Yaml input #125

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Unit tests

	on:
	push:
	branches: [ "master" ]
	pull_request:
	branches: [ "master" ]

	permissions:
	contents: read

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python 3.8
	uses: actions/setup-python@v3
	with:
	python-version: "3.8"
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest tox
	sudo apt-get install -y minimap2 samtools
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Lint with flake8
	run: \|
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: \|
	python -m tox

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