Update to README & allows pipeline to evaluate .Rtab gene presence ma… #9

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: CI

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

	jobs:
	test:

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11"]

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v3
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install .
	- name: run help
	run: \|
	panqc --help
	- name: run test data
	run: \|
	cd tests/data
	time panqc nrc -a TestSet1.InputAsmPaths.tsv -r TestSet1.pan_genome_reference.fa.gz -m TestSet1.gene_presence_absence.csv -o test_results/

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