Update Modules Template #1

	name: Update Modules Template

	on:
	schedule:
	- cron: "0 0 * * *"
	workflow_dispatch:

	jobs:
	update_modules:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

	- name: Set up Python
	uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
	with:
	python-version: "3.x"

	- name: Install nf-core
	run: pip install nf-core

	- name: Update modules
	run: nf-core modules update --all
	working-directory: nf-core/pipeline-template

	- name: Update subworkflows
	run: nf-core subworkflows update --all
	working-directory: nf-core/pipeline-template

	# Commit the changes
	- name: Commit changes
	run: \|
	git config user.email "[email protected]"
	git config user.name "nf-core-bot"
	git add .
	git status
	git commit -m "[automated] Fix code linting"

	# Open a new PR to dev with the changes
	- name: Create PR
	run: \|
	git checkout -b update-modules
	git push origin update-modules
	gh pr create --title "Update modules in template" --body "This PR updates the modules in the pipeline template" --base dev --head update-modules

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