ci: refactor e2e tests #1

	# Testing for pipeline python wrapper and scripts used inside rules

	name: Juno_mapping test

	on: [pull_request]

	env:
	KRAKEN_DEFAULT_DB: /home/runner/kraken-database

	jobs:
	singularity_end_to_end:
	runs-on: ${{ matrix.config.os }}
	strategy:
	fail-fast: false
	matrix:
	config:
	- {os: ubuntu-latest}
	name: Singularity Juno_mapping pipeline ${{ matrix.config.os }}

	steps:
	- uses: actions/checkout@v2
	- uses: eWaterCycle/setup-singularity@v7
	with:
	singularity-version: 3.8.7
	- name: Install Conda environment with Micromamba
	uses: mamba-org/setup-micromamba@v1
	with:
	cache-downloads: true
	environment-file: envs/juno_mapping.yaml
	- name: Cache minikraken
	id: cache-minikraken
	uses: actions/cache@v3
	with:
	path: ${{ env.KRAKEN_DEFAULT_DB }}
	key: minikraken-${{ runner.os }}
	- name: Download k2 database
	if: steps.cache-minikraken.outputs.cache-hit != 'true'
	run: \|
	mkdir -pv ${{ env.KRAKEN_DEFAULT_DB }}
	cd ${{ env.KRAKEN_DEFAULT_DB }}
	curl -k https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20220908.tar.gz > k2_viral_20220908.tar.gz
	tar zxvf k2_viral_20220908.tar.gz
	ls -lh
	- name: Conda list
	shell: bash -l {0}
	run: conda list
	- name: Test juno_mapping pipeline using singularity.
	shell: bash -l {0}
	run: pytest -v tests/test_pipeline_singularity.py
	- name: Test the juno_mapping wrapper
	shell: bash -l {0}
	run: pytest -v tests/test_juno_mapping.py

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