Tests

chore(main): updated workflow-catalog.yml #76

	name: Tests

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]


	jobs:
	Formatting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Formatting
	uses: github/super-linter@v4
	env:
	VALIDATE_ALL_CODEBASE: false
	DEFAULT_BRANCH: main
	GITHUB_TOKEN: ${{ secrets.PAT_TOKEN }}
	VALIDATE_SNAKEMAKE_SNAKEFMT: true

	Linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Lint workflow
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: workflow/Snakefile
	args: "--lint"



	Testing:
	runs-on: ubuntu-latest
	needs:
	- Linting
	- Formatting
	steps:
	- uses: actions/checkout@v4


	- name: Test workflow
	uses: snakemake/[email protected]
	with:
	directory: '.test'
	snakefile: 'workflow/Snakefile'
	args: "--dry-run --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
	stagein: \|
	echo "Current working directory: $(pwd)"
	echo "Listing contents of current directory:"
	ls -R
	echo "Listing contents of .test directory:"
	ls -R .test
	echo "Listing contents of .test/config directory:"
	ls -R .test/config
	echo "Listing contents of .test/data directory:"
	ls -R .test/data
	- name: Test report
	uses: snakemake/[email protected]
	with:
	directory: '.test'
	snakefile: 'workflow/Snakefile'
	args: "--report report.zip"

Provide feedback