Updated bowtie2 setting to be compatible with long reads #25

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

	name: Python application

	on:
	push:
	branches: [ "master", "v2.0.0" ]
	pull_request:
	branches: [ "master", "v2.0.0" ]

	permissions:
	contents: read

	jobs:
	build:

	runs-on: ubuntu-22.04

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.12
	uses: actions/setup-python@v4
	with:
	python-version: "3.12"
	- name: Install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install samtools bowtie2 mash bcftools ncbi-blast+ seqtk libcurl4-openssl-dev libssl-dev ca-certificates -y
	sudo apt-get install python3-pip python3-dev python3-pandas python3-requests python3-biopython -y
	python3 -m pip install --upgrade pip setuptools
	pip3 install pytest
	if [ -f requirements.txt ]; then
	pip3 install -r requirements.txt;
	else
	pip3 install -e .
	fi
	ectyper_init
	- name: Test with pytest
	run: \|
	pytest -o log_cli=true --basetemp=tmp-pytest

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