Add metacells to GHA and handle small data #4

	# This is a workflow to run the metacells 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 metacells analysis module
	env:
	MODULE_PATH: analyses/metacells
	AWS_DEFAULT_REGION: us-east-2

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

	on:
	workflow_dispatch:
	workflow_call:
	pull_request:
	branches:
	- main
	paths:
	- "analyses/metacells/**"

	jobs:
	run-module:
	if: github.repository_owner == 'AlexsLemonade'
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -el {0}

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

	# Downloading just one sample for initial testing
	- name: Download test data
	run: ./download-data.py --test-data --format AnnData --sample SCPCS000001

	- name: Set up conda
	uses: conda-incubator/setup-miniconda@v3

	- name: Install and activate locked conda environment
	run: \|
	conda install conda-lock
	conda-lock install --name test ${MODULE_PATH}/conda-lock.yml

	- name: Run analysis module
	run: \|
	cd ${MODULE_PATH}
	# run module script here
	bash run-metacells.sh

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