update dependancies, implement vcf output #35

	name: CI

	# Controls when the action will run.
	on:
	# Triggers the workflow on push or pull request events but only for the main branch
	push:
	branches: [main, master]
	pull_request:
	branches: [main, master]

	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:

	# A workflow run is made up of one or more jobs that can run sequentially or in parallel
	jobs:
	Formatting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- uses: psf/black@stable
	with:
	options: ". --check --verbose"

	Linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- name: Test linting
	uses: snakemake/snakemake-github-action@v1.23.0
	with:
	directory: .
	snakefile: workflow/Snakefile
	args: "--lint"

	run-workflow:
	needs: Formatting
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- name: Test CI
	uses: snakemake/snakemake-github-action@v1.23.0
	with:
	directory: .
	snakefile: workflow/Snakefile

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