hello-clusters notebook: Perform and evaluate clustering #21

	# This is a workflow to run the hello-clusters module
	#
	# Analysis modules are run based on three triggers:
	# - Manual trigger
	# - On pull requests where code in the module has changed
	# - As a reusable workflow called from a separate workflow which periodically runs all modules
	#
	# At initialization, only the manual trigger is active

	name: Run hello-clusters analysis module
	env:
	MODULE_PATH: analyses/hello-clusters
	AWS_DEFAULT_REGION: us-east-2

	concurrency:
	# only one run per branch at a time
	group: "run_hello-clusters_${{ github.ref }}"
	cancel-in-progress: true

	on:
	workflow_dispatch:
	workflow_call:
	pull_request:
	branches:
	- main
	paths:
	- analyses/hello-clusters/**
	- "!analyses/hello-clusters/Dockerfile"
	- "!analyses/hello-clusters/.dockerignore"
	- .github/workflows/run_hello-clusters.yml

	jobs:
	run-module:
	if: github.repository_owner == 'AlexsLemonade'
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Set up R
	uses: r-lib/actions/setup-r@v2
	with:
	r-version: 4.4.0
	use-public-rspm: true

	- name: Set up pandoc
	uses: r-lib/actions/setup-pandoc@v2

	- name: Install additional system dependencies
	run: \|
	sudo apt-get install -y libcurl4-openssl-dev libglpk40

	- name: Set up renv
	uses: r-lib/actions/setup-renv@v2
	with:
	working-directory: ${{ env.MODULE_PATH }}

	- name: Download test data
	run: ./download-data.py --test-data --format SCE --samples SCPCS000001

	- name: Run analysis module
	run: \|
	cd ${MODULE_PATH}
	./run_hello-clusters.sh

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