patch - Concatenate Microbial fastq files #17714

	name: CG CI

	on:
	pull_request:
	push:
	branches:
	- master

	jobs:
	tests-coverage:
	runs-on: 8_core_linux

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

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"

	- name: Install and configure Poetry
	uses: snok/install-poetry@v1
	with:
	virtualenvs-create: false

	- name: Cache dependencies
	uses: actions/cache@v4
	id: cache
	with:
	path: ${{ env.pythonLocation }}
	key: ${{ env.pythonLocation }}-${{ hashFiles('**/poetry.lock') }}

	- name: Install Dependencies
	if: steps.cache.outputs.cache-hit != 'true'
	run: poetry install --no-interaction

	- name: Test with Pytest & Coveralls
	run: \|
	pytest -n logical --cov=cg/
	coveralls
	env:
	COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}

	finish:
	needs: tests-coverage
	runs-on: ubuntu-latest
	steps:
	- name: Coveralls Finished
	uses: coverallsapp/[email protected]
	with:
	github-token: ${{ secrets.github_token }}
	parallel-finished: true

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