Tests

ci: conda strict channel priority #3

	# Run tests over snakefile workflow
	---
	name: Tests

	on: # yamllint disable-line rule:truthy
	push:
	branches: [main, devel]
	pull_request:
	branches: [main, devel]

	env:
	CACHE_NUMBER: 0 # Increment this number to invalidate the cache

	jobs:

	Pre-Commit:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	lfs: 'true'
	- name: Run pre-commit on all files
	uses: pre-commit/[email protected]
	with:
	extra_args: --all-files

	Testing:
	runs-on: ubuntu-latest
	needs:
	- Pre-Commit
	steps:

	- name: Checkout
	uses: actions/checkout@v4
	with:
	lfs: 'true'

	- name: Set up caches
	uses: actions/cache@v4
	with:
	path: \|
	.snakemake/conda
	~/.cache/pre-commit/
	key: snakemake-conda-${{ env.CACHE_NUMBER }}

	- name: Set up channel priority
	run: conda config --set channel_priority strict

	- name: Clean conda cache
	run: conda clean --all --yes

	- name: Test workflow - Preprocess
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: workflow/Snakefile
	args: >
	--use-conda
	--show-failed-logs
	--cores 3
	--conda-cleanup-pkgs cache
	--latency-wait 5
	all

	- uses: actions/upload-artifact@v4
	if: failure()
	with:
	name: results
	path: \|
	results/*/.log
	# results/
	# reports/
	# !*/.cram
	# !*/.fq.gz
	# !*/.bam
	# !*/.bt2

Provide feedback