genome test is now correct #3

	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: Checkout code
	uses: actions/checkout@v4
	- name: Set up SSH # for cloning private test_sequencing_runs repo
	uses: webfactory/ssh-agent@v0.8.0
	with:
	ssh-private-key: ${{ secrets.ACTIONS_SSH_PRIVATE_KEY }}
	- name: Setup miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	auto-update-conda: true
	miniforge-variant: Mambaforge
	channels: conda-forge, bioconda, defaults
	auto-activate-base: true
	use-mamba: true
Check failure on line 44 in .github/workflows/test.yml View workflow run for this annotation GitHub Actions / .github/workflows/test.yml Invalid workflow file `You have an error in your yaml syntax on line 44`
	- name: Install Nextflow
	run: conda install -y -c bioconda nextflow=${{ matrix.NXF_VER }}
	- name: Run nf test
	run: \|
	sudo apt-get install libxml2-utils
	bash run_test.sh

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