adding serum_filter tool to workflow #3

	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
	environment-file: environment.yml
	activate-environment: cdiff_pipeline
	python-version: ${{ matrix.python-version }}

	# step 3
	- name: Install custom tool
	run: \|
	git clone https://github.com/ssi-dk/serum_readfilter
	cd serum_readfilter
	pip install .
	cd ..

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

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

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