Checkpoint #13

	name: "Copilot Setup Steps"

	# Automatically run the setup steps when they are changed to allow for easy validation, and
	# allow manual testing through the repository's "Actions" tab
	on:
	workflow_dispatch:
	push:
	paths:
	- .github/workflows/copilot-setup-steps.yml
	pull_request:
	paths:
	- .github/workflows/copilot-setup-steps.yml

	jobs:

	copilot-setup-steps:
	runs-on: ubuntu-latest

	permissions:
	contents: read

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

	# More info on options: https://github.com/conda-incubator/setup-miniconda
	- name: Install conda dependencies for main env
	uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: ""
	auto-activate-base: true
	show-channel-urls: true
	auto-update-conda: true
	conda-remove-defaults: true

	- name: Create all conda envs
	shell: bash -l {0}
	run: \|
	conda env create -f envs/env.yaml
	conda activate tcrtrifold-experiments
	pip install -e .
	conda deactivate
	conda env create -f envs/nf-core.yaml

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