Merge pull request #272 from danilodileo/add-spades-options #816

	name: nf-core linting
	# This workflow is triggered on pushes and PRs to the repository.
	# It runs the `nf-core lint` and markdown lint tests to ensure
	# that the code meets the nf-core guidelines.
	on:
	push:
	branches:
	- dev
	pull_request:
	release:
	types: [published]

	jobs:
	pre-commit:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- 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

	nf-core:
	runs-on: ubuntu-latest
	steps:
	- name: Check out pipeline code
	uses: actions/checkout@v4

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v1

	- uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	architecture: "x64"

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install nf-core

	- name: Run nf-core lint
	env:
	GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
	run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md

	- name: Save PR number
	if: ${{ always() }}
	run: echo ${{ github.event.pull_request.number }} > PR_number.txt

	- name: Upload linting log file artifact
	if: ${{ always() }}
	uses: actions/upload-artifact@v4
	with:
	name: linting-logs
	path: \|
	lint_log.txt
	lint_results.md
	PR_number.txt

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