run workflow with conda envs #144

	name: run workflow with conda envs
	on:
	push:
	branches: [main, dev]
	pull_request:
	branches: [main, dev]
	release:
	types: [published]
	schedule:
	- cron: '0 3 * * 3,6'
	jobs:
	run-integration-tests-with-conda-install:
	name: ${{ matrix.os }} - Workflow with snakemake conda envs
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -el {0}
	strategy:
	fail-fast: false
	matrix:
	os: [
	"ubuntu-latest",
	"macos-13",
	# "windows-latest" # rrcovNA cannot be build from source on windows-server
	]
	python-version: ["3.10"]
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Set up Miniconda
	# ! change action https://github.com/mamba-org/setup-micromamba
	uses: conda-incubator/setup-miniconda@v3
	with:
	miniforge-variant: Mambaforge
	use-mamba: true
	channel-priority: disabled
	python-version: ${{ matrix.python-version }}
	environment-file: snakemake_env.yml
	activate-environment: snakemake
	auto-activate-base: true
	- name: inspect-conda-environment
	run: \|
	conda info
	conda list
	- name: Dry-run workflow
	run: \|
	cd project
	snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml -n --use-conda
	- name: Run demo workflow (integration test)
	continue-on-error: true
	run: \|
	cd project
	snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda
	- name: Run demo workflow again (in case of installation issues)
	run: \|
	cd project
	snakemake -p -c1 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda

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