Updating docs to match the code. #775

	name: PHGv2 CI

	on:
	workflow_dispatch:
	pull_request:
	types:
	- opened
	- synchronize
	branches:
	- main
	paths:
	- 'src/**'

	jobs:
	test:
	name: PHGv2 CI
	runs-on: ubuntu-latest
	permissions:
	contents: read
	checks: write # See: https://github.com/mikepenz/action-junit-report/issues/23#issuecomment-1412597753
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-activate-base: true
	activate-environment: ""
	miniconda-version: "latest"
	- name: Run Conda
	run: conda env create --solver=libmamba --file src/main/resources/phg_environment.yml
	- name: Run RopeBWT Conda
	run: conda env create --solver=libmamba --file src/main/resources/phg_ropebwt_environment.yml
	- name: Set up Java
	uses: actions/setup-java@v3
	with:
	distribution: temurin
	java-version: 17
	cache: 'gradle'
	- name: Update applications.conf
	run: src/scripts/update_applications_conf.sh
	- name: Build with Gradle
	run: ./gradlew clean build --no-daemon
	- name: Run Kover XML report
	run: ./gradlew koverXMLReport
	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v3
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	with:
	files: build/reports/kover/report.xml
	- name: Publish Test Report
	uses: mikepenz/action-junit-report@v3
	if: success() \|\| failure()
	with:
	report_paths: '*/build/test-results/test/TEST-.xml'
	check_name: PHGv2 Test Report
	job_summary: true
	detailed_summary: true

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