Catch and handle weird r-utils edge case #79

	name: Tests

	on:
	push:
	branches:
	- main
	- featurecount
	- develop
	pull_request:
	branches_ignore: []

	jobs:
	formatting:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout with submodules
	uses: actions/checkout@v3
	with:
	submodules: recursive
	fetch-depth: 0
	- name: Formatting
	uses: github/super-linter@v5
	env:
	VALIDATE_ALL_CODEBASE: false
	DEFAULT_BRANCH: featurecount
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	VALIDATE_SNAKEMAKE_SNAKEFMT: true
	linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Linting
	uses: snakemake/[email protected]
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--configfile .test/configs/star_config.yaml --lint"

	run-workflow:
	runs-on: ubuntu-latest
	needs:
	- linting
	- formatting
	steps:
	- name: Checkout repository
	uses: actions/checkout@v3
	- name: Test workflow (nogenes)
	uses: snakemake/[email protected]
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--configfile .test/configs/nogenes.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --latency-wait 30"
	- name: Test workflow (bam)
	uses: snakemake/[email protected]
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--configfile .test/configs/bam2bakR.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --latency-wait 30"
	- name: Test workflow (star)
	uses: snakemake/[email protected]
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--configfile .test/configs/star_config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --latency-wait 30"

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