Add exome depth functionality as per v44.8.0 #146

	name: Automated scripts

	on:
	push:
	branches:
	- master
	- Production
	- 'feature/**'
	- 'v4*'
	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.10.6']

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python3 -m pip install --upgrade pip
	pip3 install flake8==6.0.0 wheel==0.38.4 pytest==7.2.1
	pip3 install -r requirements.txt
	echo "dummytoken" > /home/runner/work/.dnanexus_auth_token
	echo "dummypw" > /home/runner/work/.amazon_email_pw
	echo "dummyuser" > /home/runner/work/.amazon_email_username
	# - name: Lint with flake8
	# run: \|
	# # stop the build if there are:
	# # - syntax errors (E9)
	# # - common assertion and comparison gotchas (F63)
	# # - control flow gotchas (F7)
	# # - undefined names (F82)
	# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	# flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	# We do not want it to run the email tests because the credentials are not stored in GitHub
	run: \|
	python3 -m pytest -v -k 'not email and not test_bcl2fastq_installed_pass'

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