Adapter screen for long sequencing adaptors #21

	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 == 'plant-food-research-open/assemblyqc'
	runs-on: ubuntu-latest
	steps:
	# Use the @nf-core-bot token to check out so we can push later
	- uses: actions/checkout@v4
	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 }}

	- name: Set up Python 3.11
	uses: actions/setup-python@v5
	with:
	python-version: 3.11
	cache: "pip"

	- name: Install pre-commit
	run: pip install pre-commit

	- name: Run pre-commit
	run: pre-commit run --all-files \|\| echo "status=fail" >> $GITHUB_ENV

	- name: Commit & push changes
	if: env.status == 'fail'
	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 linting with pre-commit"
	git push

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