wes and wgs samples in hail search #518

	name: Hail Search Unit Tests

	# Run the test suite on pushes (incl. merges) to master and dev
	# Run the test suite when a PR is opened, pushed to, or reopened
	on:
	push:
	branches:
	- master
	- dev
	paths:
	- 'hail_search/**'
	pull_request:
	types: [opened, synchronize, reopened]
	paths:
	- 'hail_search/**'

	jobs:
	hail_search:
	runs-on: ubuntu-latest
	container: hailgenetics/hail:0.2.128

	steps:
	- uses: actions/checkout@v2
	- name: Install dependencies
	run: \|
	python3 -m pip install --upgrade pip wheel
	pip install -r hail_search/requirements-test.txt
	- name: Run coverage tests
	run: \|
	export HAIL_SEARCH_DATA_DIR=./hail_search/fixtures
	export REFERENCE_DATASETS_DIR=./hail_search/fixtures/reference_data
	export MAX_GENE_INTERVALS=3
	export MACHINE_MEM=24
	export JAVA_OPTS_XSS=16M
	coverage run --source="./hail_search" --omit="./hail_search/__main__.py","./hail_search/test_utils.py" -m pytest hail_search/
	coverage report --fail-under=99

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