test

Workaround for srst2 mkfifo failure when using latest Nextflow and Singularity #62

	# Runs test related tasks.

	name: test

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

	jobs:
	test:

	runs-on: ubuntu-22.04

	steps:
	- uses: actions/checkout@v2
	- uses: actions/setup-python@v4
	with:
	python-version: 3.9
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest pytest-cov
	pip install biopython pandas
	- 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: \|
	python3 -m pytest --cov=./ --cov-report=xml
	- uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	env_vars: OS,PYTHON
	name: codecov-upload
	fail_ci_if_error: true
	verbose: true
	- uses: actions/setup-java@v3
	with:
	distribution: 'zulu'
	java-version: '17'
	- name: Install Nextflow
	run: \|
	# Install latest version of Nextflow
	curl -s https://get.nextflow.io \| bash
	sudo mv nextflow /usr/bin
	- name: Regression tests
	run: ./tests/regression_tests.sh

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