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Update Modules Template #254

Update Modules Template

Update Modules Template #254

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@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Set up Python
uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # 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