Detect doublets in ScPCA data #23

	# This is a workflow to run the doublet-detection module
	# This module has both an renv and a conda environment
	#
	# 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

	name: Run doublet-detection analysis module
	env:
	MODULE_PATH: analyses/doublet-detection
	AWS_DEFAULT_REGION: us-east-1

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

	on:
	workflow_dispatch:
	workflow_call:
	pull_request:
	branches:
	- main
	paths:
	- analyses/doublet-detection/**

	jobs:
	run-module:
	if: github.repository_owner == 'AlexsLemonade'
	runs-on: ubuntu-latest
	container: public.ecr.aws/openscpca/doublet-detection:latest
	defaults:
	run:
	shell: bash -el {0}

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

	- name: Download test data in SCE format
	run: \|
	conda activate openscpca-doublet-detection
	./download-data.py --test-data --format SCE

	- name: Run doublet-detection module
	run: \|
	projects=$(basename -a data/current/SCPCP*)

	cd ${MODULE_PATH}
	for project in $projects; do
	bash run_doublet-detection-scpca.sh $project
	done

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