	JAVA_DISTRO: zulu

	jobs:
	pipeline-test:
	name: Pipeline tests
	runs-on: ubuntu-latest
	needs: workflow-test

	strategy:
	fail-fast: false
	matrix:
	profile:
	- gemflux
	- starrsem
	- starflux
	- markdup
	- rmdup
	- ihec

	steps:
	- uses: actions/checkout@v4
	- name: Set up Java
	uses: actions/setup-java@v4
	with:
	distribution: ${{ env.JAVA_DISTRO }}
	java-version: ${{ env.JAVA_VERSION }}
	java-package: jre
	- name: Setup Nextflow
	uses: nf-core/setup-nextflow@v2
	- name: Install nf-test
	uses: nf-core/setup-nf-test@v1
	- name: Run tests
	run: nf-test test --tag pipeline --profile +${CI_PROFILE}
	env:
	CI_PROFILE: ${{ matrix.profile }}

	workflow-test:
	name: Workflow tests
	runs-on: ubuntu-latest
	needs: module-test

	steps:
	- uses: actions/checkout@v4
	- name: Set up Java
	uses: actions/setup-java@v4
	with:
	distribution: ${{ env.JAVA_DISTRO }}
	java-version: ${{ env.JAVA_VERSION }}
	java-package: jre
	- name: Setup Nextflow
	uses: nf-core/setup-nextflow@v2
	- name: Install nf-test
	uses: nf-core/setup-nf-test@v1
	- name: Run tests
	run: nf-test test --tag workflow

	module-test:
	name: Module tests
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4
	- name: Set up Java
	uses: actions/setup-java@v4
	with:
	distribution: ${{ env.JAVA_DISTRO }}
	java-version: ${{ env.JAVA_VERSION }}
	java-package: jre
	- name: Setup Nextflow
	uses: nf-core/setup-nextflow@v2
	- name: Install nf-test
	uses: nf-core/setup-nf-test@v1
	- name: Run tests
	run: nf-test test --tag module

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