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Pipeline template: New pre-commit hooks (large files, merge conflicts) #3935

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Pipeline template: New pre-commit hooks (large files, merge conflicts) #3935

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a95fbb8
Add new pre-commit hooks to pipeline template: Exclude large files an…
MatthiasZepper Nov 26, 2025
4babb88
[automated] Update CHANGELOG.md
nf-core-bot Nov 26, 2025
0295768
Add custom pre-commit hook to check for a pipeline output directory.
MatthiasZepper Nov 27, 2025
8022ab4
Add '.hooks/block_pipeline_outdir.sh' to linter group for pipeline cu…
MatthiasZepper Nov 27, 2025
7a2291e
Exclude assets folder from file size check.
MatthiasZepper Dec 11, 2025
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Add custom pre-commit hook to check for a pipeline output directory.
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@MatthiasZepper
MatthiasZepper committed Dec 11, 2025
commit 0295768abe7da16262801771dcf9d1e4114262c4
30 changes: 30 additions & 0 deletions nf_core/pipeline-template/.hooks/block_pipeline_outdir.sh
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@@ -0,0 +1,30 @@
#!/usr/bin/env bash
# This hook is used to block commits if they include staged files inside a directory
# which also contains a subdirectory called `pipeline_info`. The purpose of this is to
# prevent users from inadvertently committing output from pipeline test runs inside the
# development directory.

set -e

# list staged files
staged_files="$(git diff --cached --name-only)"

status=0

for file in $staged_files; do
file_dir=$(dirname "$file")

# Walk up the directory tree and check if the current directory contains a subdirectory called `pipeline_info`
# or the staged file is itself inside a directory called `pipeline_info`.
while [ "$file_dir" != "." ] && [ "$file_dir" != "/" ]; do
if [ $(basename "$file_dir") == "pipeline_info" ] || [ -d "$file_dir/pipeline_info" ]; then
echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself."
echo "Use 'git restore --staged <file>...' to remove the output files from the staging area before proceeding."
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@prototaxites prototaxites Dec 10, 2025

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Can this also print out the offending path?

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@MatthiasZepper MatthiasZepper Dec 11, 2025

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We could change the script to print out $file, yes.

However, I reckon that people may typically have added their whole output folder to the staging area and then it is more effective to remove all relevant files at once instead single files. I would, though, not want to make the call what that top-level folder is.

status=1
break
fi
file_dir=$(dirname "$file_dir")
done
done

exit "$status"
6 changes: 6 additions & 0 deletions nf_core/pipeline-template/.pre-commit-config.yaml
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Expand Up @@ -35,3 +35,9 @@ repos:
docs/.*\.(svg|pdf)$
)$
- id: check-merge-conflict
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@mashehu mashehu Nov 26, 2025

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we have already https://nf-co.re/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests/merge_markers, but this is a nicer approach

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@MatthiasZepper MatthiasZepper Nov 26, 2025

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The main motivation for this PR was evidently the check-added-large-files. Phil just recommended to use the other one as well, because he has it on the MultiQC repo.

If you think that I shouldn't bundle them in one PR to allow separate decisions, I am fine with removing it as well.

- repo: local
hooks:
- id: block-pipeline-outdir
name: Prevent committing output from pipeline test runs to the pipeline code itself
entry: ./.hooks/block_pipeline_outdir.sh
language: script