update complex piped subprocess commands, needs testing #38

	name: Test Aviary with Setup-Miniconda From Marketplace
	on: [push, pull_request]

	jobs:
	miniconda:
	name: Miniconda ${{ matrix.os }}
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -l {0}
	strategy:
	matrix:
	python-version: ["3.10"]
	steps:
	- uses: actions/checkout@v2
	- name: Set up environment with Python ${{ matrix.python-version }}
	uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: test
	environment-file: aviary.yml
	python-version: ${{ matrix.python-version }}
	miniforge-variant: Mambaforge
	auto-activate-base: false
	channels: conda-forge,bioconda
	channel-priority: true
	- run: \|
	conda info
	conda list
	conda config --set channel_priority strict
	- name: Install Aviary
	run: \|
	pip install -e .
	- name: Run unit tests
	run: \|
	aviary -h
	python test/test_assemble.py
	python test/test_recover.py
	python test/test_run_checkm.py -b

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