complete snakemake workflow #82

	# This modules will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: Python application

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install pytest cython pytest-cov pytest-xdist
	python -m pip install -e .
	- name: Test with pytest
	run: \|
	python -m pytest -n auto tests/ --junitxml=junit/test-results.xml --cov=lapa --cov-report=xml
	- uses: actions/upload-artifact@v2
	with:
	name: test-coverage
	path: coverage.xml

	upload-to-codecov:
	needs: [build]
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v2
	- name: Download artifacts
	uses: actions/download-artifact@v2
	- name: Upload to Codecov
	uses: codecov/codecov-action@v1

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