Phyloseq object creation will fail if any samples have all reads removed by the tax filtering step #575

	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/ampliseq'
	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

	# Check that we actually need to fix something
	- name: Run 'prettier --check'
	id: prettier_status
	run: \|
	if prettier --check ${GITHUB_WORKSPACE}; then
	echo "result=pass" >> $GITHUB_OUTPUT
	else
	echo "result=fail" >> $GITHUB_OUTPUT
	fi

	- name: Run 'prettier --write'
	if: steps.prettier_status.outputs.result == 'fail'
	run: prettier --write ${GITHUB_WORKSPACE}

	- name: Commit & push changes
	if: steps.prettier_status.outputs.result == 'fail'
	run: \|
	git config user.email "[email protected]"
	git config user.name "nf-core-bot"
	git config push.default upstream
	git add .
	git status
	git commit -m "[automated] Fix linting with Prettier"
	git push

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