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Small patch to fix release CI/CD tests #35

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Merged
ypriverol merged 3 commits into from
Apr 6, 2026
Merged

Small patch to fix release CI/CD tests #35

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7601371
fix: skip linting comment when triggered by release events
ypriverol Apr 6, 2026
b54dcf3
Merge remote-tracking branch 'origin/main' into dev
ypriverol Apr 6, 2026
2a88236
fix: exclude linting.yml from nf-core files_unchanged check
ypriverol Apr 6, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/linting.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ jobs:
run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md

- name: Save PR number
if: ${{ always() }}
if: ${{ always() && github.event.pull_request.number }}
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@coderabbitai coderabbitai bot Apr 6, 2026

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⚠️ Potential issue | 🟠 Major

Line 69 causes template drift and keeps files_unchanged lint failing

This condition is not needed anymore now that linting_comment.yml safely skips invalid/missing PR numbers, and it appears to be the reason the nf-core template check is failing in this PR.

Suggested template-compatible fix 
-      - name: Save PR number
-        if: ${{ always() && github.event.pull_request.number }}
+      - name: Save PR number
+        if: ${{ always() }}
         run: echo ${{ github.event.pull_request.number }} > PR_number.txt

Based on learnings: Run nf-core pipelines lint before merging code to ensure pipeline standards compliance (use --release flag for master branch PRs).

🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In @.github/workflows/linting.yml at line 69, The linting job contains an
unnecessary PR-number guard (the line with the if-condition checking
github.event.pull_request.number) which causes template drift and breaks the
nf-core template check; remove that conditional so the step runs under the
workflow's existing guards (or replace it with a simple always() check) to allow
linting_comment.yml to handle missing/invalid PR numbers and restore template
compatibility.

run: echo ${{ github.event.pull_request.number }} > PR_number.txt

- name: Upload linting log file artifact
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11 changes: 7 additions & 4 deletions .github/workflows/linting_comment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,17 +21,20 @@ jobs:
id: pr_number
run: |
if [ ! -f linting-logs/PR_number.txt ]; then
echo "PR number file not found"
exit 1
echo "No PR number file found (not a PR event), skipping comment"
echo "skip=true" >> $GITHUB_OUTPUT
exit 0
fi
PR_NUM=$(cat linting-logs/PR_number.txt)
if ! [[ "$PR_NUM" =~ ^[0-9]+$ ]]; then
echo "Invalid PR number: $PR_NUM"
exit 1
echo "Invalid PR number: $PR_NUM, skipping comment"
echo "skip=true" >> $GITHUB_OUTPUT
exit 0
fi
echo "pr_number=$PR_NUM" >> $GITHUB_OUTPUT

- name: Post PR comment
if: ${{ steps.pr_number.outputs.skip != 'true' }}
uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
with:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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1 change: 1 addition & 0 deletions .nf-core.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ lint:
- .github/PULL_REQUEST_TEMPLATE.md
- .github/CONTRIBUTING.md
- .github/workflows/branch.yml
- .github/workflows/linting.yml
- .github/workflows/linting_comment.yml
- .github/.dockstore.yml
- docs/README.md
Expand Down
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