Annotate and rank SNVs per family #1509

	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]
	workflow_dispatch:

	env:
	NXF_ANSI_LOG: false
	NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
	NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
	NFTEST_VER: "0.9.2"

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

	permissions:
	checks: write

	jobs:
	test:
	name: ${{ matrix.tags }} \| ${{ matrix.profile }} \| NF-${{ matrix.NXF_VER }}
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	NXF_VER:
	- "24.04.2"
	- "latest-everything"
	tags:
	- "samplesheet"
	- "samplesheet_multisample_bam"
	- "samplesheet_multisample_ont_bam"
	- "SHORT_VARIANT_CALLING"
	- "SNV_ANNOTATION"
	- "CALL_SVS"
	- "ANNOTATE_SVS"
	- "RANK_VARIANTS"
	- "CALL_REPEAT_EXPANSIONS"
	- "METHYLATION"
	profile:
	- "docker"

	steps:
	- name: Check out pipeline code
	uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
	with:
	fetch-depth: 0

	- name: Set up Nextflow
	uses: nf-core/setup-nextflow@v2
	with:
	version: "${{ matrix.NXF_VER }}"

	- uses: nf-core/setup-nf-test@v1
	with:
	version: ${{ env.NFTEST_VER }}
	install-pdiff: true

	- uses: actions/setup-python@v4
	with:
	python-version: "3.11"
	architecture: "x64"

	- name: Run nf-test
	run: \|
	nf-test test \
	--ci \
	--changed-since HEAD^ \
	--verbose \
	--tag ${{ matrix.tags }} \
	--profile "+${{ matrix.profile }}" \
	--junitxml=test.xml

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