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Merged
mashehu merged 3 commits into from
Mar 5, 2026
Merged

nf-core bot: collect all snapshots before commiting #4082

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1d7ae33
nf-core bot: collect all snapshots before commiting
mashehu Mar 5, 2026
32db391
[automated] Update CHANGELOG.md
nf-core-bot Mar 5, 2026
e701623
Merge branch 'dev' into try-to-fix-update-snapshot-action
mashehu Mar 5, 2026
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41 changes: 34 additions & 7 deletions .github/workflows/update-template-snapshots.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -118,11 +118,19 @@ jobs:
nf-test test \
--profile=+docker \
--verbose
--update-snapshot

- name: Update nf-test snapshot
- name: Copy snapshot to .github/snapshots
if: steps.nf-test.outcome == 'success'
run: |
cp ${{ github.workspace }}/create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap
cp create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap .github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap

- name: Upload snapshot artifact
if: steps.nf-test.outcome == 'success'
uses: actions/upload-artifact@v4
with:
name: snapshot-${{ matrix.TEMPLATE }}
path: .github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap

# indication that the run has finished
- name: react if finished succesfully
Expand All @@ -132,15 +140,34 @@ jobs:
comment-id: ${{ github.event.comment.id }}
reactions: "+1"

commit-snapshots:
needs: [prepare-matrix, update-snapshots]
runs-on: ubuntu-latest
if: always() && needs.update-snapshots.result != 'skipped'
steps:
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
with:
token: ${{ secrets.nf_core_bot_auth_token }}

- name: Checkout Pull Request
run: gh pr checkout ${{ github.event.issue.number }}
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

- name: Download all snapshot artifacts
uses: actions/download-artifact@v4
with:
pattern: snapshot-*
path: .github/snapshots/
merge-multiple: true

- name: Commit & push changes
id: commit-and-push
if: steps.nf-test.outcome == 'success'
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 add .github/snapshots/
git diff --staged --quiet && echo "No snapshot changes to commit" && exit 0
git commit -m "[automated] Update Template snapshots"
git push

Expand All @@ -160,7 +187,7 @@ jobs:
reactions: confused

- name: react if snapshots were not updated
if: steps.commit-and-push.outcome == 'failure'
if: steps.commit-and-push.outcome == 'failure'
uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
with:
issue-number: ${{ github.event.issue.number }}
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@
- Update GitHub Actions ([#4067](https://github.com/nf-core/tools/pull/4067))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.15.4 ([#4069](https://github.com/nf-core/tools/pull/4069))
- bump nf-test to 0.9.4 ([#4079](https://github.com/nf-core/tools/pull/4079))
- nf-core bot: collect all snapshots before commiting ([#4082](https://github.com/nf-core/tools/pull/4082))
- Update GitHub Actions to v4 (major) ([#4081](https://github.com/nf-core/tools/pull/4081))

### Linting
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