Fix ci #14

	name: Run basic tests for Lemur

	on:
	push:
	branches: [ "main" ]
	pull_request:
	branches: [ "main" ]

	jobs:
	test:
	name: Test Lemur executable
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -l {0}

	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest, macos-latest]

	steps:
	- uses: actions/checkout@v3
	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	environment-file: ./lemur.yml
	activate-environment: lemur-env
	python-version: 3.9

	- name: Create output folder
	run: \|
	mkdir ./examples/example-output

	- name: Run Lemur
	run: ./lemur -i ./examples/example-data/example.fastq
	-o ./examples/example-output
	-d ./examples/example-db
	--tax-path ./examples/example-db/taxonomy.tsv
	-r species
	--verbose;

	- name: Check that output was produced
	id: check_files
	uses: andstor/[email protected]
	with:
	files: "./examples/example-output/P_rgs_df.tsv, ./examples/example-output/relative_abundance.tsv, ./examples/example-output/relative_abundance-species.tsv"
	fail: true

	- name: Check if outputed profile matches reference
	uses: LouisBrunner/[email protected]
	with:
	old: ./examples/example-output-ref/relative_abundance.tsv
	new: ./examples/example-output/relative_abundance.tsv
	mode: strict
	tolerance: same
	output: ./examples/example-output/relative_abundance_diff.txt

	- name: Archive production artifacts
	uses: actions/upload-artifact@v3
	with:
	name: lemur-out-log
	path: ./examples/example-output/*
	retention-days: 5

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