added files for make test #1

	name: ecoli food bourne infection workflow

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

	jobs:
	build:
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -l {0}
	strategy:
	matrix:
	os: ["ubuntu-latest"]
	python-version: ["3.11"]

	steps:
	# step 1: checkout repository
	- name: Checkout repository
	uses: actions/checkout@v3

	# step 2 use environment.yml dependencies to create conda environment
	- name: Set up miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}

	# step 3: Create the conda environment manually
	- name: Create conda environment
	run: \|
	conda create --name cdiff_pipeline picard gatk4 biopython ruamel.yaml kraken bwa samtools

	# step 4
	- name: Run test script
	run: \|
	conda activate cdiff_pipeline
	make test

	# consider adding the webhook to https://github.com/ssi-dk/bifrost_sp_cdiff/

Provide feedback