add conda channels for samtools, scanpy, muon #79

	name: hadge test workflow
	on:
	push:
	pull_request:
	jobs:
	test_genetic:
	name: Run pipeline in genetic mode with test data
	runs-on: ubuntu-latest
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@v4
	- name: Setup conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	miniconda-version: "latest"
	channels: conda-forge, bioconda
	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v1
	- name: Set up Python to install gdown
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: "pip"
	- name: Download test dataset
	run: bash ${GITHUB_WORKSPACE}/test_data/download_data.sh
	- name: Run pipeline with test data
	run: \|
	nextflow run ${GITHUB_WORKSPACE} -profile test,conda --mode genetic --souporcell False --generate_anndata False
	test_hashing:
	name: Run pipeline in hashing mode with test data
	runs-on: ubuntu-latest
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@v3
	- name: Setup conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	miniconda-version: "latest"
	channels: conda-forge, bioconda
	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v1
	- name: Set up Python to install gdown
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: "pip"
	- name: Download test dataset
	run: bash ${GITHUB_WORKSPACE}/test_data/download_data.sh
	- name: Run pipeline with test data
	run: \|
	nextflow run ${GITHUB_WORKSPACE} -profile test,conda --mode hashing --generate_anndata False

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