Merge pull request #142 from maxulysse/fix_dbsnp_known_indels_usage #323

	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:
	name: Run pipeline with test data
	# 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 == 'nf-core/rnavar') }}"
	runs-on: ubuntu-latest
	strategy:
	matrix:
	NXF_VER:
	- "23.04.0"
	- "latest-everything"
	test:
	- "default"
	- "annotation"
	- "removeduplicates"
	- "skipbasecalib"
	- "bamcsiindex"
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

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

	- name: Disk space cleanup
	uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: "3.x"

	- name: Install dependencies
	run: python -m pip install --upgrade pip pytest-workflow

	- name: Run pipeline with tests settings
	run: TMPDIR=~ PROFILE=docker pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes

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