Fixing GPU support with parabricks #99

	name: rna-seq-pop-single-end

	on: pull_request

	jobs:
	run-workflow:
	runs-on: ubuntu-latest
	steps:
	- name: Set up python3
	uses: actions/setup-python@v2
	with:
	python-version: '3.9' # Version range or exact version of a Python version to use, using SemVer's version range syntax

	- name: Checkout repository
	uses: actions/checkout@v2
	with:
	submodules: recursive

	- name: cp results book yamls
	run: cp docs/rna-seq-pop-results/_toc.yml docs/rna-seq-pop-results/_config.yml .test/docs/rna-seq-pop-results

	- name: cp landing page
	run: cp docs/rna-seq-pop-results/landing-page.md .test/docs/rna-seq-pop-results

	- name: Test workflow single-end
	uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
	with:
	directory: '.test'
	snakefile: 'workflow/Snakefile'
	args: "--cores 4 --use-conda --configfile .test/config/config_single_end.yaml --conda-cleanup-pkgs cache"
	stagein:
	"
	conda config --set channel_priority flexible
	"

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