Bump github/super-linter from 4 to 7 #40

	name: MosaiCatcher basic checks with snakemake v8

	on:
	push:
	branches:
	- "**"
	schedule:
	- cron: "0 0 * * 0"

	jobs:
	Testing-basic-v8:
	runs-on: ubuntu-latest
	# needs:
	# - Formatting
	# - Linting
	steps:
	- name: Checkout repository with submodules
	uses: actions/checkout@v4
	with:
	submodules: recursive
	# lfs: true

	- name: Git Submodule Update
	run: \|
	# git pull --recurse-submodules
	git submodule update --remote --recursive --force --init

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"

	- name: List contents of .tests
	run: \|
	tree -h .tests

	- name: Show config file
	run: \|
	cat .tests/config/simple_config_mosaicatcher.yaml

	- name: List contents of workflow/data
	run: \|
	tree -h workflow/data

	- name: Add Conda to system path
	run: echo "$CONDA/bin" >> $GITHUB_PATH

	- name: Install dependencies
	run: conda install -c conda-forge mamba

	- name: Setup Snakemake
	run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

	- name: List options of workflow
	run: \|
	snakemake --cores 1 --config list_commands=True --verbose --debug

	- name: Run workflow
	run: \|
	snakemake --cores 1 --sdm conda --configfile .tests/config/simple_config_mosaicatcher.yaml \
	--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

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