Add BCLConvert support #65

	name: Run tests
	on: [push, pull_request]
	jobs:
	run-tests:
	runs-on: ubuntu-22.04
	env:
	NXF_VER: 21.04.1
	NXF_ANSI_LOG: false
	steps:
	- name: Check out repository code
	uses: actions/checkout@v2

	- name: Cache singularity images
	uses: actions/[email protected]
	with:
	path: work/singularity
	key: singularity-${{ hashFiles('config/nextflow_config/singularity.config') }}
	restore-keys: singularity-

	- name: Install Singularity
	uses: eWaterCycle/setup-singularity@v7
	with:
	singularity-version: 3.8.3

	- name: Install Nextflow
	env:
	CAPSULE_LOG: none
	run: \|
	curl -fsSL https://github.com/nextflow-io/nextflow/releases/download/v24.10.4/nextflow -o nextflow \| bash
	sudo mv nextflow /usr/local/bin/

	- name: Make Nextflow binary executable
	run: chmod +x /usr/local/bin/nextflow

	- name: Set up python
	uses: actions/setup-python@v2
	with:
	python-version: 3.13
	architecture: x64

	- name: Install build dependencies and upgrade pip
	run: \|
	# Install system packages needed to build wheels for packages like lxml as it's missig in pytho 3.13
	sudo apt-get update
	sudo apt-get install -y build-essential libxml2-dev libxslt1-dev zlib1g-dev
	# Install latest build tools and PEP 517 build dependencies
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install build hatchling setuptools-scm

	- name: Install test requirements
	run: \|
	# Install Python requirements for tests
	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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