Add tests for resfinderv4.5 fastq output resolves #86 #74

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

	name: test_package

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

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.7, 3.8]

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest
	pip install .
	- name: Lint hAMRonization library with flake8
	run: \|
	pushd hAMRonization
	# 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=20 --max-line-length=127 --statistics
	popd
	- name: Run sanity tests
	run: \|
	pushd test
	pytest
	popd
	- name: Run crude test of CLI parser for all tools
	run: \|
	pushd test
	bash run_integration_test.sh
	popd
	#- name: Validate all harmonized .json files with SALAD schema
	# run: \|
	# pip install schema_salad
	# pushd test/data
	# for f in *.harmonized.json; do schema-salad-tool ../../schema/antimicrobial_resistance_genomic_analysis_result.schema.yml ${f}; done

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