Merge pull request #91 from AfshinLab/add-testdata #529

	name: CI

	on:
	push:
	branch:
	- main
	pull_request:
	branch:
	- main
	schedule:
	- cron: 0 7 10 * *

	jobs:
	Linting:
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v3
	- name: Setup Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.6
	architecture: x64
	- name: Install flake8
	run:
	pip install flake8
	- name: Run flake8
	run: \|
	flake8 src/ tests/
	flake8 --select=W292 --filename '.yaml,.yml'

	Testing:
	needs:
	- Linting
	name: Run pipeline
	timeout-minutes: 15
	runs-on: ubuntu-20.04
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@v3
	- uses: conda-incubator/setup-miniconda@v3
	with:
	miniforge-version: latest
	environment-file: environment.linux-64.lock
	- name: Install test deps
	run: \|
	mamba install pytest
	# Bioconda build for deepvariant no working currently
	# see:
	# - https://github.com/bioconda/bioconda-recipes/issues/30310
	# - https://github.com/nf-core/modules/issues/1754
	# mamba install deepvariant=1.3.0
	- name: Install BLR
	run: pip install .
	- name: Run tests
	run: \|
	tests/run.sh

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