Fix Jinja2 undefined variables #20

	name: Run Integration Tests

	on:
	push:

	pull_request:
	types: [opened, reopened]

	jobs:
	build:
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -l {0}
	env:
	CRISPRESSO2_DIR: ${GITHUB_WORKSPACE}/../CRISPResso2_copy

	strategy:
	fail-fast: false

	steps:
	- uses: actions/checkout@v3

	- name: Set up Conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	mamba-version: "*"
	channels: conda-forge,bioconda,defaults
	auto-activate-base: false
	activate-environment: test_env
	environment-file: .github/envs/test_env.yml

	- name: Install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl
	pip install ydiff

	- name: Create directory for files
	run: \|
	mkdir ../CRISPResso2_copy
	cp -r * ../CRISPResso2_copy

	- name: Copy C2_tests repo
	uses: actions/checkout@v3
	with:
	repository: edilytics/CRISPResso2_tests
	token: ${{ secrets.ACCESS_CRISPRESSO2_TESTS }}
	# ref: '<BRANCH_NAME>' // Use this to specify a branch other than master

	- name: Run Basic
	run: \|
	make basic test

	- name: Run Params
	if: success() \|\| failure()
	run: \|
	make params test

	- name: Run Prime Editor
	if: success() \|\| failure()
	run: \|
	make prime-editor test

	- name: Run Batch
	if: success() \|\| failure()
	run: \|
	make batch test

	- name: Run Pooled
	if: success() \|\| failure()
	run: \|
	make pooled test

	- name: Run WGS
	if: success() \|\| failure()
	run: \|
	make wgs test

	- name: Run Compare
	if: success() \|\| failure()
	run: \|
	make compare test

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