Use nf-schema for pipeline params #56

	name: auto-format

	on:
	workflow_dispatch:
	pull_request:

	env:
	GH_TOKEN: ${{ github.token }}

	permissions:
	contents: write
	pull-requests: write

	jobs:
	auto-format:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4
	if: github.event_name == 'pull_request'
	with:
	fetch-depth: 0
	ref: ${{ github.head_ref }}
	- uses: actions/checkout@v4
	if: github.event_name == 'push'
	with:
	fetch-depth: 0
	ref: ${{ github.ref_name }}
	- uses: actions/setup-python@v4
	with:
	python-version: 3.11
	- name: Install nextflow
	uses: nf-core/setup-nextflow@v1
	- name: git config
	run: \|
	git config --global user.name "github-actions[bot]"
	git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install .[dev]

	- name: Write nf-schema docs
	run: \|
	nf-core pipelines schema docs -f -x markdown -o docs/params.md
	echo "<!-- this doc is generated by: nf-core pipelines schema docs -->" >> docs/params.md

	- name: Format
	uses: pre-commit/[email protected]
	continue-on-error: true

	- name: commit & push
	run: \|
	git add docs/params.md
	git commit -m "ci: 📑 update params docs with 'nf-core pipelines schema docs'" \|\| echo "nothing to commit"

	git add .
	git commit -m "ci: 🤖 format everything with pre-commit" \|\| echo "nothing to commit"
	git push \|\| echo "nothing to push"

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