GTDBtk is being run on only one (of several) samples, even when running with the option --binning_map_mode own #812
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name: Fix linting from a comment | |
on: | |
issue_comment: | |
types: [created] | |
jobs: | |
fix-linting: | |
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords | |
if: > | |
contains(github.event.comment.html_url, '/pull/') && | |
contains(github.event.comment.body, '@nf-core-bot fix linting') && | |
github.repository == 'nf-core/mag' | |
runs-on: ubuntu-latest | |
steps: | |
# Use the @nf-core-bot token to check out so we can push later | |
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
with: | |
token: ${{ secrets.nf_core_bot_auth_token }} | |
# indication that the linting is being fixed | |
- name: React on comment | |
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
with: | |
comment-id: ${{ github.event.comment.id }} | |
reactions: eyes | |
# Action runs on the issue comment, so we don't get the PR by default | |
# Use the gh cli to check out the PR | |
- name: Checkout Pull Request | |
run: gh pr checkout ${{ github.event.issue.number }} | |
env: | |
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | |
# Install and run pre-commit | |
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
with: | |
python-version: "3.12" | |
- name: Install pre-commit | |
run: pip install pre-commit | |
- name: Run pre-commit | |
id: pre-commit | |
run: pre-commit run --all-files | |
continue-on-error: true | |
# indication that the linting has finished | |
- name: react if linting finished succesfully | |
if: steps.pre-commit.outcome == 'success' | |
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
with: | |
comment-id: ${{ github.event.comment.id }} | |
reactions: "+1" | |
- name: Commit & push changes | |
id: commit-and-push | |
if: steps.pre-commit.outcome == 'failure' | |
run: | | |
git config user.email "core@nf-co.re" | |
git config user.name "nf-core-bot" | |
git config push.default upstream | |
git add . | |
git status | |
git commit -m "[automated] Fix code linting" | |
git push | |
- name: react if linting errors were fixed | |
id: react-if-fixed | |
if: steps.commit-and-push.outcome == 'success' | |
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
with: | |
comment-id: ${{ github.event.comment.id }} | |
reactions: hooray | |
- name: react if linting errors were not fixed | |
if: steps.commit-and-push.outcome == 'failure' | |
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
with: | |
comment-id: ${{ github.event.comment.id }} | |
reactions: confused | |
- name: react if linting errors were not fixed | |
if: steps.commit-and-push.outcome == 'failure' | |
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
with: | |
issue-number: ${{ github.event.issue.number }} | |
body: | | |
@${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. | |
See [CI log](https://github.com/nf-core/mag/actions/runs/${{ github.run_id }}) for more details. |