Tests

fix: remove checkpoint in dorado_demux to speed up workflow, closes #32 #103

	name: Tests

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

	jobs:
	Formatting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Formatting
	uses: super-linter/super-linter@v7
	env:
	VALIDATE_ALL_CODEBASE: false
	DEFAULT_BRANCH: main
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	VALIDATE_SNAKEMAKE_SNAKEFMT: true
	VALIDATE_YAML_PRETTIER: true

	Linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Lint workflow
	uses: snakemake/snakemake-github-action@v2
	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/snakemake-github-action@v2
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--sdm conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n"

	- name: Test report
	uses: snakemake/snakemake-github-action@v2
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--cores 2 --report report.zip"

Provide feedback