minor fix for avoid non-matching variants going through allele_qc to throw error in mr #521
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name: Update documentation | |
on: | |
pull_request_target: | |
paths-ignore: | |
- .github/* | |
- .gitignore | |
- README.md | |
jobs: | |
update_documentation: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout pull request branch | |
uses: actions/checkout@v3 | |
with: | |
token: ${{ secrets.CI_TOKEN }} | |
fetch-depth: 0 | |
repository: ${{ github.event.pull_request.head.repo.full_name }} | |
ref: ${{ github.event.pull_request.head.ref }} | |
- name: Create YAML from recipe | |
run: | | |
cp .github/environment/environment.yaml /tmp/environment.yaml | |
grep -v '{%' < .github/recipe/meta.yaml | yq .requirements.host | sed 's/^/ /' >> /tmp/environment.yaml | |
- name: Setup micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: /tmp/environment.yaml | |
generate-run-shell: true | |
- name: Update documentation | |
shell: micromamba-shell {0} | |
run: R -e "devtools::document()" | |
- name: Commit changes to documentation | |
uses: EndBug/add-and-commit@v9 | |
with: | |
push: true | |
message: Update documentation |