Tests

fix for reading data from a folder #33

	name: Tests

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

	jobs:
	tests:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python 3.11
	uses: actions/setup-python@v2
	with:
	python-version: 3.11
	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH
	- name: Install dependencies
	run: \|
	conda install -c conda-forge mamba
	# - name: Lint with flake8
	# run: \|
	# mamba install flake8
	# # 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: Setup snakemake and workflow dependencies
	run: \|
	mamba install -c conda-forge -c bioconda pytest snakemake singularity snakefmt
	pip install .
	- name: Lint with snakemake and snakefmt
	run: \|
	snakemake --lint
	snakefmt workflow
	- name: Integration dry-run test
	run: \|
	snakemake -np

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