Major refactor + add Vardict caller #608

	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

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

	jobs:
	test_all:
	name: Run nf-test with ${{ matrix.test }}-${{ matrix.NXF_VER }}
	# Only run on push if this is the nf-core dev branch (merged PRs)
	if: "${{ github.event_name != 'push' \|\| (github.event_name == 'push' && github.repository == 'CenterForMedicalGeneticsGhent/nf-cmgg-germline') }}"
	runs-on: ubuntu-latest
	strategy:
	matrix:
	NXF_VER:
	- "23.04.0"
	- "latest-everything"
	test:
	- "vardict"
	- "haplotypecaller"
	- "fails"
	- "annotate_test"
	- "filter_test"
	- "gemini_test"
	- "full_wes"
	- "full_wgs"
	- "only_call"
	steps:
	- name: Free some space
	run: \|
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf /opt/ghc
	sudo rm -rf "/usr/local/share/boost"
	sudo rm -rf "$AGENT_TOOLSDIRECTORY"

	- name: Check out pipeline code
	uses: actions/checkout@v3

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v1
	with:
	version: "${{ matrix.NXF_VER }}"

	- name: Install nf-test
	run: \|
	conda install -c bioconda nf-test

	- name: Run pipeline with test data
	run: \|
	$CONDA/bin/nf-test test --tag ${{ matrix.test }} --junitxml=default.xml

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

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