Add complete template for nf-core/mag pipeline execution #656

	name: python_lint

	on:
	push:
	branches: "**"
	pull_request:
	types: [opened, reopened, synchronize, closed]
	branches: "**"

	jobs:
	flake8_py3:
	runs-on: ubuntu-latest
	steps:
	- name: Setup Python
	uses: actions/setup-python@v1
	with:
	python-version: 3.9.x
	architecture: x64
	- name: Checkout PyTorch
	uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- name: Install flake8
	run: pip install flake8
	- name: Check for Python file changes
	id: file_check
	uses: tj-actions/changed-files@v44
	with:
	sha: ${{ github.event.pull_request.head.sha }}
	files: \|
	**.py
	- name: Run flake8
	if: steps.file_check.outputs.any_changed == 'true'
	run: flake8 --ignore E501,W503,E203,W605
	- name: No Python files changed
	if: steps.file_check.outputs.any_changed != 'true'
	run: echo "No Python files have been changed."

	black_lint:
	runs-on: ubuntu-latest
	steps:
	- name: Setup
	uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- name: Install black in jupyter
	run: pip install black[jupyter]
	- name: Check for Python file changes
	id: file_check
	uses: tj-actions/changed-files@v44
	with:
	sha: ${{ github.event.pull_request.head.sha }}
	files: '**.py'
	- name: Check code lints with Black
	if: steps.file_check.outputs.any_changed == 'true'
	uses: psf/black@stable
	- name: No Python files changed
	if: steps.file_check.outputs.any_changed != 'true'
	run: echo "No Python files have been changed."

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