Update parseFiles.sh #30

	---
	name: Lint Code Base

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

	jobs:
	linter:
	runs-on: ubuntu-latest

	defaults:
	run:
	shell: bash -l {0}

	permissions:
	contents: read
	packages: read
	# To report GitHub Actions status checks
	statuses: write

	steps:
	- name: Checkout Code
	uses: actions/checkout@v4

	# - name: Install conda environment dependencies
	# uses: conda-incubator/setup-miniconda@v2
	# with:
	# miniforge-version: latest
	# miniforge-variant: Mambaforge
	# mamba-version: "*"
	# channels: conda-forge,bioconda
	# channel-priority: strict
	# activate-environment: JupyText
	# auto-update-conda: true
	# environment-file: tests/conda_snk_env.yaml

	# - name: Set up Python
	# uses: actions/setup-python@v5
	# with:
	# python-version: '3.12'
	# architecture: 'x64'

	- name: Super-linter
	uses: super-linter/[email protected]
	env:
	VALIDATE_ALL_CODEBASE: false
	DEFAULT_BRANCH: main

	VALIDATE_SNAKEMAKE_SNAKEFMT: true
	#VALIDATE_SNAKEMAKE_LINT: true
	VALIDATE_R: true
	VALIDATE_CLANG_FORMAT: true
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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