Snakedeploy Tests #3

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Workflow file for this run

.github/workflows/snakedeploy_tests.yaml at 8f557a9

	name: Snakedeploy

	on:
	push:
	pull_request:

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}

	jobs:
	runtime_tests:
	env:
	THREADS: 5

	strategy:
	max-parallel: 5
	fail-fast: false
	matrix:
	# python-version: [ "3.11"]
	virus: ["hiv"]
	#, "sars-cov-2"]

	runs-on: ubuntu-latest

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Checkout test data
	uses: actions/checkout@v3
	with:
	sparse-checkout: \|
	tests
	sparse-checkout-cone-mode: false
	lfs: false
	# NOTE to save on bandwidth costs, GitHub Action will not use GitHub's own LFS

	- name: Install conda environment dependencies
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-version: latest
	miniforge-variant: Mambaforge
	# python-version: ${{ matrix.python-version }}
	mamba-version: "*"
	channels: conda-forge,bioconda
	channel-priority: strict
	activate-environment: snakemake
	auto-update-conda: true
	environment-file: tests/conda_snakedeploy_env.yaml

	- name: Snakedeploy
	# snakedeploy will issue error message if workflow/ or config/ exist, i.e. if tests/ was not sparsely checked out
	run: \|
	snakedeploy deploy-workflow "$(git remote get-url origin)" . --branch "$(git rev-parse HEAD)"

	- name: Configure
	run: \|
	virus="${{ matrix.virus }}"
	threads="${THREADS}"
	trim_primers="false"

	# samples data
	data_root="tests/data/${virus}"
	mkdir -p samples
	mv -v "${data_root}"/*/ samples/

	if [ -e "${data_root}/samples.tsv" ]; then
	mv -v "${data_root}/samples.tsv" samples/
	# automatically turn trimming on if 4-columns format in TSV
	# shellcheck disable=SC2162
	while read s b l p o; do
	# no proto?
	if [[ -z "${p}" ]]; then
	continue
	fi

	# proto => trim!
	trim_primers="true"
	echo "with trimming"
	break

	: "${s} ${b} ${l} ${o}" are unused
	done < "samples/samples.tsv"
	fi

	# configuration file
	cat > config/config.yaml <<CONFIG
	general:
	virus_base_config: "${virus}"

	output:
	snv: true
	local: true
	global: false
	visualization: true
	diversity: true
	QA: true
	upload: true
	trim_primers: ${trim_primers}

	upload:
	orig_cram: true

	snv:
	threads: ${threads}
	CONFIG

	# does this test data provides extra configuration options
	if [ -e "${data_root}/config-extra.yaml" ]; then
	echo "with extra config:"
	cat "${data_root}/config-extra.yaml"
	echo
	# recursively merge using go-yq
	yq eval-all --inplace '. as $item ireduce ({}; . * $item )' config/config.yaml "${data_root}/config-extra.yaml"
	fi

	# Display config
	echo
	echo "Configuration:"
	echo
	yq config/config.yaml

	- name: Run test
	run:
	echo "Run on ${THREADS} cores"
	PYTHONUNBUFFERED=1 snakemake \
	--use-conda \
	--cores "${THREADS}" \
	--dry-run

	echo
	cat config/samples.tsv
	echo

	PYTHONUNBUFFERED=1 snakemake \
	--use-conda \
	--cores "${THREADS}" \
	-p \
	--keep-going

	- name: Archive test results
	uses: actions/upload-artifact@v3
	with:
	name: test_output
	path: \|
	./*
	!./.git
	!./.snakemake/conda/*/
	if-no-files-found: ignore