respect indentation on version bump #2110

	name: Fix linting from a comment
	on:
	issue_comment:
	types: [created]

	jobs:
	deploy:
	# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
	if: >
	contains(github.event.comment.html_url, '/pull/') &&
	contains(github.event.comment.body, '@nf-core-bot fix linting') &&
	github.repository == 'nf-core/tools'
	runs-on: ubuntu-latest
	steps:
	# Use the @nf-core-bot token to check out so we can push later
	- uses: actions/checkout@v3
	with:
	token: ${{ secrets.nf_core_bot_auth_token }}

	# Action runs on the issue comment, so we don't get the PR by default
	# Use the gh cli to check out the PR
	- name: Checkout Pull Request
	run: gh pr checkout ${{ github.event.issue.number }}
	env:
	GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

	- uses: actions/setup-node@v3

	- name: Install Prettier
	run: npm install -g prettier @prettier/plugin-php

	- name: Run 'prettier --write'
	run: prettier --write ${GITHUB_WORKSPACE}

	- name: Run Black
	uses: psf/black@stable
	with:
	# Override to remove the default --check flag so that we make changes
	options: "--color"

	- name: Set up Python 3.11
	uses: actions/setup-python@v4
	with:
	python-version: 3.11
	- name: python-isort
	uses: isort/isort-action@v1.0.0
	with:
	isortVersion: "latest"
	requirementsFiles: "requirements.txt requirements-dev.txt"

	- name: Commit & push changes
	run: \|
	git config user.email "core@nf-co.re"
	git config user.name "nf-core-bot"
	git config push.default upstream
	git add .
	git status
	git commit -m "[automated] Fix code linting"
	git push

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