test

Before read from file commit #19

	name: test
	# Controls when the workflow will run:
	on:
	# Triggers the workflow on push to master branch, or on pull request
	# to any branch:
	push:
	branches:
	- master
	pull_request:

	jobs:

	# label of the job:
	tests:
	name: Tests
	# containers must run in Linux based operating systems:
	runs-on: ubuntu-latest
	# Do not ignore bash profile files. From:
	# https://github.com/marketplace/actions/setup-miniconda
	# This is needed to run conda. It prevents the error:
	# CommandNotFoundError: Your shell has not been properly configured
	# to use 'conda activate'.
	strategy:
	matrix:
	NXF_VER:
	- "23.04.1"
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- name: Setup miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	miniforge-variant: Mambaforge
	channels: conda-forge, bioconda, defaults
	auto-activate-base: true
	use-mamba: true
	- name: Checkout code
	uses: actions/checkout@v4
	- name: Setup Nextflow
	uses: nf-core/[email protected]
	- name: Run test script
	run: \|
	sudo apt-get install -y libxml2-utils samtools
	bash run_test.sh

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