Update Modules Template #310

	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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

	- name: Set up Python
	uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
	with:
	python-version: "3.x"

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

	- name: Update modules
	run: nf-core modules update --all --no-preview
	working-directory: nf_core/pipeline-template

	- name: Update subworkflows
	run: nf-core subworkflows update --all --no-preview
	working-directory: nf_core/pipeline-template

	# Commit the changes
	- name: Commit changes
	run: \|
	git config user.email "core@nf-co.re"
	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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