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update_components_template.yml
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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