Merge branch 'develop-0.5.6' of https://github.com/akikuno/DAJIN2 int… #1

	name: E2E test for Stx2 deletion

	on:
	push:

	jobs:
	build:
	runs-on: ${{ matrix.os }}
	strategy:
	max-parallel: 2
	matrix:
	os: [ubuntu-latest, macos-latest]
	python-version: ["3.x"]
	name: Python ${{ matrix.python-version }} on ${{ matrix.os }}

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v4

	- name: Set up Miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: ${{ matrix.python-version }}
	miniconda-version: "latest"
	activate-environment: test-env
	channels: bioconda, conda-forge, defaults

	- name: Create conda environment and install dependencies
	run: \|
	conda create -y -n env-dajin2 python=${{ matrix.python-version }} pip pytest
	conda activate env-dajin2
	pip install -e . # Install DAJIN2 in editable mode

	- name: Download example dataset
	run: \|
	if [ ! -d example_single ]; then
	curl -LJO https://github.com/akikuno/DAJIN2/raw/main/examples/example_single.tar.gz
	tar -xf example_single.tar.gz
	fi

	- name: Run DAJIN2 with parameters
	env:
	PYTHONPATH: src
	run: \|
	time DAJIN2 \
	--control example_single/control \
	--sample example_single/sample \
	--allele example_single/stx2_deletion.fa \
	--name stx2_deletion \
	--genome mm39 \
	--threads 4 \
	--debug \|\| exit 1

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