change parameters #19

	name: Small Integration Tests

	on:
	push:
	branches: [ main, master ]
	pull_request:
	branches: [ main, master ]
	workflow_dispatch:

	permissions:
	contents: read

	jobs:
	quick-test:
	name: Quick Integration Test
	runs-on: ubuntu-latest
	timeout-minutes: 30

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Install system dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y \
	libcurl4-openssl-dev \
	libssl-dev \
	zlib1g-dev \
	libbz2-dev \
	liblzma-dev \
	samtools \
	bcftools

	- name: Install Rust toolchain
	uses: dtolnay/rust-toolchain@stable

	- name: Build project
	run: cargo build --release

	- name: Test help command
	run: \|
	cargo run --release -- --help \|\| true
	cargo run --release -- quick-start --help \|\| true
	cargo run --release -- filter --help \|\| true
	cargo run --release -- build --help \|\| true
	cargo run --release -- correct --help \|\| true
	cargo run --release -- call --help \|\| true
	cargo run --release -- asm --help \|\| true
	cargo run --release -- methyl --help \|\| true

	- name: Test Himito quick-start command
	run: \|
	if [ -f "test_data/HG005_100x.bam" ] && [ -f "test_data/HG005_100x.bai" ]; then
	cargo run --release -- quick-start \
	-i test_data/HG005_100x.bam \
	-c "chrM" \
	-k 21 \
	--sampleid HG005 \
	-r test_data/rCRS.fasta \
	--output-prefix test_output/himito_test \|\| echo "Himito test skipped - may require additional dependencies"
	else
	echo "Test data not available, skipping evaluate test"
	fi


	- name: Cleanup
	if: always()
	run: rm -rf test_output test_data

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