Filter out empty fastqs #97

	name: Run tests
	on: [push, pull_request]
	jobs:
	run-tests:
	runs-on: ubuntu-22.04
	env:
	NXF_VER: 25.10.2
	NXF_ANSI_LOG: false
	steps:
	- name: Check out repository code
	uses: actions/checkout@v6

	- name: Cache singularity/apptainer images
	uses: actions/cache@v5.0.2
	with:
	path: work/singularity
	key: singularity-${{ hashFiles('config/nextflow_config/singularity.config') }}
	restore-keys: singularity-

	- name: Install apptainer
	uses: eWaterCycle/setup-apptainer@v2
	with:
	apptainer-version: 1.3.6

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v2
	with:
	version: 25.10.2

	- name: Set up python
	uses: actions/setup-python@v6
	with:
	python-version: 3.11
	architecture: x64

	- name: Install test requirements
	run: \|
	pip install -r requirements-dev.txt

	- name: Run tests
	run: pytest tests

	- name: Run Black code formatting check
	run: black --check .

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