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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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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -20,6 +20,7 @@

### Template

- New pre-commit hooks (large files, merge conflicts) in pipeline template ([#3935](https://github.com/nf-core/tools/pull/3935))
- switch to uv and prek for pipeline linting workflow ([#3942](https://github.com/nf-core/tools/pull/3942))

### Linting
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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 "$status"
17 changes: 17 additions & 0 deletions nf_core/pipeline-template/.pre-commit-config.yaml
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Expand Up @@ -25,3 +25,20 @@ repos:
subworkflows/nf-core/.*|
.*\.snap$
)$
- id: check-added-large-files
args: [--maxkb=5000]
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@Aratz Aratz Dec 11, 2025

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Can the limit be defined as a variable somewhere and be used here? This would make it easier to adjust it for each pipeline, if necessary. Ideally it would be nice if it could be in .nf-core.yml, but I don't know if that is possible.

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@mashehu mashehu Dec 11, 2025

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without needing another script, this file would be the place.

exclude: |
(?x)^(
.*ro-crate-metadata.json$|
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@muffato muffato Dec 10, 2025

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Can the RO crate be that big ?
I guess we can accept it in on the basis it's machine generated, so its size can be considered legitimate whatever it is ?

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@MatthiasZepper MatthiasZepper Dec 11, 2025

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Yes, that was my logic. I just checked a semi-random selection of nf-core pipelines for the biggest files with the command given in the PR description and the RO-crate json was usually among the bigger files in a repo. Not that big, but I felt that it is safer to exclude it entirely as it is machine-generated.

With the nf-core downloads test I already once left everyone in a catch-22 situation where they required that test to pass to merge the template update that would correct said test to allow it to succeed. Therefore, I wanted to err on the safe site here.

.*\.snap$|
lib/nfcore_external_java_deps.jar$|
docs/.*\.(svg|pdf)$|
assets/.*$
)$
- 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
1 change: 1 addition & 0 deletions nf_core/pipelines/create/template_features.yml
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Expand Up @@ -438,6 +438,7 @@ code_quality:
- ".prettierignore"
- ".prettierrc.yml"
- ".github/workflows/fix-linting.yml"
- ".hooks/block_pipeline_outdir.sh"
short_description: "Use code linters"
description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier."
help_text: |
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